LYST Affects Lysosome Size and Quantity,but not Trafficking or Degradation Through Autophagy or Endocytosis

Mutations in the large BEACH domain‐containing protein LYST causes Chediak–Higashi syndrome. The diagnostic hallmark is enlarged lysosomes and lysosome‐related organelles in various cell types. Dysfunctional secretion of enlarged lysosome‐related organelles has been observed in cells with mutations in LYST, but the capacity of the enlarged lysosomes to degrade endogenous proteins has not been studied. Here, we show for the first time that small interfering RNA‐depletion of LYST in human cell lines recapitulates the LYST mutant phenotype of enlarged lysosomes. We found no evidence for an effect of LYST depletion on autophagy or endocytic degradation. Autophagosomes are formed in normal size and quantities and are able to fuse to the enlarged lysosomes, leading to normal rates of degradation. Degradation of the epidermal growth factor receptor (EGFR) was similarly not affected, indicating that the enlarged lysosomes are fully functional in degrading endogenous proteins. Retrograde trafficking of toxins as well as the localization of transporters of lysosomal proteins, adaptor protein‐3 (AP‐3) and cation‐independent mannose‐6‐phosphate receptor (CI‐MPR), were all found to be unaffected by LYST. Quantitative analysis of the enlarged lysosomes shows that LYST depletion causes a reduction in vesicle quantity per cell, while the total enzymatic content and vesicular pH are unaffected, supporting a role for LYST in lysosomal fission and/or fusion events.      

Drosophila mauve Mutants Reveal a Role of LYST Homologs Late in the Maturation of Phagosomes and Autophagosomes

Chediak–Higashi syndrome (CHS) is a lethal disease caused by mutations that inactivate the lysosomal trafficking regulator protein (LYST). Patients suffer from diverse symptoms including oculocutaneous albinism, recurrent infections, neutropenia and progressive neurodegeneration. These defects have been traced back to over‐sized lysosomes and lysosome‐related organelles (LROs) in different cell types. Here, we explore mutants in the Drosophila mauve gene as a new model system for CHS. The mauve gene (CG42863) encodes a large BEACH domain protein of 3535 amino acids similar to LYST. This reflects a functional homology between these proteins as mauve mutants also display enlarged LROs, such as pigment granules. This Drosophila model also replicates the enhanced susceptibility to infections and we show a defect in the cellular immune response. Early stages of phagocytosis proceed normally in mauve mutant hemocytes but, unlike in wild type, late phagosomes fuse and generate large vacuoles containing many bacteria. Autophagy is similarly affected in mauve fat bodies as starvation‐induced autophagosomes grow beyond their normal size. Together these data suggest a model in which Mauve functions to restrict homotypic fusion of different pre‐lysosomal organelles and LROs.     

A Dynamin Homolog Promotes the Transition from Hemifusion to Content Mixing in Intracellular Membrane Fusion

The convergence of the antagonistic reactions of membrane fusion and fission at the hemifusion/hemifission intermediate has generated a captivating enigma of whether Soluble N‐ethylmaleimide sensitive factor Attachment Protein Receptor (SNAREs) and dynamin have unusual counter‐functions in fission and fusion, respectively. SNARE‐mediated fusion and dynamin‐driven fission are fundamental membrane flux reactions known to occur during ubiquitous cellular communication events such as exocytosis, endocytosis and vesicle transport. Here we demonstrate the influence of the dynamin homolog Vps1 (Vacuolar protein sorting 1) on lipid mixing and content mixing properties of yeast vacuoles, and on the incorporation of SNAREs into fusogenic complexes. We propose a novel concept that Vps1, through its oligomerization and SNARE domain binding, promotes the hemifusion‐content mixing transition in yeast vacuole fusion by increasing the number of trans‐SNAREs .      

