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Article ; Online: Mechanisms Controlling Selective Elimination of Damaged Lysosomes.

Hoyer, Melissa J / Swarup, Sharan / Harper, J Wade

2022 Volume 29

Abstract: Lysosomes are subjected to physiological and patho-physiological insults over the course of their life cycle and are accordingly repaired or recycled. Lysophagy, the selective degradation of lysosomes via autophagy, occurs upon unrepairable lysosomal ... ...

Abstract	Lysosomes are subjected to physiological and patho-physiological insults over the course of their life cycle and are accordingly repaired or recycled. Lysophagy, the selective degradation of lysosomes via autophagy, occurs upon unrepairable lysosomal membrane rupture; galectins bind to glycosylated macromolecules in the lysosome lumen, orchestrating a series of cellular responses to promote autophagic recycling of damaged lysosomes and transcriptional upregulation of lysosomal genes. Damaged lysosomes are ubiquitylated, resulting in the recruitment of ubiquitin-binding autophagy receptors, which promote assembly of an autophagosome around damaged lysosomes for delivery to healthy lysosomes for degradation. Here, we review the current state of our understanding of mechanisms used to mark and eliminate damaged lysosomes, and discuss the complexities of galectin function and ubiquitin-chain linkage types. Finally, we discuss the limitations of available data and challenges with the goal of understanding the mechanistic basis of key steps in lysophagic flux.
Language	English
Publishing date	2022-08-30
Publishing country	England
Document type	Journal Article
ZDB-ID	2918626-2
ISSN	2468-8673 ; 2468-8681
ISSN (online)	2468-8673
ISSN	2468-8681
DOI	10.1016/j.cophys.2022.100590
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Article ; Online: Proteome census upon nutrient stress reveals Golgiphagy membrane receptors.

Hickey, Kelsey L / Swarup, Sharan / Smith, Ian R / Paoli, Julia C / Miguel Whelan, Enya / Paulo, Joao A / Harper, J Wade

Nature

2023 Volume 623, Issue 7985, Page(s) 167–174

Abstract: During nutrient stress, macroautophagy degrades cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodelling the ... ...

Abstract	During nutrient stress, macroautophagy degrades cellular macromolecules, thereby providing biosynthetic building blocks while simultaneously remodelling the proteome
MeSH term(s)	Animals ; Autophagy/physiology ; Autophagy-Related Protein 8 Family/metabolism ; Endoplasmic Reticulum ; Golgi Apparatus/metabolism ; Mammals/metabolism ; Membrane Proteins/metabolism ; Nutrients/metabolism ; Proteome/metabolism ; Proteomics
Chemical Substances	Autophagy-Related Protein 8 Family ; Membrane Proteins ; Proteome
Language	English
Publishing date	2023-09-27
Publishing country	England
Document type	Journal Article
ZDB-ID	120714-3
ISSN	1476-4687 ; 0028-0836
ISSN (online)	1476-4687
ISSN	0028-0836
DOI	10.1038/s41586-023-06657-6
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Article ; Online: Quantitative proteomics reveals the selectivity of ubiquitin-binding autophagy receptors in the turnover of damaged lysosomes by lysophagy.

Eapen, Vinay V / Swarup, Sharan / Hoyer, Melissa J / Paulo, Joao A / Harper, J Wade

eLife

2021 Volume 10

Abstract: Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the ... ...

Abstract	Removal of damaged organelles via the process of selective autophagy constitutes a major form of cellular quality control. Damaged organelles are recognized by a dedicated surveillance machinery, leading to the assembly of an autophagosome around the damaged organelle, prior to fusion with the degradative lysosomal compartment. Lysosomes themselves are also prone to damage and are degraded through the process of lysophagy. While early steps involve recognition of ruptured lysosomal membranes by glycan-binding galectins and ubiquitylation of transmembrane lysosomal proteins, many steps in the process, and their interrelationships, remain poorly understood, including the role and identity of cargo receptors required for completion of lysophagy. Here, we employ quantitative organelle capture and proximity biotinylation proteomics of autophagy adaptors, cargo receptors, and galectins in response to acute lysosomal damage, thereby revealing the landscape of lysosome-associated proteome remodeling during lysophagy. Among the proteins dynamically recruited to damaged lysosomes were ubiquitin-binding autophagic cargo receptors. Using newly developed lysophagic flux reporters including Lyso-Keima, we demonstrate that TAX1BP1, together with its associated kinase TBK1, are both necessary and sufficient to promote lysophagic flux in both HeLa cells and induced neurons (iNeurons). While the related receptor Optineurin (OPTN) can drive damage-dependent lysophagy when overexpressed, cells lacking either OPTN or CALCOCO2 still maintain significant lysophagic flux in HeLa cells. Mechanistically, TAX1BP1-driven lysophagy requires its N-terminal SKICH domain, which binds both TBK1 and the autophagy regulatory factor RB1CC1, and requires upstream ubiquitylation events for efficient recruitment and lysophagic flux. These results identify TAX1BP1 as a central component in the lysophagy pathway and provide a proteomic resource for future studies of the lysophagy process.
MeSH term(s)	Autophagy/genetics ; Humans ; Lysosomes/pathology ; Macroautophagy/physiology ; Protein Binding ; Proteomics ; Ubiquitin/metabolism
Chemical Substances	Ubiquitin
Language	English
Publishing date	2021-09-29
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2687154-3
ISSN	2050-084X ; 2050-084X
ISSN (online)	2050-084X
ISSN	2050-084X
DOI	10.7554/eLife.72328
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Article: Lysosomal storage disease proteo/lipidomic profiling using nMOST links ferritinophagy with mitochondrial iron deficiencies in cells lacking NPC2.

