Cited by 199Autophagy in Disease and TherapyParkinson's Disease Mechanisms and TreatmentsCellular transport and secretion

RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway

Open access
Heo, J.-M., Ordureau, A., Swarup, S., Paulo, J. A., Shen, K., Sabatini, D. M., Harper, J. W.·2018·Science Advances

Abstract

TBK1 phosphorylates RAB7A-S72 to support multiple downstream steps in PARKIN-dependent mitophagy.

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Integrity signals

Registry

Crossref · 10.1126/sciadv.aav0443

Cites

4 of 4 references verified0 citation errors · 0 not checkable

Statistics

Claims the paper makes

The claims and statistics of this paper haven’t been checked yet.

Run the check — free, no account needed. It reads the open-access text and checks the sources it cites.

A few free checks a day · papers already verified open instantly · results are public

Claims other papers make about this one

Each is checked against this paper’s own text: does it say what the citing paper says it does?

  • RAB7A is located in the HOPS, Rab proteins involved in autophagosome formation, and mitophagy core sub-groups.

    “Indeed, some genes belong to more than one category due to their multiple role (indicated in red in the Supplementary Table 1): for example, the regulator of vesicular transport “RAB7A” is located in i) the “HOPS” [32], ii) the “Rab proteins involved in autophagosome formation” [33], and iii) the “mitophagy core” [34] sub-groups.”

    From A gene toolbox for monitoring autophagy transcription (2021) · cites this paper as [34]

Self-check

Percentages, sums and reported differences re-computed from the paper’s own numbers.

The self-check needs the paper’s full text.