Global Analysis of Fission Yeast Mating Genes Reveals New Autophagy Factors

Macroautophagy (autophagy) is crucial for cell survival during starvation and plays important roles in animal development and human diseases. Molecular understanding of autophagy has mainly come from the budding yeast Saccharomyces cerevisiae, and it remains unclear to what extent the mechanisms are the same in other organisms. Here, through screening the mating phenotype of a genome-wide deletion collection of the fission yeast Schizosaccharomyces pombe, we obtained a comprehensive catalog of autophagy genes in this highly tractable organism, including genes encoding three heretofore unidentified core Atg proteins, Atg10, Atg14, and Atg16, and two novel factors, Ctl1 and Fsc1. We systematically examined the subcellular localization of fission yeast autophagy factors for the first time and characterized the phenotypes of their mutants, thereby uncovering both similarities and differences between the two yeasts. Unlike budding yeast, all three Atg18/WIPI proteins in fission yeast are essential for autophagy, and we found that they play different roles, with Atg18a uniquely required for the targeting of the Atg12–Atg5·Atg16 complex. Our investigation of the two novel factors revealed unforeseen autophagy mechanisms. The choline transporter-like protein Ctl1 interacts with Atg9 and is required for autophagosome formation. The fasciclin domain protein Fsc1 localizes to the vacuole membrane and is required for autophagosome-vacuole fusion but not other vacuolar fusion events. Our study sheds new light on the evolutionary diversity of the autophagy machinery and establishes the fission yeast as a useful model for dissecting the mechanisms of autophagy.     

Tying trafficking to fusion and fission at the mighty mitochondria

The mitochondrion is a unique organelle that serves as the main site of ATP generation needed for energy in the cell. However, mitochondria also play essential roles in cell death through apoptosis and necrosis, as well as a variety of crucial functions related to stress regulation, autophagy, lipid synthesis and calcium storage. There is a growing appreciation that mitochondrial function is regulated by the dynamics of its membrane fusion and fission; longer, fused mitochondria are optimal for ATP generation, whereas fission of mitochondria facilitates mitophagy and cell division. Despite the significance of mitochondrial homeostasis for such crucial cellular events, the intricate regulation of mitochondrial fusion and fission is only partially understood. Until very recently, only a single mitochondrial fission protein had been identified. Moreover, only now have researchers turned to address the upstream machinery that regulates mitochondrial fusion and fission proteins. Herein, we review the known GTPases involved in mitochondrial fusion and fission, but also highlight recent studies that address the mechanisms by which these GTPases are regulated. In particular, we draw attention to a substantial new body of literature linking endocytic regulatory proteins, such as the retromer VPS35 cargo selection complex subunit, to mitochondrial homeostasis. These recent studies suggest that relationships and cross‐regulation between endocytic and mitochondrial pathways may be more widespread than previously assumed.      

Distinct complexes of yeast Snx4 family SNX‐BARs mediate retrograde trafficking of Snc1 and Atg27

The yeast SNX4 sub‐family of sorting nexin containing a Bin‐Amphiphysin‐Rvs domain (SNX‐BAR) proteins, Snx4/Atg24, Snx41 and Atg20/Snx42, are required for endocytic recycling and selective autophagy. Here, we show that Snx4 forms 2 functionally distinct heterodimers: Snx4‐Atg20 and Snx4‐Snx41. Each heterodimer coats an endosome‐derived tubule that mediates retrograde sorting of distinct cargo; the v‐SNARE, Snc1, is a cargo of the Snx4‐Atg20 pathway, and Snx4‐Snx41 mediates retrograde sorting of Atg27, an integral membrane protein implicated in selective autophagy. Live cell imaging of individual endosomes shows that Snx4 and the Vps5‐Vps17 retromer SNX‐BAR heterodimer operate concurrently on a maturing endosome. Consistent with this, the yeast dynamin family protein, Vps1, which was previously shown to promote fission of retromer‐coated tubules, promotes fission of Snx4‐Atg20 coated tubules. The results indicate that the yeast SNX‐BAR proteins coat 3 distinct types of endosome‐derived carriers that mediate endosome‐to‐Golgi retrograde trafficking.      

