Autophagy

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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.

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.

• 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.
• Depositor: Dr. Noboru Mizushima

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.

• 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.
• Depositor: Dr. Takahiro Seki

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.

• Depositor: Dr. Itaru Hamachi

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.

• Depositor: Dr. Keiji Kimura

List of gene resources

• Human gene resources
  

  Gene
  AMBRA1	ATG2A	ATG2B	ATG3
  ATG4A	ATG4B	ATG4C	ATG4D
  ATG5	ATG7	ATG9A	ATG10
  ATG12	ATG13	ATG14	ATG16L1
  ATG16L2	ATG101	BECN1	GABARAP
  GABARAPL1	GABARAPL2	IFNG	INS
  MAP1LC3A	MAP1LC3B	PIK3C3	PIK3R4
  PRKAA1	RB1CC1	ULK1	ULK2
  ULK3	VMP1	WDR45	WDR45B
  WIPI1	WIPI2	ZFYVE1

• Mouse gene resources
  

  Gene
  Ambra1	Atg2a	Atg2b	Atg3
  Atg4b	Atg4c	Atg4d	Atg5
  Atg7	Atg12	Atg13	Atg16l1
  Becn1	Gabarapl1	Gabarapl2	Ifng
  Ins1	Kdelr1	Map1lc3a	Map1lc3b
  Pik3r4	Prkaa1	Rb1cc1	Ulk1
  Ulk2	Vmp1	Wdr45b	Wipi1
  Wipi2

• S. pombe gene resources
  

  Gene
  atg1	atg3	atg4	atg5
  atg6	atg7	atg8	atg12
  atg13	atg17	atg18	pik3
  ppk19	SPAC458.06	vac8

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)

• Experimental Animal Division
• Cell Engineering Division

(GSB0021e, T.M. 2014.10.13)

2019.04.24