Cites

Flagged first, then by citations

Research works printed but not linked: 47

  1. [1]Pickles S., Vigié P., Youle R. J., Mitophagy and quality control mechanisms in mitochondrial maintenance. Curr. Biol. 28, R170– R185 (2018). 29462587 PMC7255410
  2. [2]Harper J. W., Ordureau A., Heo J.-M., Building and decoding ubiquitin chains for mitophagy. Nat. Rev. Mol. Cell. Biol. 19, 93– 108 (2018). 29358684
  3. [3]Sekine S., Youle R. J., PINK1 import regulation; a fine system to convey mitochondrial stress to the cytosol. BMC Biol. 16, 2 (2018). 29325568 PMC5795276
  4. [4]Yamano K., Matsuda N., Tanaka K., The ubiquitin signal and autophagy: An orchestrated dance leading to mitochondrial degradation. EMBO Rep. 17, 300– 316 (2016). 26882551 PMC4772979
  5. [5]Wong Y. C., Holzbaur E. L. F., Optineurin is an autophagy receptor for damaged mitochondria in parkin-mediated mitophagy that is disrupted by an ALS-linked mutation. Proc. Natl. Acad. Sci. U.S.A. 111, E4439– 4448 (2014). 25294927 PMC4210283
  6. [6]Lazarou M., Sliter D. A., Kane L. A., Sarraf S. A., Wang C., Burman J. L., Sideris D. P., Fogel A. I., Youle R. J., The ubiquitin kinase PINK1 recruits autophagy receptors to induce mitophagy. Nature 524, 309– 314 (2015). 26266977 PMC5018156
  7. [7]Heo J.-M., Ordureau A., Paulo J. A., Rinehart J., Harper J. W., The PINK1-PARKIN mitochondrial ubiquitylation pathway drives a program of OPTN/NDP52 recruitment and TBK1 activation to promote mitophagy. Mol. Cell 60, 7– 20 (2015). 26365381 PMC4592482
  8. [8]Moore A. S., Holzbaur E. L., Dynamic recruitment and activation of ALS-associated TBK1 with its target optineurin are required for efficient mitophagy. Proc. Natl. Acad. Sci. U.S.A. 113, E3349– 3358 (2016). 27247382 PMC4914160
  9. [10]Stolz A., Ernst A., Dikic I., Cargo recognition and trafficking in selective autophagy. Nat. Cell Biol. 16, 495– 501 (2014). 24875736
  10. [11]Grumati P., Dikic I., Ubiquitin signaling and autophagy. J. Biol. Chem. 293, 5404– 5413 (2018). 29187595 PMC5900779
  11. [12]Wild P., Farhan H., McEwan D. G., Wagner S., Rogov V. V., Brady N. R., Richter B., Korac J., Waidmann O., Choudhary C., Dötsch V., Bumann D., Dikic I., Phosphorylation of the autophagy receptor optineurin restricts Salmonella growth. Science 333, 228– 233 (2011). 21617041 PMC3714538
  12. [14]Gleason C. E., Ordureau A., Gourlay R., Arthur J. S., Cohen P., Polyubiquitin binding to optineurin is required for optimal activation of TANK-binding kinase 1 and production of interferon β. J. Biol. Chem. 286, 35663– 35674 (2011). 21862579 PMC3195586
  13. [15]Thurston T. L. M., Boyle K. B., Allen M., Ravenhill B. J., Karpiyevich M., Bloor S., Kaul A., Noad J., Foeglein A., Matthews S. A., Komander D., Bycroft M., Randow F., Recruitment of TBK1 to cytosol-invading Salmonella induces WIPI2-dependent antibacterial autophagy. EMBO J. 35, 1779– 1792 (2016). 27370208 PMC5010046
  14. [16]Yamano K., Fogel A. I., Wang C., van der Bliek A. M., Youle R. J., Mitochondrial Rab GAPs govern autophagosome biogenesis during mitophagy. eLife 3, e01612 (2014). 24569479 PMC3930140
  15. [17]Yamano K., Wang C., Sarraf S. A., Munch C., Kikuchi R., Noda N. N., Hizukuri Y., Kanemaki M. T., Harper W., Tanaka K., Matsuda N., Youle R. J., Endosomal Rab cycles regulate Parkin-mediated mitophagy. eLife 7, e31326 (2018). 29360040 PMC5780041
  16. [18]Jimenez-Orgaz A., Kvainickas A., Nägele H., Denner J., Eimer S., Dengjel J., Steinberg F., Control of RAB7 activity and localization through the retromer-TBC1D5 complex enables RAB7-dependent mitophagy. EMBO J. 37, 235– 254 (2018). 29158324 PMC5770787
  17. [19]Hegedus K., Takáts S., Boda A., Jipa A., Varga K., Kovács A. L., Juhász G., The Ccz1-Mon1-Rab7 module and Rab5 control distinct steps of autophagy. Mol. Biol. Cell 27, 3132– 3142 (2016). 27559127 PMC5063620