Mitochondrial fusion, fission and autophagy as a quality control axis: The bioenergetic view

The mitochondrial life cycle consists of frequent fusion and fission events. Ample experimental and clinical data demonstrate that inhibition of either fusion or fission results in deterioration of mitochondrial bioenergetics. While fusion may benefit mitochondrial function by allowing the spreading of metabolites, protein and DNA throughout the network, the functional benefit of fission is not as intuitive. Remarkably, studies that track individual mitochondria through fusion and fission found that the two events are paired and that fusion triggers fission. On average each mitochondrion would go though ~ 5 fusion:fission cycles every hour. Measurement of Δψ_m during single fusion and fission events demonstrates that fission may yield uneven daughter mitochondria where the depolarized daughter is less likely to become involved in a subsequent fusion and is more likely to be targeted by autophagy. Based on these observations we propose a mechanism by which the integration of mitochondrial fusion, fission and autophagy forms a quality maintenance mechanism. According to this hypothesis pairs of fusion and fission allow for the reorganization and sequestration of damaged mitochondrial components into daughter mitochondria that are segregated from the networking pool and then becoming eliminated by autophagy.     

Promiscuous and specific phospholipid binding by domains in ZAC,a membrane-associated Arabidopsis protein with an ARF GAP zinc finger and a C2 domain

Arabidopsis proteins were predicted which share an 80 residue zinc finger domain known from ADP-ribosylation factor GTPase-activating proteins (ARF GAPs). One of these is a 37 kDa protein, designated ZAC, which has a novel domain structure in which the N-terminal ARF GAP domain and a C-terminal C2 domain are separated by a region without homology to other known proteins. Zac promoter/-glucuronidase reporter assays revealed highest expression levels in flowering tissue, rosettes and roots. ZAC protein was immuno-detected mainly in association with membranes and fractionated with Golgi and plasma membrane marker proteins. ZAC membrane association was confirmed in assays by a fusion between ZAC and the green fluorescence protein and prompted an analysis of the in vitro phospholipid-binding ability of ZAC. Phospholipid dot-blot and liposome-binding assays indicated that fusion proteins containing the ZAC-C2 domain bind anionic phospholipids non-specifically, with some variance in Ca²⁺ and salt dependence. Similar assays demonstrated specific affinity of the ZAC N-terminal region (residues 1–174) for phosphatidylinositol 3-monophosphate (PI-3-P). Binding was dependent in part on an intact zinc finger motif, but proteins containing only the zinc finger domain (residues 1–105) did not bind PI-3-P. Recombinant ZAC possessed GTPase-activating activity on Arabidopsis ARF proteins. These data identify a novel PI-3-P-binding protein region and thereby provide evidence that this phosphoinositide is recognized as a signal in plants. A role for ZAC in the regulation of ARF-mediated vesicular transport in plants is discussed.     

The heptad repeat domain 1 of Mitofusin has membrane destabilization function in mitochondrial fusion

Mitochondria are double‐membrane‐bound organelles that constantly change shape through membrane fusion and fission. Outer mitochondrial membrane fusion is controlled by Mitofusin, whose molecular architecture consists of an N‐terminal GTPase domain, a first heptad repeat domain (HR1), two transmembrane domains, and a second heptad repeat domain (HR2). The mode of action of Mitofusin and the specific roles played by each of these functional domains in mitochondrial fusion are not fully understood. Here, using a combination of in situ and in vitro fusion assays, we show that HR1 induces membrane fusion and possesses a conserved amphipathic helix that folds upon interaction with the lipid bilayer surface. Our results strongly suggest that HR1 facilitates membrane fusion by destabilizing the lipid bilayer structure, notably in membrane regions presenting lipid packing defects. This mechanism for fusion is thus distinct from that described for the heptad repeat domains of SNARE and viral proteins, which assemble as membrane‐bridging complexes, triggering close membrane apposition and fusion, and is more closely related to that of the C‐terminal amphipathic tail of the Atlastin protein.     

