Quantitative Proteome Analysis of Atg5 -Deficient Mouse Embryonic Fibroblasts Reveals the Range of the Autophagy-Modulated Basal Cellular Proteome

Abstract

Autophagy performs housekeeping functions for cells and maintains a functional mode by degrading damaged proteins and organelles and providing energy under starvation conditions. The process is tightly regulated by the evolutionarily conserved Atg genes, of which Atg5 is one such crucial mediator. Here, we have done a comprehensive quantitative proteome analysis of mouse embryonic fibroblasts that lack a functional autophagy pathway (Atg5 knockout). We observe that 14% of the identified cellular proteome is remodeled, and several proteins distributed across diverse cellular processes with functions in signaling, cell adhesion, development, and immunity show either higher or lower levels under autophagy-deficient conditions. These cells have lower levels of crucial immune proteins that are required to mount a protective inflammatory response. This study will serve as a valuable resource to determine the role of autophagy in modulating specific protein levels in cells.

Lycium barbarum polysaccharide protects against ethanol‐induced spermiotoxicity and testicular degeneration in Immp2l +/− mice

“…Tandem Mass Tag was applied (Park et al, 2019; Sharma et al, 2019) for the analysis of testis proteins in our study. The results revealed 114 differentially expressed proteins between ethanol group and control, including 64 upregulated proteins (56.14% of those that were differentially expressed) and 50 downregulated proteins (43.86%).…”

Activation of cGAS/STING pathway upon paramyxovirus infection

“…Upon infection of MeV and/or NiV in mouse and/or human cells, the absence of cGAS/STING pathway affects IFNβ response and to a lower and more variable extent IFNα response. Owing to cell-dependent ability to produce IFNα, a different outcome may reflect higher expression of IRF-7 in pMEFs ( Sharma et al., 2019 ) compared with THP-1 cells ( Green et al., 2020 ). Indeed, whereas activation of the IFNβ gene optimally relies on IRF3 homodimers or IRF3/IRF7 heterodimers and NF-κB ( Honda et al., 2005 ; Wathelet et al., 1998 ), the one for IFNα genes relies mostly relies on IRF7 homodimers ( Yeow et al., 2000 ).…”

Proteomic landscape of Japanese encephalitis virus-infected fibroblasts

“…The experimental system was designed for eight-plex TMT-based mass spectrometry analysis. The PCA plot, schematic workflow for eight-plex TMT-based proteomics, detailed description of the sample preparation, mass spectrometry data acquisition, database search and quantification are described in our previous study [18]. For this study, we have analysed four samples comprising two biological replicates each of uninfected and JEV-infected MEFs.…”

“…After the required hours post-infection, supernatant was collected for plaque assay and cells were harvested for RNA isolation, Western blotting or immunostaining according to the design of experiment. Western blots were performed as described previously [18].…”