  18. [20]Lamb C. A., Yoshimori T., Tooze S. A., The autophagosome: Origins unknown, biogenesis complex. Nat. Rev. Mol. Cell Biol. 14, 759– 774 (2013). 24201109
  19. [21]Steger M., Tonelli F., Ito G., Davies P., Trost M., Vetter M., Wachter S., Lorentzen E., Duddy G., Wilson S., Baptista M. A., Fiske B. K., Fell M. J., Morrow J. A., Reith A. D., Alessi D. R., Mann M., Phosphoproteomics reveals that Parkinson’s disease kinase LRRK2 regulates a subset of Rab GTPases. eLife 5, e12813 (2016). 26824392 PMC4769169
  20. [22]Purlyte E., Dhekne H. S., Sarhan A. R., Gomez R., Lis P., Wightman M., Martinez T. N., Tonelli F., Pfeffer S. R., Alessi D. R., Rab29 activation of the Parkinson’s disease-associated LRRK2 kinase. EMBO J. 37, 1– 18 (2018). 29212815 PMC5753036
  21. [24]Tsun Z. Y., Bar-Peled L., Chantranupong L., Zoncu R., Wang T., Kim C., Spooner E., Sabatini D. M., The folliculin tumor suppressor is a GAP for the RagC/D GTPases that signal amino acid levels to mTORC1. Mol. Cell 52, 495– 505 (2013). 24095279 PMC3867817
  22. [25]Shen K., Choe A., Sabatini D. M., Intersubunit crosstalk in the Rag GTPase heterodimer enables mTORC1 to respond rapidly to amino acid availability. Mol. Cell 68, 552– 565.e8 (2017). 29056322 PMC5674802
  23. [26]McAlister G. C., Nusinow D. P., Jedrychowski M. P., Wühr M., Huttlin E. L., Erickson B. K., Rad R., Haas W., Gygi S. P., MultiNotch MS3 enables accurate, sensitive, and multiplexed detection of differential expression across cancer cell line proteomes. Anal. Chem. 86, 7150– 7158 (2014). 24927332 PMC4215866
  24. [27]Ordureau A., Sarraf S. A., Duda D. M., Heo J. M., Jedrychowski M. P., Sviderskiy V. O., Olszewski J. L., Koerber J. T., Xie T., Beausoleil S. A., Wells J. A., Gygi S. P., Schulman B. A., Harper J. W., Quantitative proteomics reveal a feedforward mechanism for mitochondrial PARKIN translocation and ubiquitin chain synthesis. Mol. Cell 56, 360– 375 (2014). 25284222 PMC4254048
  25. [28]Pfeffer S. R., Structural clues to Rab GTPase functional diversity. J. Biol. Chem. 280, 15485– 15488 (2005). 15746102
  26. [29]Wandinger-Ness A., Zerial M., Rab proteins and the compartmentalization of the endosomal system. Cold Spring Harb. Perspect. Biol. 6, a022616 (2014). 25341920 PMC4413231
  27. [30]Weintz G., Olsen J. V., Frühauf K., Niedzielska M., Amit I., Jantsch J., Mages J., Frech C., Dölken L., Mann M. M., Lang R., The phosphoproteome of toll-like receptor-activated macrophages. Mol. Syst. Biol. 6, 371 (2010). 20531401 PMC2913394
  28. [31]Trost M., English L., Lemieux S., Courcelles M., Desjardins M., Thibault P., The phagosomal proteome in interferon-gamma-activated macrophages. Immunity 30, 143– 154 (2009). 19144319
  29. [32]Toyofuku T., Morimoto K., Sasawatari S., Kumanogoh A., Leucine-rich repeat kinase 1 regulates autophagy through turning on TBC1D2-dependent Rab7 inactivation. Mol. Cell. Biol. 35, 3044– 3058 (2015). 26100023 PMC4525318
  30. [33]Rose C. M., Isasa M., Ordureau A., Prado M. A., Beausoleil S. A., Jedrychowski M. P., Finley D. J., Harper J. W., Gygi S. P., Highly multiplexed quantitative mass spectrometry analysis of ubiquitylomes. Cell Syst. 3, 395– 403.e4 (2016). 27667366 PMC5241079
  31. [34]Lai Y.-C., Kondapalli C., Lehneck R., Procter J. B., Dill B. D., Woodroof H. I., Gourlay R., Peggie M., Macartney T. J., Corti O., Corvol J.-C., Campbell D. G., Itzen A., Trost M., Muqit M. M. K., Phosphoproteomic screening identifies Rab GTPases as novel downstream targets of PINK1. EMBO J. 34, 2840– 2861 (2015). 26471730 PMC4654935
  32. [35]Aerni H. R., Shifman M. A., Rogulina S., O’Donoghue P., Rinehart J., Revealing the amino acid composition of proteins within an expanded genetic code. Nucleic Acids Res. 43, e8 (2015). 25378305 PMC4333366
