Defining and measuring autophagosome flux—concept and reality

Autophagy. 2014;10(11):2087-96. doi: 10.4161/15548627.2014.973338.


The autophagic system is involved in both bulk degradation of primarily long-lived cytoplasmic proteins as well as in selective degradation of cytoplasmic organelles. Autophagic flux is often defined as a measure of autophagic degradation activity, and a number of methods are currently utilized to assess autophagic flux. However, despite major advances in measuring various molecular aspects of the autophagic machinery, we remain less able to express autophagic flux in a highly sensitive, robust, and well-quantifiable manner. Here, we describe a conceptual framework for defining and measuring autophagosome flux at the single-cell level. The concept discussed here is based on the theoretical framework of metabolic control analysis, which distinguishes between the pathway along which there is a flow of material and the quantitative measure of this flow. By treating the autophagic system as a multistep pathway with each step characterized by a particular rate, we are able to provide a single-cell fluorescence live-cell imaging-based approach that describes the accurate assessment of the complete autophagosome pool size, the autophagosome flux, and the transition time required to turn over the intracellular autophagosome pool. In doing so, this perspective provides clarity on whether the system is at steady state or in a transient state moving towards a new steady state. It is hoped that this theoretical account of quantitatively measuring autophagosome flux may contribute towards a new direction in the field of autophagy, a standardized approach that allows the establishment of systematic flux databases of clinically relevant cell and tissue types that serve as important model systems for human pathologies.

Keywords: CMA, chaperone-mediated autophagy; GFP, green fluorescent protein; J, flux; LC3, microtubule-associated protein 1 light chain 3; TEM, transmission electron microscopy; nA, number of autophagosomes; τ, transition time.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Autophagy*
  • Cytoplasm / metabolism
  • Humans
  • Lysosomes / physiology
  • Macrolides / chemistry
  • Microscopy, Electron, Transmission
  • Microscopy, Fluorescence
  • Microtubule-Associated Proteins / metabolism
  • Phagosomes
  • Time Factors


  • MAP1LC3A protein, human
  • Macrolides
  • Microtubule-Associated Proteins
  • bafilomycin A