Chediak-Higashi syndrome: a clinical and molecular view of a rare lysosomal storage disorder

Chediak Higashi syndrome (CHS) is a rare, autosomal recessive disorder that affects multiple systems of the body. Patients with CHS exhibit hypopigmentation of the skin, eyes and hair, prolonged bleeding times, easy bruisability, recurrent infections, abnormal NK cell function and peripheral neuropathy. Morbidity results from patients succumbing to frequent bacterial infections or to an "accelerated phase" lymphoproliferation into the major organs of the body. Current treatment for the disorder is bone marrow transplant, which alleviates the immune problems and the accelerated phase, but does not inhibit the development of neurologic disorders that grow increasingly worse with age. There are several animal models of CHS, the beige mouse being the most characterized. Positional cloning and YAC complementation resulted in the identification of the Beige and CHS1/LYST genes. These genes encode a cytosolic protein of 430,000 Da. Sequence analysis identified three conserved regions in the protein: a HEAT repeat motif at the amino-terminus that contains several a helices, a BEACH domain containing the amino acid sequence WIDL, and a WD40 repeat motif, which is described as a protein-protein interaction domain. The presence of the BEACH and WD40 domains defines a family of genes that encode extremely large proteins.     

Regulation and Function of Autophagy during Cell Survival and Cell Death

Autophagy is an important catabolic process that delivers cytoplasmic material to the lysosome for degradation. Autophagy promotes cell survival by elimination of damaged organelles and proteins aggregates, as well as by facilitating bioenergetic homeostasis. Although autophagy has been considered a cell survival mechanism, recent studies have shown that autophagy can promote cell death. The core mechanisms that control autophagy are conserved between yeast and humans, but animals also possess genes that regulate autophagy that are not present in yeast. These regulatory differences may be explained by the need to control autophagy in a cell context-specific manner in multicellular animals, such as during cell survival and cell death. Autophagy was thought to be a bulk cytoplasmic degradation mechanism, but recent studies have shown that specific cargo is recruited for degradation. This suggests the possibility that either cell survival or death may be regulated by selective autophagic clearance of cytoplasmic material. Here we summarize the mechanisms that regulate autophagy and how they may contribute to cell survival and death.Autophagy (self-eating) is an evolutionarily conserved catabolic process that is used to deliver cytoplasmic materials, including organelles and proteins, to the lysosome for degradation. Three types of autophagy have been described, including macroautophagy, microautophagy, and chaperone-mediated autophagy (Mizushima and Komatsu 2011). Although macroautophagy involves the fusion of the double membrane autophagosome and lysosomes, microautophagy is poorly understood and thought to involve direct uptake of material by the lysosome via a process that appears similar to pinocytosis. By contrast, chaperone-mediated autophagy is a biochemical mechanism to import proteins into the lysosome; it depends on a signature sequence and interaction with protein chaperones. Here we will focus on macroautophagy (hereafter called autophagy) because of our knowledge of this process in cell survival and cell death.Autophagy was likely first observed when electron microscopy was used to observe “dense bodies” containing mitochondria in mouse kidneys (Clark 1957). Five years later, it was reported that rat hepatocytes exposed to glucagon possessed membrane-bound vesicles that were rich in mitochondria and endoplasmic reticulum (Ashford and Porter 1962). Almost simultaneously, it was shown that these membrane-bound vesicles contained lysosomal hydrolases (Novikoff and Essner 1962). In 1965 de Duve coined the term “autophagy” (Klionsky 2008).The delivery of cytoplasmic material to the lysosome by autophagy involves membrane formation and fusion events (Fig. 1). First an isolation membrane, also known as a phagophore, must be initiated from a membrane source known as the phagophore assembly site (PAS). de Duve suggested that the smooth endoplasmic reticulum could be the source of autophagosome membrane (de Duve and Wattiaux 1966), and subsequent studies have supported this possibility (Dunn 1990; Axe et al. 2008). Although controversial, mitochondria and plasma membrane could also supply membranes for the formation of the autophagosomes under different conditions (Hailey et al. 2010; Ravikumar et al. 2010). The elongating isolation membrane surrounds cargo that is ultimately enclosed in the double membrane autophagosome. Once the autophagosome is formed, it fuses with lysosomes (known as the vacuole in yeasts and plants) to form autolysosomes in which the cargo is degraded by lysosomal hydrolases. At this stage lysosomes must reform so that subsequent autophagy may occur (Yu et al. 2010).Open in a separate windowFigure 1.Macroautophagy (autophagy) delivers cytoplasmic cargo to lysosomes for degradation, and involves membrane formation and fusion. The isolation membrane is initiated from a membrane source known as the from the phagophore assembly site (PAS). The isolation membrane surrounds cargo, including organelles and proteins, to form a double membrane autophagosome. Autophagosomes fuse with lysosomes to form autolysosomes in which the cargo is degraded by lysosomal hydrolases.     

