Peroxisomal Atg37 binds Atg30 or palmitoyl-CoA to regulate phagophore formation during pexophagy

Autophagy is a membrane trafficking pathway that sequesters proteins and organelles into autophagosomes. The selectivity of this pathway is determined by autophagy receptors, such as the Pichia pastoris autophagy-related protein 30 (Atg30), which controls the selective autophagy of peroxisomes (pexophagy) through the assembly of a receptor protein complex (RPC). However, how the pexophagic RPC is regulated for efficient formation of the phagophore, an isolation membrane that sequesters the peroxisome from the cytosol, is unknown. Here we describe a new, conserved acyl-CoA–binding protein, Atg37, that is an integral peroxisomal membrane protein required specifically for pexophagy at the stage of phagophore formation. Atg30 recruits Atg37 to the pexophagic RPC, where Atg37 regulates the recruitment of the scaffold protein, Atg11. Palmitoyl-CoA competes with Atg30 for Atg37 binding. The human orthologue of Atg37, acyl-CoA–binding domain containing protein 5 (ACBD5), is also peroxisomal and is required specifically for pexophagy. We suggest that Atg37/ACBD5 is a new component and positive regulator of the pexophagic RPC.

Download Full-text

Structural and biochemical advances on the recruitment of the autophagy-initiating ULK and TBK1 complexes by autophagy receptor NDP52

Science Advances ◽

10.1126/sciadv.abi6582 ◽

2021 ◽

Vol 7 (33) ◽

pp. eabi6582

Author(s):

Tao Fu ◽

Mingfang Zhang ◽

Zixuan Zhou ◽

Ping Wu ◽

Chao Peng ◽

...

Keyword(s):

Protein Complex ◽

Coiled Coil ◽

Aminobutyric Acid ◽

Gamma Aminobutyric Acid ◽

Related Protein ◽

Binding Region ◽

Receptor Associated Protein ◽

Selective Autophagy ◽

Specific Association ◽

Molecular Bases

The recruitment of Unc-51-like kinase and TANK-binding kinase 1 complexes is essential for Nuclear dot protein 52-mediated selective autophagy and relies on the specific association of NDP52, RB1-inducible coiled-coil protein 1, and Nak-associated protein 1 (5-azacytidine-induced protein 2, AZI2). However, the underlying molecular mechanism remains elusive. Here, we find that except for the NDP52 SKIP carboxyl homology (SKICH)/RB1CC1 coiled-coil interaction, the LC3-interacting region of NDP52 can directly interact with the RB1CC1 Claw domain, as that of NAP1 FIP200-binding region (FIR). The determined crystal structures of NDP52 SKICH/RB1CC1 complex, NAP1 FIR/RB1CC1 complex, and the related NAP1 FIR/Gamma-aminobutyric acid receptor-associated protein complex not only elucidate the molecular bases underpinning the interactions of RB1CC1 with NDP52 and NAP1 but also reveal that RB1CC1 Claw and Autophagy-related protein 8 family proteins are competitive in binding to NAP1 and NDP52. Overall, our findings provide mechanistic insights into the interactions of NDP52, NAP1 with RB1CC1 and ATG8 family proteins.

Download Full-text

70-kDa peroxisomal membrane protein related protein (P70R/ABCD4) localizes to endoplasmic reticulum not peroxisomes, and NH2-terminal hydrophobic property determines the subcellular localization of ABC subfamily D proteins

Experimental Cell Research ◽

10.1016/j.yexcr.2008.10.031 ◽

2009 ◽

Vol 315 (2) ◽

pp. 190-205 ◽

Cited By ~ 36

Author(s):

Yoshinori Kashiwayama ◽

Midori Seki ◽

Akina Yasui ◽

Yoshiyuki Murasaki ◽

Masashi Morita ◽

...

Keyword(s):

Endoplasmic Reticulum ◽

Membrane Protein ◽

Subcellular Localization ◽

Related Protein ◽

Hydrophobic Property ◽

Peroxisomal Membrane ◽

Peroxisomal Membrane Protein

Download Full-text

Formation of the peroxisome lumen is abolished by loss of Pichia pastoris Pas7p, a zinc-binding integral membrane protein of the peroxisome.

