Gene Engineering Division > Gene Set Collection > Autophagy

Autophagy

The 2016 Nobel Prize in Physiology or Medicine was awarded to Dr. Yoshinori Ohsumi “for his discoveries of mechanisms for autophagy” [1]. Genetic resources for autophagy study are available. Looking forward to receiving your request.

Resarch Tools of Autophagy and Mitophagy

Visualizing and Modulating Mitophagy for Therapeutic Studies of Neurodegeneration.

Katayama, H., Hama, H., Nagasawa, K., Kurokawa, H., Sugiyama, M., Ando, R., Funata, M., Yoshida, N., Homma, M., Nishimura, T., Takahashi, M., Ishida, Y., Hioki, H., Tsujihata, Y., Miyawaki, A. Cell 181 (5): 1176-1187.e16 (2020). PubMed PMID 32437660.

Catalog no. Name of resource Description
RDB18222 SRAI_pcDNA3 Expression vector of fluorescent protein, SRAI (signal-retaining autophagy indicator) for autophagy sensor.
RDB18223 mito-SRAI_pcDNA3 Expression vector of fluorescent protein, mito-SRAI (signal-retaining autophagy indicator) for quantitative visualizing mitophagy.
RDB18684 pAAV2-TRE-mito-SRAI-BGHpA AAV2 expression vector of mito-SRAI (signal-retaining autophagy indicator) driven by the tetracyclin-responsive element promoter.

Glycolytic suppression dramatically changes the intracellular metabolic profile of multiple cancer cell lines in a mitochondrial metabolism-dependent manner.

Shiratori, R., Furuichi, K., Yamaguchi, M., Miyazaki, N., Aoki, H., Chibana, H., Ito, K., Aoki, S. Sci. Rep. 9 (1): 18699 (2019). PubMed PMID 31822748.

Catalog no. Name of resource Description
RDB18369 mitoKeima-Red Expression vector encoding mitochondrially targeted Keima-Red (mitoKeima-Red).

An Autophagic Flux Probe that Releases an Internal Control.

Kaizuka, T., Morishita, H., Hama, Y., Tsukamoto, S., Matsui, T., Toyota, Y., Kodama, A., Ishihara, T., Mizushima, T., Mizushima, N.
Mol. Cell 64 (4): 835-849 (2016). PubMed PMID 27818143.

Catalog no. Name of resource Description
RDB14601 pMRX-IP-GFP-LC3-RFP Fluorescent probe to evaluate autophagic flux by the rat LC3 fused with GFP and RFP.
RDB14600 pMRX-IP-GFP-LC3-RFP-LC3 delta G Fluorescent probe to evaluate autophagic flux by the rat LC3 fused with GFP and RFP.
  • In order to visualize autophagosome and observe autophagy, MAP1LC3 (LC3) fused with fluorescent proteins as a probe are used. However, the fluorescence of the probe attenuates during autophagy progresses and it is not suitable for quantitative assay of autophagy.
  • Dr. Noboru Mizushima and his colleagues at the University of Tokyo developed a new probe that can expresses GFP-LC3 and RFP-LC3 delta G (lacking glycine (G) at the LC 3 end) simultaneously at equimolar amounts. As autophagy progresses, the fluorescence of GFP-LC3 decays whereas that of RFP-LC3 delta G remains in the cytoplasm as an internal standard. Therefor, the activity of autophagy can be quantified evaluated by the fluorescence intensity ratio of GFP/RFP.
  • Using this probe, autophagic flux was measured in mouse and zebrafish embryos and tissues as well as cultured cells. This is also suitable for analysis of large number of samples.

Establishment of a novel fluorescence-based method to evaluate chaperone-mediated autophagy in a single neuron.

Seki, T., Yoshino, K.I., Tanaka, S., Dohi, E., Onji, T., Yamamoto, K., Hide, I., Paulson, H.L., Saito, N., Sakai, N.
PLoS One 7 (2): e31232 (2012). PubMed PMID 22363588.

Catalog no. Name of resource Description
RDB15088 pcDNA5-GAPDH-HaloTag Expression vector for the visualization of chaperone-mediated autophagy (CMA).
  • The GAPDH-HT indicator is a chaperone-mediated autophagy (CMA) marker consisting of HaloTag and GAPDH which is a typical substrate of CMA. The CMA activity in the cells can be evaluated by using GAPDH-HT indicator and an appropriate under the fluorescent-labeled HaloTag ligand.

References and Related Articles:

  • Sato, M. et al. Fluorescent-based evaluation of chaperone-mediated autophagy and microautophagy activities in cultured cells. Genes Cells 21 (8): 861-873, 2016. PubMed PMID: 27377049

A conditional proteomics approach to identify proteins involved in zinc homeostasis.

Miki, T., Awa, M., Nishikawa, Y., Kiyonaka, S., Wakabayashi, M., Ishihama, Y., Hamachi, I.
Nat. Methods 13 (11): 931-937 (2016). PubMed PMID 27617391.

Catalog no. Name of resource Description
RDB15159 mCherry-LC3B Autophagosome marker. Expression vector of rat Microtubule-associated proteins 1A/1B light chain 3B (LC3B), mCherry tag.

The nucleolar protein nucleophosmin is essential for autophagy induced by inhibiting Pol I transcription.

Katagiri, N., Kuroda, T., Kishimoto, H., Hayashi, Y., Kumazawa, T., Kimura, K.
Sci. Rep. 5: 8903 (2015). PubMed PMID 25754892.

Catalog no. Name of resource Description
RDB13435 pEGFP-C1-hLC3B Indicator of autophagy. Expression clone of human LC3B in mammalian cells.

A sensitive and quantitative technique for detecting autophagic events based on lysosomal delivery.

Katayama, H., Kogure, T., Mizushima, N., Yoshimori, T., Miyawaki, A.
Chem. Biol. 18 (8): 1042-1052 (2011). PubMed PMID 21867919.

Catalog no. Name of resource Description
RDB15236 mKeima (h)/pCS2 Expression vector of monomeric Keima-Red (mKeima).
RDB15237 dKeima (h)/pCS2 Expression vector of dimeric Keima-Red (dKeima).
RDB15238 mt-mKeima (h)/pIND(SP1) Expression vector of monomeric Keima-Red (mKeima) with mitochondria localization signal.
RDB15456 mt-mKeima/pcDNA3 Expression vector of monomeric Keima-Red (mKeima) with mitochondria localization signal.

 

List of gene resources

References

  1. The 2016 Nobel Prize in Physiology or Medicine
  2. Tsukada, M., FEBS Lett. 333 (1-2): 169-174 (1993).
  3. Kabeya, Y., Biochem. Biophys. Res. Commun. 356 (2): 405-410 (2007).
  4. Mizushima, N., Annu. Rev. Cell Dev. Biol. 27: 107-132 (2011).
  5. KEGG Pathway – Autophagy – animal
  6. KEGG Pathway – Autophagy – yeast
  7. KEGG Pathway – Autophagy – other

Other Resources (Riken BRC)

Link to KEGG Pathway – Mitophagy Pathway
List of gene resources
Human [open/close]

Mouse [open/close]

KEGG orthology [open/close]

(GSB0021e, T.M. 2014.10.13)

2022.04.16



 

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