News

Just released on BioRxiv - our latest work from Team Lysophagy (Vinay, Sharan, and Melissa) describing a proteomic analysis of lysophagy using proximity biotinylation and lyso-IP. We identified TAX1BP1 as a critical cargo adaptor involved in lysophagic flux, as measured using a new lyso-Keima assay. {https://www.biorxiv.org/content/10.1101/2021.07.19.452535v1}

Introducing Frances Hundley, a new postdoc in the lab who comes to us from the Toczyski lab at UCSF, and Julia Paoli, a research assistant, who comes to us from the University of Illinois. Welcome to you both!!

Many CONGRATULATIONS! to Walter, who has been named a 2020 STAT Wunderkinds! Great news...https://www.statnews.com/wunderkinds/​​

Check out out paper with Rachel Green identifying EDF1 as a key regulator of ribosome collisions - great application fo TMT proteomics to discovery new proteins in polysomes (EDF1). https://elifesciences.org/articles/58828

Congratulations to our neighbors in the Shao lab for the great collaboration with Alban in the lab on the identiifcation of ATP13A1 as a transmembrane dislocase that removes mislocalized tail-anchored proteins from the ER. Such mis-localized proteins include those that normally are localized to mitochondria. Thanks for the great collaboration! https://pubmed.ncbi.nlm.nih.gov/32973005/

Very happy to announce that Kelsey Hickey and Felix Kraus have joined the lab. Kelsey was a graduate student in Jonathan Weissman's lab at UCSF and worked on ribosomal quality control (RQC), including a recent paper in Mol Cell. Felix was a graduate student in Mike Ryan's lab in Melbourne and worked on Dynamin and mitochondrial fission/fusion dynamics. Welsome to both!!

Congratulations to Heeseon and Alban on the publication of their new paper in Nature! An H, Ordureau A, Körner M, Paulo JA, Harper JW. Systematic quantitative analysis of ribosome inventory during nutrient stress. Nature. 2020;583(7815):303-309. doi:10.1038/s41586-020-2446-y

Excited to have Ellen Goodall (from Andy Martin's lab at Berkeley) join the lab as a post-doc and Alex Panov join the lab as a graduate student from the BBS program.

Excited to have Melissa Hoyer join the lab! Recent alum from Gia Voeltz's lab (UC Boulder).

Congratulations to Heeseon and Alban on the publication of their new paper in Molecular Cell identifying a new ER-phagy receptor TEX264. An H, Ordureau A, Paulo JA, Shoemaker CJ, Denic V, Harper JW. TEX264 Is an Endoplasmic Reticulum-Resident ATG8-Interacting Protein Critical for ER Remodeling during Nutrient Stress. Mol Cell. 2019 Apr 11. pii: S1097-2765(19)30258-8. doi: 10.1016/j.molcel.2019.03.034. [Epub ahead of print]

Congratulations to Jin-mi, whose paper on TBK1 and RAB7A appeared recently in Science Advances. In this work, we identify S72 in RAB7A as a target of TBK1 in response to mitochondrial depolarization and activation of the PARKIN pathway for mitophagy. Heo et al., RAB7A phosphorylation by TBK1 promotes mitophagy via the PINK-PARKIN pathway. Science Advances (http://advances.sciencemag.org/content/4/11/eaav0443).

Alban's paper describing digital snapshots of PARKIN activity on mitochondria using Parallel Reaction Monitoring is out in Molecular Cell: Dynamics of PARKIN-Dependent Mitochondrial Ubiquitylation in Induced Neurons and Model Systems Revealed by Digital Snapshot Proteomics. Mol Cell. (2018) 70:211-227.

Our new review on the Parkin-Pink1 pathway is out in a special issue of Nature Reviews - Molecular Cell Biology focused on mitochondrial biology. Check it out!  http://www.nature.com.ezp-prod1.hul.harvard.edu/nrm/journal/v19/n2/index...

Heeseon's paper on ribophagy is now out in Nature Cell Biology...

