Quantitative analysis of plant ER architecture and dynamics

Nature Communications
Charlotte PainMark Fricker

Abstract

The endoplasmic reticulum (ER) is a highly dynamic polygonal membrane network composed of interconnected tubules and sheets (cisternae) that forms the first compartment in the secretory pathway involved in protein translocation, folding, glycosylation, quality control, lipid synthesis, calcium signalling, and metabolon formation. Despite its central role in this plethora of biosynthetic, metabolic and physiological processes, there is little quantitative information on ER structure, morphology or dynamics. Here we describe a software package (AnalyzER) to automatically extract ER tubules and cisternae from multi-dimensional fluorescence images of plant ER. The structure, topology, protein-localisation patterns, and dynamics are automatically quantified using spatial, intensity and graph-theoretic metrics. We validate the method against manually-traced ground-truth networks, and calibrate the sub-resolution width estimates against ER profiles identified in serial block-face SEM images. We apply the approach to quantify the effects on ER morphology of drug treatments, abiotic stress and over-expression of ER tubule-shaping and cisternal-modifying proteins.

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Citations

Dec 8, 2019·Journal of Experimental Botany·Charlotte Pain, Verena Kriechbaumer
Dec 5, 2019·Annals of Botany·Ulla Neumann, Angela Hay
Oct 23, 2019·Journal of Microscopy·Ulla Neumann
Jun 15, 2019·Journal of Experimental Botany·Joshua J BlakesleeVerena Kriechbaumer
Sep 5, 2020·Annual Review of Genetics·Hao Xu, George W Bassel
Sep 1, 2020·Wiley Interdisciplinary Reviews. Systems Biology and Medicine·Wenjing LiGe Yang
Dec 29, 2020·Journal of Experimental Botany·Elina WelchenDaniel H Gonzalez
Apr 2, 2021·Plant Physiology·Zhiqi LiuLiwen Jiang
Jul 24, 2021·Journal of Plant Physiology·Jingze ZangPengwei Wang
Oct 12, 2021·The Plant Cell·Byung-Ho KangBethany Karlin Zolman
Nov 28, 2021·The Plant Journal : for Cell and Molecular Biology·Enrico CorteseLorella Navazio

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Methods Mentioned

BETA
transgenic
confocal microscopy
electron microscopy
imaging techniques
super-resolution microscopy
PCR

Software Mentioned

Amira
IMOD
MatLab
GIMP
MATLAB Vision Toolbox
AnalyzER

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