Selected Publications

The ER membrane protein complex restricts mitophagy by controlling BNIP3 turnover.
Delgado JM, Wallace Shepard L, Lamson SW, Liu SL, Shoemaker CJ
EMBO J. 2024. Jan;43(1):32-60. doi: 10.1038/s44318-023-00006-z. Epub 2023 Dec 15.

How mitophagy induction is spatiotemporally controlled remains poorly understood. Here, constitutive delivery of two mitophagy receptors, BNIP3 and BNIP3L/NIX, to lysosomes is shown to control mitophagy in an autophagy-independent manner.

PMID: 38177312

Receptor-mediated clustering of FIP200 bypasses the role of LC3 lipidation in autophagy.
Ohnstad AE, Delgado JM, North BJ, Nasa I, Kettenbach AN, Schultz SW, Shoemaker CJ
EMBO J. 2020 Dec 15;39(24):e104948. doi: 10.15252/embj.2020104948. Epub 2020 Nov 23.

In the absence of LC3 lipidation, receptor-mediated clustering of upstream autophagy factors is sufficient to induce local autophagosome formation and enforce cargo specificity.

PMID: 33226137

TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress.
An H, Ordureau A, Paulo JA, Shoemaker CJ, Denic V, Harper JW
Mol Cell. 2019 Jun 6;74(5):891-908.e10. doi: 10.1016/j.molcel.2019.03.034. Epub 2019 Apr 18.
PMID: 31006537

CRISPR screening using an expanded toolkit of autophagy reporters identifies TMEM41B as a novel autophagy factor.
Shoemaker CJ, Huang TQ, Weir NR, Polyakov NJ, Schultz SW, Denic V
PLoS Biol. 2019 Apr;17(4):e2007044. doi: 10.1371/journal.pbio.2007044. Epub 2019 Apr 1.

Here, we set out to build new reporters for studying mammalian autophagy by genetic screening. This approach allowed us to carry out genome-wide CRISPR-mediated knockout screens that recovered virtually all known mammalian autophagy-related (ATG) factors. In addition, we uncovered several uncharacterized proteins, including the endoplasmic reticulum (ER) transmembrane protein 41B (TMEM41B), which we went on to show is required for normal growth of autophagosome precursor membranes around their targets.

PMID: 30933966

A molecular switch for selective autophagosome formation.
Kamber RA, Shoemaker CJ, Denic V
Autophagy. 2015 Nov 2;11(11):2132-2133.
PMID: 26649944

Receptor-Bound Targets of Selective Autophagy Use a Scaffold Protein to Activate the Atg1 Kinase.
Kamber RA, Shoemaker CJ, Denic V
Mol Cell. 2015 Aug 6;59(3):372-81. doi: 10.1016/j.molcel.2015.06.009. Epub 2015 Jul 9.

We find that a key function of target-bound autophagy receptors is to activate the autophagy kinase, Atg1, via interactions with the scaffold protein Atg11. Our work thus reveals a mechanism by which target recognition coordinates the earliest steps in autophagosome biogenesis.

PMID: 26166702


For a full list of publications, click here.