Kraus, Felix / He, Yuchen / Swarup, Sharan / Overmyer, Katherine A / Jiang, Yizhi / Brenner, Johann / Capitanio, Cristina / Bieber, Anna / Jen, Annie / Nightingale, Nicole M / Anderson, Benton J / Lee, Chan / Paulo, Joao A / Smith, Ian R / Plitzko, Jürgen M / Schulman, Brenda A / Wilfling, Florian / Coon, Joshua J / Wade Harper, J

bioRxiv : the preprint server for biology

2024

Abstract: Lysosomal storage diseases (LSDs) comprised ~50 monogenic diseases characterized by the accumulation of cellular material in lysosomes and associated defects in lysosomal function, but systematic molecular phenotyping is lacking. Here, we develop a ... ...

Abstract	Lysosomal storage diseases (LSDs) comprised ~50 monogenic diseases characterized by the accumulation of cellular material in lysosomes and associated defects in lysosomal function, but systematic molecular phenotyping is lacking. Here, we develop a nanoflow-based multi-omic single-shot technology (nMOST) workflow allowing simultaneously quantify HeLa cell proteomes and lipidomes from more than two dozen LSD mutants, revealing diverse molecular phenotypes. Defects in delivery of ferritin and its autophagic receptor NCOA4 to lysosomes (ferritinophagy) were pronounced in NPC2
Language	English
Publishing date	2024-03-27
Publishing country	United States
Document type	Preprint
DOI	10.1101/2024.03.26.586828
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Article ; Online: Wnt/Wingless signaling in Drosophila.

Swarup, Sharan / Verheyen, Esther M

Cold Spring Harbor perspectives in biology

2012 Volume 4, Issue 6

Abstract: The Wingless (Wg) pathway represents one of the best-characterized intercellular signaling networks. Studies performed in Drosophila over the last 30 years have contributed to our understanding of the role of Wg signaling in the regulation of tissue ... ...

Abstract	The Wingless (Wg) pathway represents one of the best-characterized intercellular signaling networks. Studies performed in Drosophila over the last 30 years have contributed to our understanding of the role of Wg signaling in the regulation of tissue growth, polarity, and patterning. These studies have revealed mechanisms conserved in the vertebrate Wnt pathways and illustrate the elegance of using the Drosophila model to understand evolutionarily conserved modes of gene regulation. In this article, we describe the function of Wg signaling in patterning the Drosophila embryonic epidermis and wing imaginal disc. As well, we present an overview of the establishment of the Wg morphogen gradient and discuss the differential modes of Wg-regulated gene expression.
MeSH term(s)	Animals ; Drosophila/metabolism ; Drosophila Proteins/metabolism ; Models, Theoretical ; Signal Transduction ; Wnt Proteins/metabolism ; Wnt1 Protein/metabolism
Chemical Substances	Drosophila Proteins ; Wnt Proteins ; Wnt1 Protein ; wg protein, Drosophila
Language	English
Publishing date	2012-06-01
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't ; Review
ISSN	1943-0264
ISSN (online)	1943-0264
DOI	10.1101/cshperspect.a007930
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Article ; Online: Spatial snapshots of amyloid precursor protein intramembrane processing via early endosome proteomics.

Park, Hankum / Hundley, Frances V / Yu, Qing / Overmyer, Katherine A / Brademan, Dain R / Serrano, Lia / Paulo, Joao A / Paoli, Julia C / Swarup, Sharan / Coon, Joshua J / Gygi, Steven P / Wade Harper, J

Nature communications

2022 Volume 13, Issue 1, Page(s) 6112

Abstract: Degradation and recycling of plasma membrane proteins occurs via the endolysosomal system, wherein endosomes bud into the cytosol from the plasma membrane and subsequently mature into degradative lysosomal compartments. While methods have been developed ... ...

