244 Matching Annotations
  1. Mar 2023
    1. This finding suggests that Arf6 is preferentially recruited to sites of active actin polymerization.

      Couldn't there still be active actin polymerization by formins and the like in other parts of the cell? I think you could add that the active actin polymerization is Arp2/3 complex-mediated.

    2. Loss of Arf6 significantly increased the amount of clathrin in sprouts as compared with controls

      Does loss of Arf6 cause differences in Arp2/3 complex recruitment to clathrin sites?

    3. actin protein mCherry-Arp2

      Is this the actin-related protein Arp2 that is a part of the Arp2/3 complex? I think this is an important distinction that you might take advantage of and discuss a little bit more here.

  2. Feb 2023
    1. Importantly, the width of the bleached region did not change significantly over time (Fig. S2)

      In figure 1D, it looks like the width of the bleached region didn't change, but it looks like the overall intensity of the signal around the whole GUV deceases - do you think this is from cycling through depolymerization, then monomeric actin, then repolymerizing at the bleached spot?

    2. This indicates that the fluorescence recovery was dominated by exchange of actin monomers or filaments with the GUV lumen via turnover, rather than by lateral diffusion of actin along the membrane.

      I think this FRAP experiment is really cool, and definitely important to show that the actin at the cortex turns over. Also, really cool that the turnover is close to that of living cells even without debranching, severing, disassembling proteins! Can you distinguish between filamentous actin and monomeric actin with your labelling technique? (It might be worth mentioning how you're labelling the actin here.) I'm curious what the ratio of G-actin to F-actin looks like and how this might affect turnover. You have a really great paragraph about this in discussion, but might be useful to mention briefly here.

    3. Introduction

      This is a really interesting paper with a really cool technique, some beautiful images, and a ton of data that tells us a lot about the mechanics of cell protrusions. Additionally, their GUVs with minimal actin cortices could be a super useful tool for better understanding what different proteins and combinations of proteins are doing at the cortex.

    4. No protrusions occurred when actin polymerized in the GUV lumen, showing that Arp2/3-driven actin polymerization at the membrane drives protrusion formation (Fig. S7 B).

      Did you do any experiments where you polymerized actin filaments with the Arp2/3 complex, but with non-membrane anchored VCAs?

    5. time-lapse imaging revealed that GUV shapes often remained unchanged over many minutes

      Interesting.. I'd expect these structures to be really dynamic. Is the turnover of actin at the membrane decreased in these deflated GUVs?

    6. fragmented the actin cortex by laser ablatio

      I was still kind of questioning if the GUV misshaping was really due to the actin vs just having extra membrane around (even though you had the bare GUVs being more spherical), but this experiment and the CytoD experiment are really convincing. Although I wonder if you could include a quantification of roundness or a similar parameter pre and post ablation?

    7. most of the cortex-bearing GUVs were frozen in highly irregular shapes, showing sharp corners (pink arrows in Fig. 2A), bleb-like protrusions (yellow arrows), long and thin protrusions (cyan arrows), or highly anisotropic shapes (yellow asterisk).

      How often did you see these different morphologies? I'm curious if some are more common than others.

    8. To selectively restrict actin nucleation to the membrane as in cells (26), we used a 10xHis-tagged VCA construct that binds to nickel-chelating lipids in the membrane.

      Really clever way to drive formation of an actin cortex at the membrane of the GUVs. But obviously VCAs aren't attached to the membrane like this in biological systems, so are there biological consequences that might affect some of this data? I think it would be interesting to hear a little bit about this in the discussion maybe?

  3. Dec 2022
    1. The direct observation of this reaction in TIRF microscopy revealed a progressive reorganization of the branched actin network by Δmod, V1ab4 and VASP

      I think it would go a long way to support your concluding hypotheses if you did a quantification of branching for Figure 6C because it is a little hard to make out with the density of the filaments and because it is so important for your conclusions.

    2. The fact that VASP and α-catenin/Δmod, which are not known to interact directly, stimulated actin assembly in a synergistic manner was not expected, but suggests that these two ABPs cooperate when combined in the same protein complex.

      It would be interesting to look at direct binding between these proteins, especially because they are mutants that might not behave quite as expected.

    3. These findings shed light on the molecular mechanisms by which actin regulators synergistically control the transition of actin architecture and dynamics that accompanies the formation and maturation of AJs.

      This is a very interesting paper looking out how different actin binding proteins work together to regulate actin in specific functions!

    4. Finally, our biochemical study must be placed in the context of cell-cell junctions

      I think it would be useful to talk again about the effect of the different constructs that you used in the context of what that means biologically in the cell.

