Fluid mechanics of luminal transport in actively contracting endoplasmic reticulum
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Curated by eLife
eLife assessment
This study explores the physical principles underlying fluid flow and luminal transport within the endoplasmic reticulum; its important contribution is to highlight the strong physical constraints imposed by viscous dissipation in nanoscopic tubular networks. In particular, the work presents convincing evidence that commonly discussed mechanisms such as tubular contraction are unlikely to be at the origin of the observed transport velocities. As this study is solely theoretical and concerned with order of magnitude estimates, its main conclusions await experimental validation. The work will be of relevance to cell biologists and physicists interested in organelle dynamics.
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Abstract
The Endoplasmic Reticulum (ER), the largest cellular compartment, harbours the machinery for the biogenesis of secretory proteins, lipids, calcium storage/mobilisation and detoxification. It is shaped as layered membranous sheets interconnected with a network of tubules extending throughout the cell. Understanding the influence of the ER morphology dynamics on molecular transport may offer clues to rationalising neuro-pathologies caused by ER morphogen mutations. It remains unclear, however, how the ER facilitates its intra-luminal mobility and homogenises its content, and the minuscule spatial and temporal scales relevant to the ER nanofluidics limit empirical studies. To surmount this barrier, here we exploit the principles of viscous fluid dynamics to generate a theoretical physical model emulating in-silico the content motion in actively contracting nanoscopic tubular networks. The computational model reveals the luminal particle speeds, and their impact in facilitating active transport, of the active contractile behaviour of the different ER components along various time-space parameters. The results of the model indicate that reproducing transport with velocities similar to those reported experimentally in single particle tracking would require unrealistically high values of tubule contraction site length and rate. Considering further nanofluidic scenarios, we show that width contractions of the ER’s flat domains (perinuclear sheets) generate fast-decaying flows with only a short-range effect on luminal transport. Only contraction of peripheral sheets can reproduce experimental measurements, provided they are able to contract fast enough.
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Author Response
Reviewer #1 (Public Review):
Theoretical principles of viscous fluid mechanics are used here to assess likely mechanisms of transport in the ER. A set of candidate mechanisms is evaluated, making good use of imaging to represent ER network geometries. Evidence is provided that the contraction of peripheral sheets provides a much more credible mechanism than the contraction of individual tubules, junctions, or perinuclear sheets.
The work has been conducted carefully and comprehensively, making good use of underlying physical principles. There is a good discussion of the role of slip; sensible approximations (low volume fraction, small particle size, slender geometries, pragmatic treatment of boundary conditions) allow tractable and transparent calculations; clear physical arguments provide useful bounds; stochastic …
Author Response
Reviewer #1 (Public Review):
Theoretical principles of viscous fluid mechanics are used here to assess likely mechanisms of transport in the ER. A set of candidate mechanisms is evaluated, making good use of imaging to represent ER network geometries. Evidence is provided that the contraction of peripheral sheets provides a much more credible mechanism than the contraction of individual tubules, junctions, or perinuclear sheets.
The work has been conducted carefully and comprehensively, making good use of underlying physical principles. There is a good discussion of the role of slip; sensible approximations (low volume fraction, small particle size, slender geometries, pragmatic treatment of boundary conditions) allow tractable and transparent calculations; clear physical arguments provide useful bounds; stochastic and deterministic features of the problem are well integrated.
We thank the reviewer for their positive assessment of our work.
There are just a couple of areas where more discussion might be warranted, in my view.
(1) The energetic cost of tubule contraction is estimated, but I did not see an equivalent estimate for the contraction of peripheral sheets. It might be helpful to estimate the energetic cost of viscous dissipation in generated flows at higher frequencies.
This is a good point. We will also include an energetic cost estimate for the contractions of peripheral sheets in the revised manuscript.
The mechanism of peripheral sheet contraction is unclear: do ATP-driven mechanisms somehow interact with thermal fluctuations of membranes?
The new energetic estimates in the revision might help constrain possible hypotheses for the mechanism(s) driving peripheral sheet contraction, and suggest if a dedicated ATP-driven mechanism is required.
(2) Mutations are mentioned in the abstract but not (as far as I could see) later in the manuscript. It would be helpful if any consequences for pathologies could be developed in the text.
We are grateful for this suggestion. The need to rationalise pathology associated with the subtle effects of ER-morphogens’ mutations is indeed pointed out as one factor motivating the study of the interplay between ER structure and performance. In the revised manuscript, we plan to include a brief discussion potentially linking ER morphogenes’ malfunction to luminal transport, integrating additional freshly published data.
Reviewer #2 (Public Review):
Summary:
This study explores theoretically the consequences of structural fluctuations of the endoplasmic reticulum (ER) morphology called contractions on molecular transport. Most of the manuscript consists of the construction of an interesting theoretical flow field (physical model) under various hypothetical assumptions. The computational modeling is followed by some simulations
Strengths:
The authors are focusing their attention on testing the hypothesis that a local flow in the tubule could be driven by tubular pinching. We recall that trafficking in the ER is considered to be mostly driven by diffusion at least at a spatial scale that is large enough to account for averaging of any random flow occurring from multiple directions [note that this is not the case for plants].
We thank the reviewer. We have indeed explored here the possibilities of active transport, focusing especially on transport over the length scale of single tubules, as a result of structural fluctuations, and found tubular pinching to be ineffective compared to e.g. peripheral sheets fluctuations. In the revised version we plan to add text mentioning what is known about the ER in plants.
Weaknesses:
The manuscript extensively details the construction of the theoretical model, occupying a significant portion of the manuscript. While this section contains interesting computations, its relevance and utility could be better emphasized, perhaps warranting a reorganization of the manuscript to foreground this critical aspect.