Abstract	Degradation and recycling of plasma membrane proteins occurs via the endolysosomal system, wherein endosomes bud into the cytosol from the plasma membrane and subsequently mature into degradative lysosomal compartments. While methods have been developed for rapid selective capture of lysosomes (Lyso-IP), analogous methods for isolation of early endosome intermediates are lacking. Here, we develop an approach for rapid isolation of early/sorting endosomes through affinity capture of the early endosome-associated protein EEA1 (Endo-IP) and provide proteomic and lipidomic snapshots of EEA1-positive endosomes in action. We identify recycling, regulatory and membrane fusion complexes, as well as candidate cargo, providing a proteomic landscape of early/sorting endosomes. To demonstrate the utility of the method, we combined Endo- and Lyso-IP with multiplexed targeted proteomics to provide a spatial digital snapshot of amyloid precursor protein (APP) processing by β and γ-Secretases, which produce amyloidogenic Aβ species, and quantify small molecule modulation of Secretase action on endosomes. We anticipate that the Endo-IP approach will facilitate systematic interrogation of processes that are coordinated on EEA1-positive endosomes.
MeSH term(s)	Amyloid Precursor Protein Secretases/metabolism ; Amyloid beta-Peptides/metabolism ; Amyloid beta-Protein Precursor/metabolism ; Endosomes/metabolism ; Membrane Proteins/metabolism ; Proteomics
Chemical Substances	Amyloid beta-Peptides ; Amyloid beta-Protein Precursor ; Membrane Proteins ; Amyloid Precursor Protein Secretases (EC 3.4.-)
Language	English
Publishing date	2022-10-16
Publishing country	England
Document type	Journal Article ; Research Support, N.I.H., Extramural ; Research Support, Non-U.S. Gov't
ZDB-ID	2553671-0
ISSN	2041-1723 ; 2041-1723
ISSN (online)	2041-1723
ISSN	2041-1723
DOI	10.1038/s41467-022-33881-x
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Article ; Online: Genome-wide identification of phospho-regulators of Wnt signaling in Drosophila.

Swarup, Sharan / Pradhan-Sundd, Tirthadipa / Verheyen, Esther M

Development (Cambridge, England)

2015 Volume 142, Issue 8, Page(s) 1502–1515

Abstract: Evolutionarily conserved intercellular signaling pathways regulate embryonic development and adult tissue homeostasis in metazoans. The precise control of the state and amplitude of signaling pathways is achieved in part through the kinase- and ... ...

Abstract	Evolutionarily conserved intercellular signaling pathways regulate embryonic development and adult tissue homeostasis in metazoans. The precise control of the state and amplitude of signaling pathways is achieved in part through the kinase- and phosphatase-mediated reversible phosphorylation of proteins. In this study, we performed a genome-wide in vivo RNAi screen for kinases and phosphatases that regulate the Wnt pathway under physiological conditions in the Drosophila wing disc. Our analyses have identified 54 high-confidence kinases and phosphatases capable of modulating the Wnt pathway, including 22 novel regulators. These candidates were also assayed for a role in the Notch pathway, and numerous phospho-regulators were identified. Additionally, each regulator of the Wnt pathway was evaluated in the wing disc for its ability to affect the mechanistically similar Hedgehog pathway. We identified 29 dual regulators that have the same effect on the Wnt and Hedgehog pathways. As proof of principle, we established that Cdc37 and Gilgamesh/CK1γ inhibit and promote signaling, respectively, by functioning at analogous levels of these pathways in both Drosophila and mammalian cells. The Wnt and Hedgehog pathways function in tandem in multiple developmental contexts, and the identification of several shared phospho-regulators serve as potential nodes of control under conditions of aberrant signaling and disease.
MeSH term(s)	Animals ; Casein Kinase I/genetics ; Casein Kinase I/metabolism ; Cell Cycle Proteins/genetics ; Cell Cycle Proteins/metabolism ; Drosophila ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Hedgehog Proteins/genetics ; Hedgehog Proteins/metabolism ; Molecular Chaperones/genetics ; Molecular Chaperones/metabolism ; Receptors, G-Protein-Coupled/genetics ; Receptors, G-Protein-Coupled/metabolism ; Receptors, Notch/genetics ; Receptors, Notch/metabolism ; Smoothened Receptor ; Wings, Animal/metabolism ; Wnt Proteins/genetics ; Wnt Proteins/metabolism ; Wnt1 Protein/genetics ; Wnt1 Protein/metabolism
Chemical Substances	Cdc37 protein, Drosophila ; Cell Cycle Proteins ; Drosophila Proteins ; Hedgehog Proteins ; Molecular Chaperones ; N protein, Drosophila ; Receptors, G-Protein-Coupled ; Receptors, Notch ; Smoothened Receptor ; Wnt Proteins ; Wnt1 Protein ; smo protein, Drosophila ; wg protein, Drosophila ; hh protein, Drosophila (149291-21-4) ; Casein Kinase I (EC 2.7.11.1) ; gish protein, Drosophila (EC 2.7.11.1)
Language	English
Publishing date	2015-04-07
Publishing country	England
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	90607-4
ISSN	1477-9129 ; 0950-1991
ISSN (online)	1477-9129
ISSN	0950-1991
DOI	10.1242/dev.116715
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Article ; Online: Drosophila homeodomain-interacting protein kinase inhibits the Skp1-Cul1-F-box E3 ligase complex to dually promote Wingless and Hedgehog signaling.