    5. actin dynamics observed in cells

      I am interested what this would look like in cells! Maybe a next step?

    6. Kinetics of actin polymerization were measured in the presence of 2 μM G-actin (10% pyrene-labelled), 50 nM Arp2/3, 100 nM VCA, 5 μM Δmod, 5 μM V1ab4 and 3 μM VASP, in conditions that allow nucleation and elongation (50 mM KCl).

      Actin + Arp2/3 + VCA + delta-mod (cyan) is interesting - it looks like nucleation is delayed, but then is able to rapidly at least approach the same level as Arp2/3 + VCA. I'd love to hear some more thoughts about this.

    7. Representative epifluorescence images of Alexa-488 actin filament bundles observed alone and in the presence of all the combinations of Δmod, V1ab4 and VASP. Conditions: 1.5 μM G-actin (2%Alexa-488-labeled), 0.25 μM Δmod, 0.25 μM V1ab4 and 0.25 μM VASP. Scale bar = 15 μm.

      These are amazing!

    8. We also observed, when the three proteins were combined, an increase in the density and length of actin filaments produced in the presence of profilin

      I think this is obviously quite visible in the images, but it would be interesting to see a quantification of filament length in each case and also the occurrence of these bright bundle-like regions. I know you do this more precisely in the next section but I think this would also help set that section up a little bit.

    9. Observation of the details of single filament elongation revealed that it was regularly interrupted by marked pauses, reflecting capping events of the barbed ends by V1ab4 and Δmod

      It would be super cool to see some images along with these graphs looking at single filament elongation.

  4. Nov 2022
    1. These experiments showed that although in cultured cells ERK3 regulated the activity of both Cdc42 and Rac1, it only directly stimulated the GDP-GTP exchange of Cdc42

      I find this interesting also in terms of the effects of ERK3 knockdown on the morphology of the cells and the specific actin structures. You mentioned previously that Rac1 leads to the formation of lamellipodia and Cdc42 leads to the formation of filopodia, and looking at the images of your cells, it looks like filopodia are more affected than lamellipodia. Is that something you noticed looking through your images?

    2. Actin is one of the most abundant and highly conserved proteins with over 95% homology among all isoforms

      You might specify that this is true for human isoforms. There are lots of weird actins out there in other organisms that are well under that 95%

    3. S418D-overexpressing cells exhibited F-actin-rich protrusions

      It might be useful to quantify protrusions for all of 6F because it seems like there are definitely some big differences!

    4. These data suggest that ERK3 could function as nucleation promoting factor to promote ARP2/3-dependent actin polymerization.

      Woah! Curious if the kinase activity (that you test in the next section) is required for this change in actin polymerization?

    5. These results were corroborated by the colocalization of ERK3 with Cdc42 to the protrusions at the cell leading-edge

      It would be interesting to see this in ERK3 knockdowns as well to see if the localization of Cdc42 changes with loss of ERK3. I'm also curious about the localization of Rac1.

    6. Interestingly, we readily detected the ARP2/3 complex subunits ARP3, ARP2 and ARPC1A as well as ERK3 by immunoblots in active Rac1/Cdc42 pull-downs

      Very cool! Did you check other subunits or did they not precipitate?

    7. ERK3 knockdown significantly decreased levels of both basal and EGF-induced GTP-bound Cdc42 and Rac1 in primary (HMEC)

      Are there stats for Figure 2F? It seems like there's more variance with the Rac1 blot quantifications than with the Cdc42 blot quantifications.

    8. S189 mutants (ERK3 S189A/ERK3 S189D)

      Super interesting! Do these mutants have motility defects too?

    9. these data suggest that ERK3 likely controls actin cytoskeleton dynamics thereby influencing cell shape, motility and polarized migration.

      By eye, I agree that it looks like cell shape is altered in Figure 1A, but it would be cool to include a quantification (maybe like how round the cells are or something). I also think that Figures 1H-J are relevant here to help connect some dots for this conclusion and show that the loss of ERK3 does cause changes in specific actin dynamics that result in shape and motility defects, but you don't talk about Fig 1H-J until later. Finally, I think the conclusion about polarized migration is more relevant in the next section than at the end of this section.

    10. The actin cytoskeleton is tightly controlled by RhoGTPases, actin binding proteins and nucleation-promoting factors to perform fundamental cellular functions. Here, we show that ERK3, an atypical MAPK, directly acts as a guanine nucleotide exchange factor for Cdc42 and phosphorylates the ARP3 subunit of the ARP2/3 complex at S418 to promote filopodia formation and actin polymerization, respectively. Consistently, depletion of ERK3 prevented both basal and EGF-dependent Rac1 and Cdc42 activation, maintenance of F-actin content, filopodia formation and epithelial cell migration. Further, ERK3 protein binds directly to the purified ARP2/3 complex and augments polymerization of actin in vitro. ERK3 kinase activity is required for the formation of actin-rich protrusions in mammalian cells. These findings unveil a fundamentally unique pathway employed by cells to control actin-dependent cellular functions.