  33. [36]Marat A. L., Dokainish H., McPherson P. S., DENN domain proteins: Regulators of Rab GTPases. J. Biol. Chem. 286, 13791– 13800 (2011). 21330364 PMC3077579
  34. [37]Ordureau A., Paulo J. A., Zhang W., Ahfeldt T., Zhang J., Cohn E. F., Hou Z., Heo J.-M., Rubin L. L., Sidhu S. S., Gygi S. P., Harper J. W., Dynamics of PARKIN-dependent mitochondrial ubiquitylation in induced neurons and model systems revealed by digital snapshot proteomics. Mol. Cell 70, 211– 227 (2018). 29656925 PMC5910199
  35. [38]Ordureau A., Heo J.-M., Duda D. M., Paulo J. A., Olszewski J. L., Yanishevski D., Rinehart J., Schulman B. A., Harper J. W., Defining roles of PARKIN and ubiquitin phosphorylation by PINK1 in mitochondrial quality control using a ubiquitin replacement strategy. Proc. Natl. Acad. Sci. U.S.A. 112, 6637– 6642 (2015). 25969509 PMC4450373
  36. [40]Weishaupt J. H., Hyman T., Dikic I., Common molecular pathways in amyotrophic lateral sclerosis and frontotemporal dementia. Trends Mol. Med. 22, 769– 783 (2016). 27498188
  37. [41]Shinde S. R. Maddika S., PTEN modulates EGFR late endocytic trafficking and degradation by dephosphorylating Rab7. Nat. Commun. 7, 10689 (2016). 26869029 PMC4754336
  38. [42]Laviolette L. A., Mermoud J., Calvo I. A., Olson N., Boukhali M., Steinlein O. K., Roider E., Sattler E. C., Huang D., Teh B. T., Motamedi M., Haas W., Iliopoulos O., Negative regulation of EGFR signalling by the human folliculin tumour suppressor protein. Nat. Commun. 8, 15866 (2017). 28656962 PMC5493755
  39. [43]Wu X., Bradley M. J., Cai Y., Kümmel D., De La Cruz E. M., Barr F. A., Reinisch K. M., Insights regarding guanine nucleotide exchange from the structure of a DENN-domain protein complexed with its Rab GTPase substrate. Proc. Natl. Acad. Sci. U.S.A. 108, 18672– 18677 (2011). 22065758 PMC3219131
  40. [44]Meng J., Ferguson S. M., GATOR1-dependent recruitment of FLCN-FNIP to lysosomes coordinates Rag GTPase heterodimer nucleotide status in response to amino acids. J. Cell Biol. 217, 2765– 2776 (2018). 29848618 PMC6080935
  41. [45]Baba M., Hong S.-B., Sharma N., Warren M. B., Nickerson M. L., Iwamatsu A., Esposito D., Gillette W. K., Hopkins R. F. III, Hartley J. L., Furihata M., Oishi S., Zhen W., Burke T. R. Jr., Linehan W. M., Schmidt L. S., Zbar B., Folliculin encoded by the BHD gene interacts with a binding protein, FNIP1, and AMPK, and is involved in AMPK and mTOR signaling. Proc. Natl. Acad. Sci. U.S.A. 103, 15552– 15557 (2006). 17028174 PMC1592464
  42. [46]Behrends C., Sowa M. E., Gygi S. P., Harper J. W., Network organization of the human autophagy system. Nature 466, 68– 76 (2010). 20562859 PMC2901998
  43. [47]Starling G. P., Yip Y. Y., Sanger A., Morton P. E., Eden E. R., Dodding M. P., Folliculin directs the formation of a Rab34–RILP complex to control the nutrient-dependent dynamic distribution of lysosomes. EMBO Rep. 17, 823– 841 (2016). 27113757 PMC4893818
  44. [48]Paulo J. A., Gygi S. P., Isobaric tag-based protein profiling of a nicotine-treated alpha7 nicotinic receptor-null human haploid cell line. Proteomics 18, e1700475 (2018). 29663646 PMC5990481
  45. [49]Huttlin E. L., Jedrychowski M. P., Elias J. E., Goswami T., Rad R., Beausoleil S. A., Villén J., Haas W., Sowa M. E., Gygi S. P., A tissue-specific atlas of mouse protein phosphorylation and expression. Cell 143, 1174– 1189 (2010). 21183079 PMC3035969
  46. [50]Tyanova S., Temu T., Sinitcyn P., Carlson A., Hein M. Y., Geiger T., Mann M., Cox J., The Perseus computational platform for comprehensive analysis of (prote)omics data. Nat. Methods 13, 731– 740 (2016). 27348712
  47. [51]Aguado C., Pérez-Jiménez E., Lahuerta M., Knecht E., Isolation of lysosomes from mammalian tissues and cultured cells. Methods Mol. Biol. 1449, 299– 311 (2016). 27613045

