We have a new paper out describing how vesicles move inside cells.
The paper in a nutshell
In science-speak
We analysed how small vesicles are transported in cells. In contrast to large vesicles and organelles, which move using motors inside cells, our analysis revealed that passive diffusion is the main mode of small vesicle transport.
In normal language
Inside cells, molecules are moved in tiny transport packets called vesicles. Large vesicles are moved by motors that tug them along cellular railway tracks. We find that small vesicles instead move by diffusion – the same process that turns a whole glass of water blue after a drop of ink is added.
What did we find?
Human cells are eukaryotic. This means that inside each cell there are different compartments. These compartments are places with different jobs and they have different molecules in them. This is great for organisation, but it gives the cell a problem: how do you move molecules from one compartment to another?
Cells have evolved “membrane traffic” systems to transport molecules between compartments using vesicles. This process has been studied for many years but one question is how the vesicles move from one compartment to another.
The textbook view is that vesicles are moved by motors on cellular tracks:
While it is true that large vesicles are moved in this way, do small vesicles also move by motor-based transport?
We studied the movement of small vesicles called intracellular nanovesicles (INVs) in this paper. We found that the majority of vesicle motions are random, brownian movements. They move by diffusion!
The movie above shows that most of the motions are random. There is one long directed track which is probably a motor-driven motion, but all the rest are diffusive. There’s a lot of analysis in the paper to support this conclusion – take a look.
If vesicles undergo diffusion rather than motor transport, how do we know that this is how they transport cargo?
To look at this we needed two things: first, to look at delivery of vesicle cargo at the final destination (so that we can measure real traffic) and second, a way to alter diffusion to ask if this can alter traffic. For the first part, we discovered that INVs can fuse with the plasma membrane.
Now we had to figure out a way to alter diffusion. We came up with a trick to make the vesicles furry! Because the Stokes-Einstein equation says that a bigger a particle is, the slower it will diffuse; we realised that a furry vesicle would have slower diffusion. Using a molecular trick, we could attach protein on the outside of INVs specifically to make them furry. We checked that their diffusive movement was slowed… and… then did the experiment… and found that delivery to the cell surface was decreased.
So it seems that the diffusive movement of INVs is responsible for the traffic of the molecules that they carry.
The textbook view of vesicle transport is that it is motor-driven so the implications of diffusive vesicle movement are fun to think about!
One strong concept in membrane traffic is that a vesicle must move “from A to B” and this is usually taken to mean from “point A to point B.” Obviously, a vesicle emerges at a specific point and fuses at a single place; therefore, a random diffusion model for transport appears woefully inadequate to fulfill this function. However, the goal of membrane traffic is to transfer material from identity A to identity B. Identity B can be large expanse like the plasma membrane or it could be present intracellularly as multiple copies of compartment B. Now, we can see that random diffusion performs well; as long as the diffusion coefficient is not too low and the proximity to the target compartment is high.
from the Discussion section
The people
Méghane Sittewelle is the postdoc who did all the experiments and analysis for the paper. I helped a bit by contributing software and writing the paper. Méghane is a very talented microscopist who figured out how to image cells in just the right way to be able to track them to enable this paper to happen.
The code
All code used in the article is available here. The TrackMateR package is here or here. We made our data available here.
There’s an Easter Egg in our code: a fully fledged tracking viewer that I wrote to visualise our tracking data. There’s a lot of work behind-the-scenes to do the analysis that doesn’t make it into the paper!
The publishing process
In the preprint version of our paper, which had a slightly different title, we extrapolated our findings of diffusive vesicle motion to other transport vesicles. When we submitted the paper to a journal, we got positive reviewer comments, but one issue was how far the diffusive model could be extended to other vesicle types. We felt that this part of our paper was correct but not very well explained, which had led the reviewers to doubt whether other vesicle types also move by diffusion. The paper was duly rejected. We did some more analysis to highlight that the motion of clathrin-coated vesicles – a very well studied type of vesicle – in particular was also mainly diffusive. On submission to a different journal, the editors still felt that the case for extending the model was not strong enough. It is true that we had not gone into the same detail with other vesicle types as we had for INVs, so we accepted this criticism and changed the title of the paper to make clear that our analysis was centred on INVs. We were offered the chance to publish our paper in Life Science Alliance, an open access publication from EMBO Press, RUP and CSHLP; which we gladly accepted. LSA publishes reviewer comments for transparency. I asked them to include all of the previous reviews but they are unable to publish reviews from other journals, so our file is virtually information-free!
The citation
Sittewelle, M. & Royle, S.J. (2023) Passive diffusion accounts for the majority of intracellular nanovesicle transport. Life Science Alliance Oct 2023, 7 (1) e202302406; DOI: 10.26508/lsa.202302406
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The post title comes from “Crosstown Traffic” by The Jimi Hendrix Experience from their album “Electric Ladyland”.
Really nice – love the idea of making the vesicles furry!