      I really enjoyed reading this paper - what a great story! It really highlights how little we still know about actin regulation (even in human cells!), but it also does a great job filling in some of that knowledge with this pathway involving this atypical MAPK.

  5. Oct 2022
    1. demonstrated the effectiveness

      Do we know that SMIFH2 broadly inhibit all of the formins in Arabidopsis?

    2. We found that side-branched filaments in arp2-1 cells were significantly longer (Fig. 4 C) and filament lifetime was prolonged (Fig. 4 D) compared to the side-branched filaments in wild-type cells

      Interesting, is the hypothesis that some of these formins that nucleate filaments off the side of existing filaments are responsible for these specific branched filaments?

    3. CK-666 (0, 1, 5, 10, 50, and 100 µM)

      I think you do a great job here and in the next figure validating CK-666 (definitely showing that there isn't added effect in the Arp2/3 complex mutants is great!), but you might consider adding CK-689 as an inactive control just to cover all your bases.

    4. Simultaneous Inhibition of the Arp2/3 Complex and Formins Enhances de novo Actin Filament Nucleation in Arabidopsis thaliana

      What a cool paper! I think papers dealing with different proteins interacting with a single pool of actin are so interesting. Also super awesome that you validate CK-666 in these cells and start dealing with potential off-target effects of SMIFH2 in these cells - so much added value to the field!

    5. left-skewed

      There are a couple of these graphs where we're looking at the distribution of data and there's mention that there's more of a skew in a sample compared to another, but sometimes this is really difficult to see in the graphs. It might be useful to split out arp2 mutants vs arpc2 mutants so that we're comparing 2 instead of 4. It might also be useful if you could include some measure of skew, especially for the ones where you think there might be a difference in skew.

    6. In addition, hypocotyls of arp2-1 and arpc2 were significantly shorter than wild-type siblings at the same time points

      It would be interesting to see specific data points here instead of bars for these graphs. Based on the representative images, it looks like there could be a couple population with different lengths, especially in the arpc2 hypocotyls. If that's the case, it would also be interesting to hear why that might be.

  6. Sep 2022
    1. (b)

      Maybe i'm missing this, but I don't see Eps8 in this map. Might just be worth discussing in the text why it's not there?

    2. Arpc5

      Interesting that ARPC5 disappeared, but not ARPC5L if I'm reading that correctly?

    3. background values adjacent to the measured bands.

      I noticed in figure 4A the tubulin loading control isn't super consistent. Did you normalize to your loading control? Might also be worth doing total protein as your loading control instead of tubulin, because it is possilbe that tubulin is being affected since you're probing other cytoskeleton related proteins.

    4. we utilized an optical tweezer (OT) setup to pull nanotubes of comparable lengths to the TNTs observed on the micropatterns to monitor by confocal microscopy F-actin polymerization within the nanotube in control and CK-666-treated conditions

      This experiment is very cool, but I wonder if you could show a similar thing with naturally forming TNTs? Do you see more actin in natural TNTs when the Arp2/3 complex is inhibited? I worry that stretching the cell like this could be causing other things to happen in the cell and isn't fully representative of a TNT forming on its own.

    5. formin-specific agonist drug IMM-01

      I really like this data with the formin agonist!

    6. Upon Arp2/3 inhibition with CK-666 (6, 48), we observed a significant increase in the percent of TNT-connected cells on D15, D20 and D30 micropatterns

      It would be really great to see representative images of the data quantified in Figure 2C.

    7. this suggests an anti-correlation between regions with high Arp2/3 activity and a cell’s ability to form TNTs

      To really illustrate this it would be helpful to show a bivariate analysis between like number of lamellipodia per cell and number of TNTs per cell for 2B. Then you could actually graphically show this anti-correlation and provide a correlation coefficient to strengthen this conclusion. It would also be interesting to show this with CK-666 treatment as I wondered while reading this if the increase in TNTs/filopodia with CK-666 treatment was accompanied by a decrease in lamellipodia.

    8. Our data suggest a shift in the equilibrium (and usage of common actin proteins players) between branched and linear actin polymerization to form different cell protrusions.

      What a cool paper! Beautiful images and I love papers that deal with this concept of a limited pool of actin in the cell that is directed to its different functions by its interactions with actin binding/interacting proteins.