Cited by

Sorted by citations

  • A gene toolbox for monitoring autophagy transcription

    Bordi, M., De Cegli, R., Testa, B., Nixon, R. A., Ballabio, A., & Cecconi, F. (2021) · Cell Death & Disease · doi:10.1038/s41419-021-04121-9 · Cited by 131 · see citing works

    “Indeed, some genes belong to more than one category due to their multiple role (indicated in red in the Supplementary Table 1): for example, the regulator of vesicular transport “RAB7A” is located in i) the “HOPS” [32], ii) the “Rab proteins involved in autophagosome formation” [33], and iii) the “mitophagy core” [34]…”
    Background

Authors
Heo, J.-M., Ordureau, A., Swarup, S., Paulo, J. A., Shen, K., Sabatini, D. M., & Harper, J. W.
Affiliations
  • Harvard University (US)
  • Broad Institute (US)
Corresponding author
Harper, J. W.
Venue
Science Advances
Published
2018-11-02
Volume
4
Issue
11
Pages
eaav0443-eaav0443
ISSN
2375-2548 (ISSN-L)
OpenAlex
W2900687171
Cited by
199
References
4
Citations by year
2026: 20 · 2025: 35 · 2024: 34 · 2023: 23 · 2022: 22 · 2021: 27 · 2020: 24 · 2019: 14
FWCI
12.69
Type
journal article
Language
en
Open access
Locations
  • Science Advances (publishedVersion)
  • Europe PMC (PubMed Central) (publishedVersion, cc-by-nc)
  • PubMed Central (publishedVersion, cc-by-nc)
  • PubMed (publishedVersion)
  • DSpace@MIT (Massachusetts Institute of Technology) (submittedVersion, cc-by-nc)
Funders
  • National Institutes of Health (NS083524, GM095567, CA103866, AI47389, DK098285)
  • Howard Hughes Medical Institute
  • Michael J. Fox Foundation for Parkinson’s Research (15866)
Topics
  • Health Sciences › Medicine › Epidemiology › Autophagy in Disease and Therapy
  • Health Sciences › Medicine › Neurology › Parkinson's Disease Mechanisms and Treatments
  • Life Sciences › Biochemistry, Genetics and Molecular Biology › Cell Biology › Cellular transport and secretion
Keywords
Rab7, TBK1, mitophagy, PINK1, Parkin, protein phosphorylation, ATG9A, LRRK2, autophagy
MeSH terms
Autophagy-Related Proteins, rab7 GTP-Binding Proteins, PTEN-Induced Putative Kinase, HeLa Cells, Humans, Membrane Proteins, Mitochondria, Phosphorylation, Protein Kinases, Proto-Oncogene Proteins, Protein Serine-Threonine Kinases, rab GTP-Binding Proteins, Tumor Suppressor Proteins, Vesicular Transport Proteins, Ubiquitin-Protein Ligases, Ubiquitination, Mitophagy

About these checks

Registry, retraction, Cites and statistics results are computed, not judged, with one exception: a printed reference that no index lists is read once by a model before it counts as a citation error. Claims are extracted by a model and kept only when their quote appears verbatim in the text; each cited source is then checked, with a model’s help, for whether it says what the claim relies on. Those verdicts can be wrong — read the claim’s quote and the cited source before relying on one.

Statistics and arithmetic are recomputed, not judged.

Confidence bands are shown only for fields calibrated on our annotated test set. None is calibrated yet, so no band is shown.

What counts as a claim ›How we measure confidence ›How we check this ›

Are you an author, or do you see a problem with this page? Request a review