Single particle trajectories reveal active endoplasmic reticulum luminal flow

Holcman, David; Parutto, Pierre; Chambers, Joseph E.; Fantham, Marcus; Young, Laurence J.; Marciniak, Stefan J.; Kaminski, Clemens F.; Ron, David; Avezov, Edward

doi:10.1038/s41556-018-0192-2

Cited by 85 publications

(177 citation statements)

References 28 publications

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“…Our data does not however report directly on diffusion of the lumenal ERmoxGFP reporter in ER tubules. The relationship between RTN4a and CLIMP-63 regulation of ER nanodomains and the slower diffusion of lumenal ER reporters in ER tubules relative to cytoplasm (33) or the contractions associated with nano-peristalsis along ER tubules (18) remains to be determined.…”

Section: Discussionmentioning

confidence: 99%

“…Single particle tracking has identified active lumenal flow within ER tubules (18). By high-speed 2D STED imaging, ER lumenal periodicities are highly dynamic and present rapid oscillations ( Fig.…”

Section: Discussionmentioning

confidence: 99%

“…A more recent STED analysis identified the presence of dynamic nanoholes in peripheral ER sheets (17). Single molecule super-resolution particle tracking of an ER lumenal reporter demonstrated the existence of active ER lumenal flow in peripheral ER tubules (18) while high-speed, super resolution GI-SIM microscopy identified lumenal bulges and constrictions along ER tubules (19).…”

Section: Introductionmentioning

confidence: 98%

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Reticulon and CLIMP-63 control nanodomain organization of peripheral ER tubules

Gao

Zhu

Liu

et al. 2019

Preprint

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The endoplasmic reticulum (ER) is an expansive, membrane-enclosed organelle composed of smooth peripheral tubules and rough, ribosome-studded central ER sheets whose morphology is determined, in part, by the ER-shaping proteins, reticulon and CLIMP-63, respectively. Here, STimulated Emission Depletion (STED) super-resolution microscopy shows that reticulon4a (RTN4a) and CLIMP-63 also regulate the organization and dynamics of peripheral ER tubule nanodomains. STED imaging shows that lumenal ERmoxGFP, membrane Sec61bGFP, knock-in calreticulin-GFP and antibody-labeled ER resident proteins calnexin and derlin-1 are all localized to periodic puncta along the length of peripheral ER tubules that are not readily observable by diffraction limited confocal microscopy. RTN4a segregates away from and restricts lumenal blob length while CLIMP-63 associates with and increases lumenal blob length. RTN4a and CLIMP-63 also regulate the nanodomain distribution of ER resident proteins, being required for the preferential segregation of calnexin and derlin-1 puncta away from lumenal ERmoxGFP blobs. High-speed (40 ms/frame) live cell STED imaging shows that RTN4a and CLIMP-63 regulate dynamic nanoscale lumenal compartmentalization along peripheral ER tubules. RTN4a enhances and CLIMP-63 disrupts the local accumulation of lumenal ERmoxGFP at spatially defined sites along ER tubules. The ER shaping proteins reticulon and CLIMP-63 therefore regulate lumenal ER nanodomain heterogeneity, interaction with ER resident proteins and dynamics in peripheral ER tubules.

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Section: Discussionmentioning

confidence: 99%

Section: Discussionmentioning

confidence: 99%

Section: Introductionmentioning

confidence: 98%

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Reticulon and CLIMP-63 control nanodomain organization of peripheral ER tubules

Gao

Zhu

Liu

et al. 2019

Preprint

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“…While extracting the diffusion coefficient D c of a single chromatin locus is limited due to many factors affecting the statistical evaluation of this variable, it is possible to extract the diffusion coefficient from many different trajectories. Indeed, instead of computing the diffusion coefficient along trajectories, it is possible to combine a massive number (10 4 − 10 5 ) of super-resolution trajectories to reconstruct a diffusion map inside cellular environments, membranes and the nucleus for a variety of fluorescently tagged proteins such as histones, receptors, cytosolic proteins [48,22,21,35,23,40,46,36,32,38,33].…”

Section: Diffusion Coefficientmentioning

confidence: 99%

Single particle trajectory statistic to reconstruct chromatin organization and dynamics

Shukron

Seeber

Amitai

et al. 2019

Preprint

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Chromatin organization remains complex and far from understood. We discuss here recent statistical methods to extract biophysical parameters from in vivo single particle trajectories of loci to reconstruct chromatin reorganization in response to cellular stress such as DNA damages. We look at the methods to analyze both single loci as well as multiple loci tracked simultaneously and explain how to quantify and describe chromatin motion using a combination of extractable parameters. These parameters can be converted into information about chromatin dynamics and function. Furthermore, we discuss how the time scale of recurrent motion of a locus can be extracted and converted into local chromatin dynamics. We also discuss the effect of various sampling rates on the estimated parameters. Finally, we discuss polymer methods based on cross-linkers that account for minimal loop constraints hidden in tracked loci, that reveal chromatin organization at the 250nm spatial scale. We list and refer to some algorithm packages that are now publicly available. To conclude, chromatin organization and dynamics at hundreds of nanometers can be reconstructed from locus trajectories and predicted based on polymer models.

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“…This motion is hypothesized to increase the rate of reactions and therefore the rate of protein biosynthesis. Peristalsis of the ER tubules has also been postulated (28), although little quantitative data has yet been presented for this model.…”

Section: Introductionmentioning

confidence: 99%

Network Organisation and the Dynamics of Tubules in the Endoplasmic Reticulum

Perkins

Ducluzaux

Woodman

et al. 2020

Preprint

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The endoplasmic reticulum (ER) is a eukaryotic subcellular organelle composed of tubules and sheetlike areas of membrane connected at junctions. The tubule network is highly dynamic and undergoes rapid and continual rearrangement. There are currently few tools to evaluate network organisation and dynamics. We quantified ER network organisation in Vero and MRC5 cells, and developed a classification system for ER dynamics in live cells. The persistence length, tubule length, junction coordination number and angles of the network were quantified. Hallmarks of imbalances in ER tension, indications of interactions with microtubules and other subcellular organelles, and active reorganisation and dynamics were observed. Live cell ER tubule dynamics were classified using a Gaussian mixture model, defining tubule motion as active or thermal and conformational phase space analysis allowed this classification to be refined by tubule curvature states. STATEMENT OF SIGNIFICANCEThe endoplasmic reticulum (ER), a subcellular organelle, is an underexplored real-world example of active matter. Many processes essential to cell survival are performed by the ER, the efficacy of which may depend on its organisation and dynamics. Abnormal ER morphology is linked to diseases such as hereditary spastic paraplegias and it is possible that the dynamics are also implicated. Therefore, analysing the ER network in normal cells is important for the understanding of diseaserelated alterations. In this work, we outline the first thorough quantification methods for determining ER organisation and dynamics, deducing that tubule motion has a binary classification as active or thermal. Active reorganisation and dynamics along with indications of tension imbalances and membrane contact sites were observed.

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Single particle trajectories reveal active endoplasmic reticulum luminal flow

Cited by 85 publications

References 28 publications

Reticulon and CLIMP-63 control nanodomain organization of peripheral ER tubules

Reticulon and CLIMP-63 control nanodomain organization of peripheral ER tubules

Single particle trajectory statistic to reconstruct chromatin organization and dynamics

Network Organisation and the Dynamics of Tubules in the Endoplasmic Reticulum

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