Evolution of tools and methods for monitoring autophagic flux in mammalian cells

A fluorescence-based imaging method to measure in vitro and in vivo mitophagy using mt-Keima

(2017) Nuo Sun et al.   Nature Protocols

Guidelines for the use and interpretation of assays for monitoring autophagy (3rd edition)

(2016) Daniel J Klionsky et al.   Autophagy

Fluorescence‐based ATG8 sensors monitor localization and function of LC3/GABARAP proteins

(2016) Alexandra Stolz et al.   EMBO JOURNAL

Dedicated SNAREs and specialized TRIM cargo receptors mediate secretory autophagy

(2016) Tomonori Kimura et al.   EMBO JOURNAL

Optineurin: The autophagy connection

(2016) Hongyu Ying et al.   EXPERIMENTAL EYE RESEARCH

LC3/GABARAP family proteins: autophagy-(un)related functions

(2016) Marco B. E. Schaaf et al.   FASEB JOURNAL

Recent insights into the function of autophagy in cancer: Table 1.

(2016) Ravi Amaravadi et al.   GENES & DEVELOPMENT

Atg8 family LC3/GABARAP proteins are crucial for autophagosome–lysosome fusion but not autophagosome formation during PINK1/Parkin mitophagy and starvation

(2016) Thanh Ngoc Nguyen et al.   JOURNAL OF CELL BIOLOGY

A Cyanine Dye to Probe Mitophagy: Simultaneous Detection of Mitochondria and Autolysosomes in Live Cells

(2016) Ying Liu et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

An Autophagic Flux Probe that Releases an Internal Control

(2016) Takeshi Kaizuka et al.   MOLECULAR CELL

The ATG conjugation systems are important for degradation of the inner autophagosomal membrane

(2016) Kotaro Tsuboyama et al.   SCIENCE

Quantitative analysis of autophagic flux by confocal pH-imaging of autophagic intermediates

(2015) Giuseppe Maulucci et al.   Autophagy

A rapid and high content assay that measures cyto-ID-stained autophagic compartments and estimates autophagy flux with potential clinical applications

(2015) Sujuan Guo et al.   Autophagy

A Role for the Ancient SNARE Syntaxin 17 in Regulating Mitochondrial Division

(2015) Kohei Arasaki et al.   DEVELOPMENTAL CELL

Assays to monitor aggrephagy

(2015) Alf Håkon Lystad et al.   METHODS

Selective autophagy: Xenophagy

(2015) Kyle A. Bauckman et al.   METHODS

Regulation of endoplasmic reticulum turnover by selective autophagy

(2015) Aliaksandr Khaminets et al.   NATURE

The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy

(2015) Michael Lazarou et al.   NATURE

ATM functions at the peroxisome to induce pexophagy in response to ROS

(2015) Jiangwei Zhang et al.   NATURE CELL BIOLOGY

The role of autophagy in bacterial infections

(2015) Nayeli Shantal Castrejón-Jiménez et al.   BioScience Trends

Bcl-2-like protein 13 is a mammalian Atg32 homologue that mediates mitophagy and mitochondrial fragmentation

(2015) Tomokazu Murakawa et al.   Nature Communications

The role of autophagy in intracellular pathogen nutrient acquisition

(2015) Shaun Steele et al.   Frontiers in Cellular and Infection Microbiology

“Ciliophagy”

(2014) Suzanne M Cloonan et al.   Autophagy

Autophagic Clearance of PolyQ Proteins Mediated by Ubiquitin-Atg8 Adaptors of the Conserved CUET Protein Family

(2014) Kefeng Lu et al.   CELL

Receptor-mediated mitophagy in yeast and mammalian systems

(2014) Lei Liu et al.   CELL RESEARCH

TRIM Proteins Regulate Autophagy and Can Target Autophagic Substrates by Direct Recognition

(2014) Michael A. Mandell et al.   DEVELOPMENTAL CELL

Quantitative proteomics identifies NCOA4 as the cargo receptor mediating ferritinophagy

(2014) Joseph D. Mancias et al.   NATURE

A Super-Ecliptic, pHluorin-mKate2, Tandem Fluorescent Protein-Tagged Human LC3 for the Monitoring of Mammalian Autophagy

(2014) Isei Tanida et al.   PLoS One

Prosurvival Bcl-2 family members affect autophagy only indirectly, by inhibiting Bax and Bak

(2014) L. M. Lindqvist et al.   PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA

The Role of the Selective Adaptor p62 and Ubiquitin-Like Proteins in Autophagy

(2014) Mónika Lippai et al.   Biomed Research International

Tools and techniques to measure mitophagy using fluorescence microscopy

(2013) Nick J Dolman et al.   Autophagy

Non-autophagic roles of autophagy-related proteins

(2013) Suresh Subramani et al.   EMBO REPORTS

SQSTM1/p62 Interacts with HDAC6 and Regulates Deacetylase Activity

(2013) Jin Yan et al.   PLoS One

Dual roles of Atg8−PE deconjugation by Atg4 in autophagy

(2012) Zhong-Qiu Yu et al.   Autophagy

Mitophagy: mechanisms, pathophysiological roles, and analysis

(2012) Wen-Xing Ding et al.   BIOLOGICAL CHEMISTRY

The Hairpin-type Tail-Anchored SNARE Syntaxin 17 Targets to Autophagosomes for Fusion with Endosomes/Lysosomes

(2012) Eisuke Itakura et al.   CELL

Extracellular M. tuberculosis DNA Targets Bacteria for Autophagy by Activating the Host DNA-Sensing Pathway

(2012) Robert O. Watson et al.   CELL

NBR1 acts as an autophagy receptor for peroxisomes

(2012) E. Deosaran et al.   JOURNAL OF CELL SCIENCE

Galectin 8 targets damaged vesicles for autophagy to defend cells against bacterial invasion

(2012) Teresa L. M. Thurston et al.   NATURE

The Role of Atg Proteins in Autophagosome Formation

(2011) Noboru Mizushima et al.   Annual Review of Cell and Developmental Biology

Starch-binding domain-containing protein 1 (Stbd1) and glycogen metabolism: Identification of the Atg8 family interacting motif (AIM) in Stbd1 required for interaction with GABARAPL1

(2011) Sixin Jiang et al.   BIOCHEMICAL AND BIOPHYSICAL RESEARCH COMMUNICATIONS

NBR1 and p62 as cargo receptors for selective autophagy of ubiquitinated targets

(2011) Trond Lamark et al.   CELL CYCLE

A Sensitive and Quantitative Technique for Detecting Autophagic Events Based on Lysosomal Delivery

(2011) Hiroyuki Katayama et al.   CHEMISTRY & BIOLOGY

Image-based genome-wide siRNA screen identifies selective autophagy factors

(2011) Anthony Orvedahl et al.   NATURE

Midbody accumulation through evasion of autophagy contributes to cellular reprogramming and tumorigenicity

(2011) Tse-Chun Kuo et al.   NATURE CELL BIOLOGY

The intricacy of nuclear membrane dynamics during nucleophagy

(2011) Dalibor Mijaljica et al.   Nucleus

The emerging role of autophagy in the pathophysiology of diabetes mellitus

(2010) Claudio D. Gonzalez et al.   Autophagy

Methods in Mammalian Autophagy Research

(2010) Noboru Mizushima et al.   CELL

LC3 and GATE-16/GABARAP subfamilies are both essential yet act differently in autophagosome biogenesis

(2010) Hilla Weidberg et al.   EMBO JOURNAL

Zymophagy, a Novel Selective Autophagy Pathway Mediated by VMP1-USP9x-p62, Prevents Pancreatic Cell Death

(2010) Daniel Grasso et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

The origin of the autophagosomal membrane

(2010) Sharon A. Tooze et al.   NATURE CELL BIOLOGY

Mechanisms of mitophagy

(2010) Richard J. Youle et al.   NATURE REVIEWS MOLECULAR CELL BIOLOGY

PLIC proteins or ubiquilins regulate autophagy-dependent cell survival during nutrient starvation

(2009) Elsa-Noah N'Diaye et al.   EMBO REPORTS

Nix is a selective autophagy receptor for mitochondrial clearance

(2009) Ivana Novak et al.   EMBO REPORTS

Cathepsin B-mediated Autophagy Flux Facilitates the Anthrax Toxin Receptor 2-mediated Delivery of Anthrax Lethal Factor into the Cytoplasm

(2009) Soon-Duck Ha et al.   JOURNAL OF BIOLOGICAL CHEMISTRY

Reverse pH-Dependence of Chromophore Protonation Explains the Large Stokes Shift of the Red Fluorescent Protein mKeima

(2009) Sebastien Violot et al.   JOURNAL OF THE AMERICAN CHEMICAL SOCIETY

An Atg4B Mutant Hampers the Lipidation of LC3 Paralogues and Causes Defects in Autophagosome Closure

(2008) Naonobu Fujita et al.   MOLECULAR BIOLOGY OF THE CELL

Autophagy fights disease through cellular self-digestion

(2008) Noboru Mizushima et al.   NATURE

Midbody ring disposal by autophagy is a post-abscission event of cytokinesis

(2008) Christian Pohl et al.   NATURE CELL BIOLOGY