Swarup, Sharan / Verheyen, Esther M

Proceedings of the National Academy of Sciences of the United States of America

2011 Volume 108, Issue 24, Page(s) 9887–9892

Abstract: Drosophila Homeodomain-interacting protein kinase (Hipk) has been shown to regulate in vivo, the stability of Armadillo, the transcriptional effector of Wingless signaling. The Wingless pathway culminates in the stabilization of Armadillo that, in the ... ...

Abstract	Drosophila Homeodomain-interacting protein kinase (Hipk) has been shown to regulate in vivo, the stability of Armadillo, the transcriptional effector of Wingless signaling. The Wingless pathway culminates in the stabilization of Armadillo that, in the absence of signaling, is sequentially phosphorylated, polyubiquitinated and degraded. Loss-of-function clones for hipk result in reduced stabilized Armadillo, whereas overexpression of hipk elevates Armadillo levels to promote Wingless-responsive target gene expression. Here, we show that overexpression of hipk can suppress the effects of negative regulators of Armadillo to prevent its degradation in the wing imaginal disc. Hipk acts to stabilize Armadillo by impeding the function of the E3 ubiquitin ligase Skp1-Cul1-F-box (SCF)(Slimb), thereby inhibiting Armadillo ubiquitination and subsequent degradation. Vertebrate Hipk2 displays a similar ability to prevent β-catenin ubiquitination in a functionally conserved mechanism. We find that Hipk's ability to inhibit SCF(Slimb)-mediated ubiquitination is not restricted to Armadillo and extends to other substrates of SCF(Slimb), including the Hedgehog signaling effector Ci. Thus, similar to casein kinase 1 and glycogen synthase kinase 3, Hipk dually regulates both Wingless and Hedgehog signaling by controlling the stability of their respective signaling effectors, but it is the first kinase to our knowledge identified that promotes the stability of both Armadillo and Ci.
MeSH term(s)	Animals ; Animals, Genetically Modified ; Armadillo Domain Proteins/genetics ; Armadillo Domain Proteins/metabolism ; Blotting, Western ; COS Cells ; Cell Line ; Chlorocebus aethiops ; DNA-Binding Proteins/genetics ; DNA-Binding Proteins/metabolism ; Drosophila Proteins/genetics ; Drosophila Proteins/metabolism ; Drosophila melanogaster/cytology ; Drosophila melanogaster/genetics ; Drosophila melanogaster/metabolism ; Female ; HEK293 Cells ; Hedgehog Proteins/genetics ; Hedgehog Proteins/metabolism ; Humans ; Immunoprecipitation ; Male ; Phosphorylation ; Protein Binding ; Protein Kinases/genetics ; Protein Kinases/metabolism ; SKP Cullin F-Box Protein Ligases/genetics ; SKP Cullin F-Box Protein Ligases/metabolism ; Signal Transduction ; Transcription Factors/genetics ; Transcription Factors/metabolism ; Transfection ; Ubiquitination ; Wings, Animal/metabolism ; Wnt1 Protein/genetics ; Wnt1 Protein/metabolism
Chemical Substances	ARM protein, Drosophila ; Armadillo Domain Proteins ; DNA-Binding Proteins ; Drosophila Proteins ; Hedgehog Proteins ; Transcription Factors ; Wnt1 Protein ; ci protein, Drosophila ; wg protein, Drosophila ; hh protein, Drosophila (149291-21-4) ; SKP Cullin F-Box Protein Ligases (EC 2.3.2.27) ; Protein Kinases (EC 2.7.-) ; HIPK protein, Drosophila (EC 2.7.11.1)
Language	English
Publishing date	2011-05-31
Publishing country	United States
Document type	Journal Article ; Research Support, Non-U.S. Gov't
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1017548108
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Article: Drosophila homeodomain-interacting protein kinase inhibits the Skp1-Cul1-F-box E3 ligase complex to dually promote Wingless and Hedgehog signaling