A BAR-Domain Protein SH3P2, Which Binds to Phosphatidylinositol 3-Phosphate and ATG8, Regulates Autophagosome Formation in Arabidopsis

Autophagy is a well-defined catabolic mechanism whereby cytoplasmic materials are engulfed into a structure termed the autophagosome. In plants, little is known about the underlying mechanism of autophagosome formation. In this study, we report that SH3 DOMAIN-CONTAINING PROTEIN2 (SH3P2), a Bin-Amphiphysin-Rvs domain–containing protein, translocates to the phagophore assembly site/preautophagosome structure (PAS) upon autophagy induction and actively participates in the membrane deformation process. Using the SH3P2–green fluorescent protein fusion as a reporter, we found that the PAS develops from a cup-shaped isolation membranes or endoplasmic reticulum–derived omegasome-like structures. Using an inducible RNA interference (RNAi) approach, we show that RNAi knockdown of SH3P2 is developmentally lethal and significantly suppresses autophagosome formation. An in vitro membrane/lipid binding assay demonstrates that SH3P2 is a membrane-associated protein that binds to phosphatidylinositol 3-phosphate. SH3P2 may facilitate membrane expansion or maturation in coordination with the phosphatidylinositol 3-kinase (PI3K) complex during autophagy, as SH3P2 promotes PI3K foci formation, while PI3K inhibitor treatment inhibits SH3P2 from translocating to autophagosomes. Further interaction analysis shows that SH3P2 associates with the PI3K complex and interacts with ATG8s in Arabidopsis thaliana, whereby SH3P2 may mediate autophagy. Thus, our study has identified SH3P2 as a novel regulator of autophagy and provided a conserved model for autophagosome biogenesis in Arabidopsis.     

Different endocytic functions of AGEF-1 in C. elegans coelomocytes

Background

ADP-ribosylation factors (ARFs) are a family of small GTP-binding proteins that play roles in membrane dynamics and vesicle trafficking. AGEF-1, which is thought to act as a guanine nucleotide exchange factor of class I ARFs, is required for caveolin-1 body formation and receptor-mediated endocytosis in oocytes of Caenorhabditis elegans. This study explores additional roles of AGEF-1 in endocytic transport.

Methods

agef-1 expression was knocked down by using RNAi in C. elegans. Markers that allow analysis of endocytic transport in scavenger cells were investigated for studying the effect of AGEF-1 on different steps of membrane transport.

Results

Knockdown of AGEF-1 levels results in two apparent trafficking defects in coelomocytes of C. elegans. First, there is a delay in the uptake of solutes from the extracellular medium. Second, there is a dramatic enlargement of the sizes of lysosomes, even though lysosomal acidification is normal and degradation still occurs.

Conclusion

Our results suggest that AGEF-1 regulates endosome/lysosome fusion or fission events, in addition to earlier steps in endocytic transport.

General significance

AGEF-1 is the first identified GTPase regulator that functions at the lysosome fusion or fission stage of the endocytic pathway. Our study provides insight into lysosome dynamics in C. elegans.     