Molecular and Cellular Biology ◽

10.1128/mcb.15.11.6406 ◽

1995 ◽

Vol 15 (11) ◽

pp. 6406-6419 ◽

Cited By ~ 48

Author(s):

J E Kalish ◽

C Theda ◽

J C Morrell ◽

J M Berg ◽

S J Gould

Keyword(s):

Pichia Pastoris ◽

Membrane Protein ◽

Protein Translocation ◽

Point Mutations ◽

Integral Membrane Protein ◽

Zinc Binding ◽

Peroxisomal Membrane ◽

Peroxisomal Targeting ◽

Targeting Signal

We have cloned and sequenced PAS7, a gene required for peroxisome assembly in the yeast Pichia pastoris. The product of this gene, Pas7p, is a member of the C3HC4 superfamily of zinc-binding proteins. Point mutations that alter conserved residues of the C3HC4 motif abolish PAS7 activity and reduce zinc binding, suggesting that Pas7p binds zinc in vivo and that zinc binding is essential for PAS7 function. As with most pas mutants, pas7 cells exhibit a pronounced deficiency in import of peroxisomal matrix proteins that contain either the type 1 peroxisomal targeting signal (PTS1) or the type 2 PTS (PTS2). However, while other yeast and mammalian pas mutants accumulate ovoid, vesicular peroxisomal intermediates, loss of Pas7p leads to accumulation of membrane sheets and vesicles which lack a recognizable lumen. Thus, Pas7p appears to be essential for protein translocation into peroxisomes as well as formation of the lumen of the organelle. Consistent with these data, we find that Pas7p is an integral peroxisomal membrane protein which is entirely resistant to exogenous protease and thus appears to reside completely within the peroxisome. Our observations suggest that the function of Pas7p defines a previously unrecognized step in peroxisome assembly: formation of the peroxisome lumen. Furthermore, because the peroxisomal intermediates in the pas7 delta mutant proliferate in response to peroxisome-inducing environmental conditions, we conclude that Pas7p is not required for peroxisome proliferation.

Download Full-text

Pichia pastoris Pex14p, a phosphorylated peroxisomal membrane protein, is part of a PTS-receptor docking complex and interacts with many peroxins

Yeast ◽

10.1002/yea.711 ◽

2001 ◽

Vol 18 (7) ◽

pp. 621-641 ◽

Cited By ~ 40

Author(s):

Monique A. Johnson ◽

William B. Snyder ◽

Joan Lin Cereghino ◽

Marten Veenhuis ◽

Suresh Subramani ◽

...

Keyword(s):

Pichia Pastoris ◽

Membrane Protein ◽

Peroxisomal Membrane ◽

Peroxisomal Membrane Protein

Download Full-text

Endoplasmic Reticulum–Mitochondria Contacts Are Required for Pexophagy in Saccharomyces cerevisiae

Contact ◽

10.1177/2515256418821584 ◽

2019 ◽

Vol 2 ◽

pp. 251525641882158 ◽

Cited By ~ 4

Author(s):

Xu Liu ◽

Xin Wen ◽

Daniel J. Klionsky

Keyword(s):

Saccharomyces Cerevisiae ◽

Endoplasmic Reticulum ◽

Lipid Metabolism ◽

Membrane Protein ◽

Mutant Form ◽

Peroxisomal Membrane ◽

Cellular Homeostasis ◽

Selective Autophagy ◽

Contact Sites ◽

Autophagic Degradation

Peroxisomes play important roles in lipid metabolism. Surplus or damaged peroxisomes can be selectively targeted for autophagic degradation, a process termed pexophagy. Maintaining a proper level of pexophagy is critical for cellular homeostasis. Here, we found that endoplasmic reticulum (ER)–mitochondria contact sites are necessary for efficient pexophagy. During pexophagy, the peroxisomes destined for degradation are adjacent to the ER–mitochondria encounter structure (ERMES) that mediates the formation of ER–mitochondria contacts; disruption of the ERMES results in a severe defect in pexophagy. We show that a mutant form of Mdm34, a component of the ERMES, which impairs ERMES formation and diminishes its association with the peroxisomal membrane protein Pex11, also causes defects in pexophagy. The dynamin-related GTPase Vps1, which is specific for peroxisomal fission, is recruited to the peroxisomes at ER–mitochondria contacts by the selective autophagy scaffold Atg11 and the pexophagy receptor Atg36, facilitating peroxisome degradation.

