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Related Concept Videos

Autophagy01:27

Autophagy

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Autophagy is a self-digesting process by which a cell protects itself from threats both within and outside the cell, ranging from abnormal proteins to invading bacteria. In this process, obsolete components of the cell and invading microbes are degraded by hydrolytic enzymes active in an acidic environment of the lysosomal lumen.
An autophagic pathway consists of a series of signaling events activated in response to diverse stress and physiological conditions such as food deprivation,...
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Autophagic Cell Death01:18

Autophagic Cell Death

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Christian de Duve discovered “autophagy,” a process in which cellular components are engulfed by membrane-bound organelles called autophagosomes. The autophagosomes then fuse with lysosomes to digest the enclosed contents. Autophagy is generally activated in cells to prevent cell death. However, cell death is triggered when the damage is beyond repair.
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Delivery Pathways to the Lysosome01:36

Delivery Pathways to the Lysosome

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Eukaryotic cells use different mechanisms to eliminate toxic waste obsolete and worn-out substances. Lysosomes play a pivotal role in this, and hence, these substances are carried to the lysosome from other parts of the cell and extracellular space through different pathways. The most elaborately studied pathways to the lysosome are the endocytic pathways.
Endocytosis
In endocytosis, the cell membrane takes up macromolecules and particles from the surrounding medium. Clathrin-mediated...
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The Proteasome01:13

The Proteasome

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Eukaryotic cells can degrade proteins through several pathways. One of the most important among these is the ubiquitin-proteasome pathway. It helps the cell eliminate the misfolded, damaged, or unwarranted cytoplasmic proteins in a highly specific manner.
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Covalently Linked Protein Regulators02:04

Covalently Linked Protein Regulators

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Proteins can undergo many types of post-translational modifications, often in response to changes in their environment. These modifications play an important role in the function and stability of these proteins. Covalently linked molecules include functional groups, such as methyl, acetyl, and phosphate groups, and also small proteins, such as ubiquitin. There are around 200 different types of covalent regulators that have been identified.
These groups modify specific amino acids in a protein....
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Export of Misfolded Proteins out of the ER01:32

Export of Misfolded Proteins out of the ER

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After folding, the ER assesses the quality of secretory and membrane proteins. The correctly folded proteins are cleared by the calnexin cycle for transport to their final destination, while misfolded proteins are held back in the ER lumen. The ER chaperones attempt to unfold and refold the misfolded proteins but sometimes fail to achieve the correct native conformation. Such terminally misfolded proteins are then exported to the cytosol by ER-associated degradation or ERAD pathway for...
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Updated: Dec 20, 2025

Study of Protein-protein Interactions in Autophagy Research
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Study of Protein-protein Interactions in Autophagy Research

Published on: September 9, 2017

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Using Reactome to build an autophagy mechanism knowledgebase.

Thawfeek Mohamed Varusai1,2, Steven Jupe3, Cristoffer Sevilla1

  • 1European Molecular Biology Laboratory, European Bioinformatics Institute (EMBL-EBI), Wellcome Genome Campus, Cambridge, UK.

Autophagy
|June 4, 2020
PubMed
Summary
This summary is machine-generated.

Reactome enhances autophagy research by providing a curated knowledgebase of molecular mechanisms. This resource facilitates reliable, comprehensive, and convenient investigation of cellular recycling and stress responses.

Keywords:
AnnotationReactomeautophagybiocurationcurationenrichment analysisknowledgebasemechanistic analysismolecular reactionspathways

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Area of Science:

  • Cellular Biology
  • Molecular Mechanisms
  • Biochemistry

Background:

  • Autophagy is a fundamental cellular process for catabolism and recycling, crucial in both normal function and stress responses.
  • While molecular mechanisms of autophagy (chaperone-mediated autophagy, macroautophagy, microautophagy) are increasingly understood, reliable and comprehensive investigation methods are needed.
  • Reactome offers a freely accessible, manually curated knowledgebase of molecular events and pathways, with integrated data analysis tools.

Purpose of the Study:

  • To discuss the curation and annotation of autophagy mechanisms within the Reactome knowledgebase.
  • To demonstrate Reactome's utility in analyzing autophagy research, including genome-wide screening data.
  • To highlight Reactome as a valuable resource for advancing autophagy research.

Main Methods:

  • Manual curation of molecular events and pathways related to autophagy.
  • Organization and graphical presentation of autophagy pathways within Reactome.
  • Application of Reactome's data analysis tools (e.g., pathway enrichment, expression data overlay) to reanalyze published autophagy research.

Main Results:

  • Detailed curation and annotation of autophagy molecular mechanisms are available in Reactome.
  • Reanalysis of genome-wide CRISPR screening data using Reactome confirmed its value in autophagy research.
  • Reactome provides a structured, annotated, and analyzable platform for autophagy pathway information.

Conclusions:

  • Reactome serves as a powerful, curated resource for understanding the molecular intricacies of autophagy.
  • The knowledgebase facilitates reliable and comprehensive analysis of autophagy mechanisms and related experimental data.
  • Reactome significantly aids researchers in advancing the study of cellular recycling and stress responses through autophagy.