Functional domains of theEscherichia coli ferric uptake regulator protein (Fur)

The functions of N- and C-terminal domains of the Fur repressor ofEscherichia coli in promoter recognition and dimerization were studied. We investigated the ability of fusion proteins containing the N- or C-terminal domain of Fur to dimerize and to repress a Fur-regulatedlacZ fusion gene. The N-terminal domain, when fused to the C-terminal domain of the repressor C1857, repressed a Fur-regulatedlacZ fusion. However, the Fur-CI857 fusion was unable to complement the growth defect of anE. coli fur mutant on fumarate and succinate. The C-terminal domain of Fur, when fused to the N-terminus of CI857, repressed a P, -regulatedlacZ fusion, indicating dimerization of the chimeric protein, which is a prerequisite for Cl activity. Both fusion proteins were fully active under both iron-rich and iron-poor growth conditions. We conclude that the N-terminal domain of Fur is involved in recognition of the Fur-responsive promoter and the C-terminus mediates oligomerization of the repressor.     

A pseudo-receiver domain in Atg32 is required for mitophagy

Mitochondria are targeted for degradation by mitophagy, a selective form of autophagy. In Saccharomyces cerevisiae, mitophagy is dependent on the autophagy receptor, Atg32, an outer mitochondrial membrane protein. Once activated, Atg32 recruits the autophagy machinery to mitochondria, facilitating mitochondrial capture in phagophores, the precursors to autophagosomes. However, the mechanism of Atg32 activation remains poorly understood. To investigate this crucial step in mitophagy regulation, we examined the structure of Atg32. We have identified a structured domain in Atg32 that is essential for the initiation of mitophagy, as it is required for the proteolysis of the C-terminal domain of Atg32 and the subsequent recruitment of Atg11. The solution structure of this domain was determined by NMR spectroscopy, revealing that Atg32 contains a previously undescribed pseudo-receiver (PsR) domain. Our data suggests that the PsR domain of Atg32 regulates Atg32 activation and the initiation of mitophagy.

Abbreviations:AIM: Atg8-interacting motif; GFP: green fluorescent protein; LIR: LC3-interacting region; NMR: nuclear magnetic resonance; NOESY: nuclear Overhauser effect spectroscopy; PDB: protein data bank; PsR: pseudo-receiver; RMSD: root-mean-square deviation     

The ides of MARCH5: The E3 ligase essential for peroxisome degradation by pexophagy

A recent study by Zheng et al. (2021. J. Cell Biol. https://doi.org/10.1083/jcb.202103156) identifies the ubiquitin-protein ligase (E3) MARCH5 as a dual-organelle localized protein that not only targets to mitochondria but also to peroxisomes in a PEX19-mediated manner. Moreover, the authors demonstrate that the Torin1-dependent induction of pexophagy is executed by the MARCH5-catalyzed ubiquitination of the peroxisomal membrane protein PMP70.