Autophagy constitutes a major mechanism for recycling of long-lived or damaged proteins. Among the most long-lived and abundant cellular machines in eukaryotes are ribosomes. Multiple quality control mechanisms impinge on ribosome function, including turnover of supernumerary ribosomal subunits and defective nascent chains via the ubiquitin-proteasome system. In contrast, whether and how intact or damaged ribosomes are selectively degraded in order to recover amino acid and nucleic acid building blocks is poorly understood. While nitrogen starvation has been proposed to promote selective autophagic degradation of ribosomes (“ribophagy”) in yeast, it is unclear in mammals: 1) whether ribophagy occurs in a regulated manner, 2) whether ribophagy is promoted through agents that lead to damaged or stalled ribosomes, or particular types of proteotoxic stress, and 3) whether ribosomes and other cytosolic proteins are degraded through parallel pathways in response to proteotoxic stress or agents typically used to induce selective autophagy. Here, we employ genomically encoded mammalian Ribo-Keima reporter cell lines for both large and small ribosomal subunits to systematically quantify ribophagic flux. Ribophagy induced by starvation or mTOR inhibition is VPS34-dependent, but is largely independent of the ATG8 conjugation system. Ribophagy was not induced upon inhibition of translational elongation or nascent chain uncoupling, but was strongly activated upon proteotoxic stress by sodium arsenite and chromosome mis-segregation, dependent upon VPS34 and ATG8 conjugation. When benchmarked against several cytoplasmic Keima reporter proteins, ribophagy was found to be comparatively selective. Interestingly, we found that agents often used to induce selective autophagy also promote ribophagy and autophagic flux of other cytosolic reporters at rates similar to that seen upon induction of bulk autophagy via mTOR inhibition, suggesting widespread “by-stander” degradation during selective autophagy. This study provides the first visualization and quantification of trafficking of ribosomes to the lysosome in mammalian cells, identifies stress agents that promote this process, and demonstrates extensive “by-stander” autophagy during selective autophagy of damaged organelles.

An and Harper (2017) Systematic Analysis of Ribophagy in Human Cells Reveals By-stander Degradation During Selective Autophagy. Nature Cell Biology, online.

Laura's paper analyzing cells lacking ATG8 proteins and discovering RMC1 as a regulator of CCZ1/MON1 is out in MCB (online)...Check it out: https://www-ncbi-nlm-nih-gov.ezp-prod1.hul.harvard.edu/pubmed/29038162

BioPlex 2.0 released.....

The most recent project from the Gygi & Harper Lab’s BioPlex 2.0 (Biophysical Interactions of ORFeome-derived complexes) project, recently featured in Nature, uses affinity purification-mass spectrometry to elucidate protein interaction networks and co-complexes nucleated by more than 25% of protein-coding genes from the human genome. It is currently the largest such network assembled, consisting of 56,000 candidate interactions and more than 29,000 previously unknown co-associations.  We have provided a wealth of data related to protein localization, protein domain interactions, complexes enriched in fitness genes, and complexes liked to many human diseases. You can read further about this project here.

Congratulations to David Rhee in the Harper lab and Danny Scott in the Schulman lab for the recent publication of a paper in Cell describing ARIH1 as an RBR class ubiquitin ligase that works in unison with cullin-RING E3s to control substrate ubiquitylation. This exciting collaboration revealed a new ubiquitin transfer mechanism at play for a subset of CRLs involving CUL1, CUL2, and CUL3 based CRLs.

Congratulations to Virginia, whose paper on QIL1 mutations in patients with early onset fetal mitochondrial encephalopathy recently appeared in eLife. In this work, which was a collaboration with Manuel Schiff's lab in Paris, we found truncation mutations in QIL1 and demonstrated that cells from patients lack itochondrial cristae junctions, and loss of components of these structures. Cells and tissues from patients also have defects in complex IV activity. 

Christian's paper on the mitochondrial Unfolded Protein Response (UPR) has now appeared in Nature. Congratulations!

In this paper, we use proteomics and RNA-Seq to describe the cells response to protein misfolding in the mitochondrial matrix. We find large numbers of changes in transcription and protein content in mitochondria after acute mitochondrial misfolding. Surprisingly we found that UPRmt blocks the activity of mitochondrial RNAse P, responsible for processing mitochondrial Pre-RNA and also blocks translation in the matrix. This study provides a framework for understanding mitochondrial UPR.

Joe and Laura's analysis of NCOA4 and ferritinophagy has appeared in Elife!!! In 2014, we discovered NCOA4 and demonstrated a role for it in the targeting of ferritin to autophagosomes to control iron availability. NCOA4 binds directly to ferritin and targets it to autophagosomes, which facilitates delivery of ferritin to the lysosome wheere its degradation leads to the release of iron. However, how ferritinophagy flux is controlled and the roles of NCOA4 in iron-dependent processes are poorly understood. Through analysis of the NCOA4-FTH1 interaction, we demonstrate that direct association via a key surface arginine in FTH1 and a C-terminal element in NCOA4 is required for delivery of ferritin to the lysosome via autophagosomes. Moreover, NCOA4 abundance is under dual control via autophagy and the ubiquitin proteasome system. Ubiquitin-dependent NCOA4 turnover is promoted by excess iron and involves an iron-dependent interaction between NCOA4 and the HERC2 ubiquitin ligase. In zebrafish and cultured cells, NCOA4 plays an essential role in erythroid differentiation. This work reveals the molecular nature of the NCOA4-ferritin complex and explains how intracellular iron levels modulate NCOA4-mediated ferritinophagy in cells and in an iron-dependent physiological setting.