Swarup, Sharan / Verheyen, Esther M

Proceedings of the National Academy of Sciences of the United States of America. 2011 June 14, v. 108, no. 24

2011

Abstract	Drosophila Homeodomain-interacting protein kinase (Hipk) has been shown to regulate in vivo, the stability of Armadillo, the transcriptional effector of Wingless signaling. The Wingless pathway culminates in the stabilization of Armadillo that, in the absence of signaling, is sequentially phosphorylated, polyubiquitinated and degraded. Loss-of-function clones for hipk result in reduced stabilized Armadillo, whereas overexpression of hipk elevates Armadillo levels to promote Wingless-responsive target gene expression. Here, we show that overexpression of hipk can suppress the effects of negative regulators of Armadillo to prevent its degradation in the wing imaginal disc. Hipk acts to stabilize Armadillo by impeding the function of the E3 ubiquitin ligase Skp1-Cul1-F-box (SCF)Slimb, thereby inhibiting Armadillo ubiquitination and subsequent degradation. Vertebrate Hipk2 displays a similar ability to prevent Î²-catenin ubiquitination in a functionally conserved mechanism. We find that Hipk's ability to inhibit SCFSlimb-mediated ubiquitination is not restricted to Armadillo and extends to other substrates of SCFSlimb, including the Hedgehog signaling effector Ci. Thus, similar to casein kinase 1 and glycogen synthase kinase 3, Hipk dually regulates both Wingless and Hedgehog signaling by controlling the stability of their respective signaling effectors, but it is the first kinase to our knowledge identified that promotes the stability of both Armadillo and Ci.
Keywords	Drosophila ; adverse effects ; clones ; gene overexpression ; loss-of-function mutation ; non-specific serine/threonine protein kinase ; tau-protein kinase ; transcription (genetics) ; ubiquitin-protein ligase ; ubiquitination ; vertebrates
Language	English
Dates of publication	2011-0614
Size	p. 9887-9892.
Publishing place	National Academy of Sciences
Document type	Article
ZDB-ID	209104-5
ISSN	1091-6490 ; 0027-8424
ISSN (online)	1091-6490
ISSN	0027-8424
DOI	10.1073/pnas.1017548108
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Article: Hipk proteins dually regulate Wnt/Wingless signal transduction

Verheyen, Esther M / Swarup, Sharan / Lee, Wendy

Fly. 2012 Apr. 1, v. 6, no. 2

2012

Abstract: The Wnt/Wingless (Wg) pathway is an evolutionarily conserved signaling system that is used reiteratively, both spatially and temporally, to control the development of multicellular animals. The stability of cytoplasmic β-catenin/Armadillo, the ... ...

Abstract	The Wnt/Wingless (Wg) pathway is an evolutionarily conserved signaling system that is used reiteratively, both spatially and temporally, to control the development of multicellular animals. The stability of cytoplasmic β-catenin/Armadillo, the transcriptional effector of the pathway, is controlled by sequential N-terminal phosphorylation and ubiquitination that targets it for proteasome-mediated degradation. Orthologous members of the Homeodomain-interacting protein kinase family from Drosophila to vertebrates have been implicated in the regulation of Wnt/Wingless signaling. In Drosophila, as a consequence of Hipk activity, cells accumulate stabilized Armadillo that directs the expression of Wg-specific target genes. Hipk promotes the stabilization of Armadillo by inhibiting its ubiquitination (and hence subsequent degradation) by the SCFSˡⁱᵐᵇ E3 ubiquitin ligase complex. Vertebrate Hipk2 impedes β-catenin ubiquitination to promote its stability and the Wnt signal in a mechanism that is functionally conserved. Moreover, we describe here that Hipk proteins have a role independent of their effect on β-catenin/Armadillo stability to enhance Wnt/Wingless signaling.
Keywords	Drosophila ; cells ; degradation ; phosphorylation ; protein kinases ; proteins ; signal transduction ; transcription (genetics) ; ubiquitin-protein ligase ; ubiquitination ; vertebrates
Language	English
Dates of publication	2012-0401
Size	p. 126-131.
Publishing place	Taylor & Francis
Document type	Article
Note	NAL-light
ISSN	1933-6942
DOI	10.4161/fly.20143
Database	NAL-Catalogue (AGRICOLA)

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