Download Full-text

The myotubularin family of lipid phosphatases in disease and in spermatogenesis

Biochemical Journal ◽

10.1042/bj20101267 ◽

2010 ◽

Vol 433 (2) ◽

pp. 253-262 ◽

Cited By ~ 25

Author(s):

Dolores D. Mruk ◽

C. Yan Cheng

Keyword(s):

Membrane Trafficking ◽

Protein Tyrosine Kinase ◽

Cell Function ◽

Growth Factor Receptor ◽

Protein Family ◽

Receptor Protein ◽

Cell Junction ◽

Related Protein ◽

Unique Type ◽

Lipid Phosphatases

The MTM (myotubularin)/MTMR (myotubularin-related) protein family is comprised of 15 lipid phosphatases, of which nine members are catalytically active. MTMs are known to play a fundamental role in human physiology as gene mutations can give rise to X-linked myotubular myopathy or Charcot–Marie–Tooth disease, which manifest in skeletal muscle or in peripheral neurons respectively. Interestingly, studies have shown MTMR2 and MTMR5, two MTM family members, to be highly expressed in the testis, particularly in Sertoli and germ cells, and knockout of either gene resulted in spermatogenic defects. Other studies have shown that MTMR2 functions in endocytosis and membrane trafficking. In the testis, MTMR2 interacts and co-localizes with c-Src/phospho-Src-(Tyr416), a non-receptor protein tyrosine kinase that regulates the phosphorylation state of proteins at the apical ES (ectoplasmic specialization), a unique type of cell junction found between Sertoli cells and elongating/elongated spermatids. In the present review, we highlight recent findings that have made a significant impact on our understanding of this protein family in normal cell function and in disease, with the emphasis on the role of MTMs and MTMRs in spermatogenesis. We also describe a working model to explain how MTMR2 interacts with other proteins such as c-Src, dynamin 2, EPS8 (growth factor receptor pathway substrate 8) and ARP2/3 (actin-related protein 2/3) at the apical ES and the apical TBC (tubulobulbar complex; tubular-like invaginations that function in the disassembly of the apical ES and in the recycling of its components) to regulate spermiation at late stage VIII of the seminiferous epithelial cycle.

Download Full-text

Pex22p of Pichia pastoris, Essential for Peroxisomal Matrix Protein Import, Anchors the Ubiquitin-Conjugating Enzyme, Pex4p, on the Peroxisomal Membrane

The Journal of Cell Biology ◽

10.1083/jcb.146.1.99 ◽

1999 ◽

Vol 146 (1) ◽

pp. 99-112 ◽

Cited By ~ 67

Author(s):

Antonius Koller ◽

William B. Snyder ◽

Klaas Nico Faber ◽

Thibaut J. Wenzel ◽

Linda Rangell ◽

...

Keyword(s):

Pichia Pastoris ◽

Membrane Protein ◽

Matrix Protein ◽

Protein Import ◽

Hypothetical Protein ◽

Peroxisomal Membrane ◽

Peroxisomal Membrane Protein ◽

Ubiquitin Conjugating Enzyme ◽

Conjugating Enzyme

We isolated a Pichia pastoris mutant that was unable to grow on the peroxisome-requiring media, methanol and oleate. Cloning the gene by complementation revealed that the encoded protein, Pex22p, is a new peroxin. A Δpex22 strain does not grow on methanol or oleate and is unable to import peroxisomal matrix proteins. However, this strain targets peroxisomal membrane proteins to membranes, most likely peroxisomal remnants, detectable by fluorescence and electron microscopy. Pex22p, composed of 187 amino acids, is an integral peroxisomal membrane protein with its NH2 terminus in the matrix and its COOH terminus in the cytosol. It contains a 25–amino acid peroxisome membrane-targeting signal at its NH2 terminus. Pex22p interacts with the ubiquitin-conjugating enzyme Pex4p, a peripheral peroxisomal membrane protein, in vivo, and in a yeast two-hybrid experiment. Pex22p is required for the peroxisomal localization of Pex4p and in strains lacking Pex22p, the Pex4p is cytosolic and unstable. Therefore, Pex22p anchors Pex4p at the peroxisomal membrane. Strains that do not express Pex4p or Pex22p have similar phenotypes and lack Pex5p, suggesting that Pex4p and Pex22p act at the same step in peroxisome biogenesis. The Saccharomyces cerevisiae hypothetical protein, Yaf5p, is the functional homologue of P. pastoris Pex22p.

Download Full-text