Abstract
The endoplasmic reticulum (ER) is a complex subcellular organelle composed of diverse structures such as tubules, sheets and tubular matrices. Flaviviruses such as Zika virus (ZIKV) induce reorganization of ER membranes to facilitate viral replication. Here, using 3D super resolution microscopy, ZIKV infection is shown to induce the formation of dense tubular matrices associated with viral replication in the central ER. Viral non-structural proteins NS4B and NS2B associate with replication complexes within the ZIKV-induced tubular matrix and exhibit distinct ER distributions outside this central ER region. Deep neural networks trained to distinguish ZIKV-infected versus mock-infected cells successfully identified ZIKV-induced central ER tubular matrices as a determinant of viral infection. Super resolution microscopy and deep learning are therefore able to identify and localize morphological features of the ER and allow for better understanding of how ER morphology changes due to viral infection.
Highlights
The endoplasmic reticulum (ER) is a highly dynamic network composed of 30–100 nm ribosome-studded rough ER sheets and convoluted networks of smooth ER tubules[1,2]
2D STimulated Emission Depletion microscopy (STED) super-resolution microscopy combined with high-speed live cell or rapid fixation approaches showed that RTN and CLIMP-63 regulate the ER macrostructure of rough ER sheets vs smooth ER tubules and the nanodomain organization of sheets and tubules imaged in the cell periphery[5,6]
Zika virus (ZIKV) infection is characterized by re-organization of the ER to create replication factories and convoluted ER membranes involved in viral replication, whose ultrastructure has been elegantly characterized by E M19,25
Summary
The endoplasmic reticulum (ER) is a highly dynamic network composed of 30–100 nm ribosome-studded rough ER sheets and convoluted networks of smooth ER tubules[1,2]. 2D STimulated Emission Depletion microscopy (STED) super-resolution microscopy combined with high-speed live cell or rapid fixation approaches showed that RTN and CLIMP-63 regulate the ER macrostructure of rough ER sheets vs smooth ER tubules and the nanodomain organization of sheets and tubules imaged in the cell periphery[5,6] Increasing both 3D spatial and temporal resolution with various super resolution imaging techniques, including 3D structured illumination (SIM), grazing incidence structured illumination (GI-SIM) and lattice light sheet point accumulation for imaging in nanoscale topography (LLS-PAINT), showed that peripheral sheets were dense tubular m atrices[7]. The NS proteins form the replication complexes and play key roles in the evasion of the host innate immune response, the hijacking of host cellular pathways, and the reorganization of ER membranes to promote viral replication[24]. We use 3D STED super-resolution microscopy to show that ZIKV infection induces the reorganization of the CER to form dense tubular matrices associated with ZIKV replication sites. We further apply deep learning approaches to identify ZIKV-infected cells based on changes in ER morphology and use class activation maps (CAMs) to identify the ZIKV-induced dense tubular matrix
Sign-in/Register to view highlights & summary Sign-in/Register to access full text options 
Talk to us
Join us for a 30 min session where you can share your feedback and ask us any queries you have
Schedule a call