Overall, the manuscript appears highly technical with limited conclusive insights, particularly lacking predictions confirmed by experimental validation. There is an absence of substantial conclusions regarding molecular trafficking within the ER.
We sought to balance the theoretical/computational details of our model with the biophysical conclusions drawn from its predictions. Given the model's complexity and novelty, it was essential to elucidate the theoretical underpinnings comprehensively, in order to allow others to implement it in the future with additional, or different, parameters. To maintain clarity and focus in the main text, we have judiciously relegated extensive technical details to the methods section or supplementary materials, and divided the text into stand-alone section headings allowing the reader to skip through to conclusions.
The primary focus of our manuscript is to introduce and explore, via our theoretical model, the interplay between ER structure dynamics and molecular transport. Our approach, while in silico, generates concrete predictions about the physical processes underpinning luminal motion within the ER. For instance, our findings challenge the previously postulated role of small tubular contractions in driving luminal flow, instead highlighting the potential significance of local flat ER areas—empirically documented entities—for facilitating such motion.
Furthermore, by deducing what type of transport may or may not occur within the range of possible ER structural fluctuations, our model offers detailed predictions designed to bridge the gap between theoretical insight and experimental verification. These predictions detail the spatial and temporal parameters essential for effective transport, delineating plausible values for these parameters. We hope that the model’s predictions will invite experimentalists to devise innovative methodologies to test them. We plan to introduce text edits to the revised version to clarify these.
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eLife assessment
This study explores the physical principles underlying fluid flow and luminal transport within the endoplasmic reticulum; its important contribution is to highlight the strong physical constraints imposed by viscous dissipation in nanoscopic tubular networks. In particular, the work presents convincing evidence that commonly discussed mechanisms such as tubular contraction are unlikely to be at the origin of the observed transport velocities. As this study is solely theoretical and concerned with order of magnitude estimates, its main conclusions await experimental validation. The work will be of relevance to cell biologists and physicists interested in organelle dynamics.
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Reviewer #1 (Public Review):
Theoretical principles of viscous fluid mechanics are used here to assess likely mechanisms of transport in the ER. A set of candidate mechanisms is evaluated, making good use of imaging to represent ER network geometries. Evidence is provided that the contraction of peripheral sheets provides a much more credible mechanism than the contraction of individual tubules, junctions, or perinuclear sheets.
The work has been conducted carefully and comprehensively, making good use of underlying physical principles. There is a good discussion of the role of slip; sensible approximations (low volume fraction, small particle size, slender geometries, pragmatic treatment of boundary conditions) allow tractable and transparent calculations; clear physical arguments provide useful bounds; stochastic and deterministic …
Reviewer #1 (Public Review):
Theoretical principles of viscous fluid mechanics are used here to assess likely mechanisms of transport in the ER. A set of candidate mechanisms is evaluated, making good use of imaging to represent ER network geometries. Evidence is provided that the contraction of peripheral sheets provides a much more credible mechanism than the contraction of individual tubules, junctions, or perinuclear sheets.
The work has been conducted carefully and comprehensively, making good use of underlying physical principles. There is a good discussion of the role of slip; sensible approximations (low volume fraction, small particle size, slender geometries, pragmatic treatment of boundary conditions) allow tractable and transparent calculations; clear physical arguments provide useful bounds; stochastic and deterministic features of the problem are well integrated.
There are just a couple of areas where more discussion might be warranted, in my view.
(1) The energetic cost of tubule contraction is estimated, but I did not see an equivalent estimate for the contraction of peripheral sheets. It might be helpful to estimate the energetic cost of viscous dissipation in generated flows at higher frequencies. The mechanism of peripheral sheet contraction is unclear: do ATP-driven mechanisms somehow interact with thermal fluctuations of membranes?
(2) Mutations are mentioned in the abstract but not (as far as I could see) later in the manuscript. It would be helpful if any consequences for pathologies could be developed in the text.
-
Reviewer #2 (Public Review):
Summary:
This study explores theoretically the consequences of structural fluctuations of the endoplasmic reticulum (ER) morphology called contractions on molecular transport. Most of the manuscript consists of the construction of an interesting theoretical flow field (physical model) under various hypothetical assumptions. The computational modeling is followed by some simulations
Strengths:
The authors are focusing their attention on testing the hypothesis that a local flow in the tubule could be driven by tubular pinching. We recall that trafficking in the ER is considered to be mostly driven by diffusion at least at a spatial scale that is large enough to account for averaging of any random flow occurring from multiple directions [note that this is not the case for plants].
Weaknesses:
The manuscript …
Reviewer #2 (Public Review):
Summary:
This study explores theoretically the consequences of structural fluctuations of the endoplasmic reticulum (ER) morphology called contractions on molecular transport. Most of the manuscript consists of the construction of an interesting theoretical flow field (physical model) under various hypothetical assumptions. The computational modeling is followed by some simulations
Strengths:
The authors are focusing their attention on testing the hypothesis that a local flow in the tubule could be driven by tubular pinching. We recall that trafficking in the ER is considered to be mostly driven by diffusion at least at a spatial scale that is large enough to account for averaging of any random flow occurring from multiple directions [note that this is not the case for plants].
Weaknesses:
The manuscript extensively details the construction of the theoretical model, occupying a significant portion of the manuscript. While this section contains interesting computations, its relevance and utility could be better emphasized, perhaps warranting a reorganization of the manuscript to foreground this critical aspect.
Overall, the manuscript appears highly technical with limited conclusive insights, particularly lacking predictions confirmed by experimental validation. There is an absence of substantial conclusions regarding molecular trafficking within the ER.
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