Recent research has begun to slowly elucidate the complex processes that underlie selective autophagic degradation of mammalian peroxisomes. The study by Zheng et al. (1) sheds a light on the mechanism underlying pexophagy, which is induced by mTOR (mechanistic target of rapamycin) inactivation (2). The ubiquitously conserved serine/threonine kinase mTOR has a central function in integrating diverse growth signals and orchestrating their physiological effect on a cellular level, while blocking cell growth–restricting mechanisms like the different autophagy pathways (3). Previous work has demonstrated that amino acid starvation could induce mTOR inhibition-dependent peroxisome degradation by up-regulating the activity of the peroxisomal protein ubiquitin (E3) ligase PEX2 (4), which was especially of interest as PEX2 is also required for peroxisomal matrix protein import during the formation of the organelle (5). However, while these data suggested that the dual function of PEX2 might mark it as a point of convergence for the balance of peroxisome formation and degradation, the Zheng et al. study has identified a role for the E3 ligase MARCH5 (membrane-associated RING-CH 5; 1) that aims at a different aspect of peroxisome biology.Zheng et al. identified the peroxisomal proteins PEX3, PEX19, and PMP70 as close interaction partners of MARCH5 (1). The authors could demonstrate a PEX19-dependent localization of a portion of the MARCH5 population to peroxisomes. Here, MARCH5 can bind and polyubiquitinate the abundant peroxisomal membrane protein PMP70. While it is clear that the increased level of polyubiquitinated PMP70 molecules marks peroxisomes for recognition by ubiquitin-binding autophagy receptors that link the target organelle to the autophagosomal membrane, the identity of the E2 enzyme involved in ubiquitin chain generation as well as the ubiquitin adaptors are unknown (Fig. 1). However, based on published research, NBR1 or p62 are good candidates for the adaptors that engage the autophagy machinery (2). Moreover, the Zheng et al. study demonstrates that MARCH5-mediated polyubiquitination of PMP70 is induced by the mTOR inhibitor Torin1. In return, the described Torin1-induced pexophagy was shown to rely on the peroxisomal localization and activity of the catalytic RING domain of MARCH5 (1).Open in a separate windowFigure 1.The small molecule Torin1 can inhibit the kinase mTOR, resulting in a relief of the mTOR-dependent block of MARCH5 targeting to peroxisomes. MARCH5 is inserted into the peroxisomal membrane in a PEX19- and PEX3-dependent manner. MARCH5 ubiquitinates the abundant peroxisomal membrane protein PMP70 with the help of an unknown ubiquitin (Ub)-conjugating enzyme (E2). The ubiquitinated PMP70 molecules are recognized by ubiquitin-binding autophagy receptors, like NBR1 or p62, that link the organelle to the autophagosome, resulting in the autophagic degradation of the peroxisome via pexophagy.It is interesting to note that the opponent of pexophagy-linked ubiquitin signals on peroxisomes was already identified as the deubiquitinating enzyme USP30 (6). This combination is even more relevant when considering that MARCH5 and USP30 were described as an antagonizing enzyme pair that regulates the autophagic degradation of mitochondria via mitophagy (6). The function of MARCH5 is also linked to other mitochondrial ubiquitination factors, like the E3 ligase Parkin. While both enzymes can contribute to mitophagy induction by ubiquitinating proteins of the outer mitochondrial membrane, they can also modify each other. MARCH5 ubiquitinates Parkin in order to restrict the number of Parkin molecules during mitophagy and to prevent Parkin-mediated cell death (7).After mitophagy induction, Parkin can ubiquitinate MARCH5, which results in the p97-mediated membrane extraction of MARCH5 and a PEX3/PEX16-dependent redistribution of MARCH5 to peroxisomes (8). This mechanism was assumed to rescue MARCH5 from degradation by mitophagy. It will be important to elucidate if there is mechanistic overlap between the Parkin-mediated (8) and the Torin1-dependent (1) targeting of MARCH5. Moreover, it will be interesting to determine if MARCH5 is also engaged in an interplay with the peroxisomal E3 ligases PEX2, PEX10, PEX12, or TRIM37.Mitochondria and peroxisomes share basic components of their fission machineries. Both organelles use the membrane proteins FIS1 and mitochondrial fission factor for the targeting of the membrane-constricting GTPase DRP1 (DLP1; 9). In the case of the mitochondria, MARCH5 can ubiquitinate DRP1 and FIS1 for proteasomal degradation in order to limit mitochondrial However, other data indicate the existence of a feedback mechanism, as DRP1 can also negatively influence MARCH5 activity. In addition, MARCH5 not only limits mitochondrial fission, but also represents a basic requirement for this process. This complex relationship of MARCH5 with mitochondrial fission proteins suggests that it performs a central role in the fine-tuning of the basic regulatory aspects of mitochondrial division (10). Therefore, future studies might not only establish a potential role of MARCH5 in peroxisomal fission but might also uncover aspects that could enable further insights into the related process in mitochondria.The different roles of MARCH5 in organelle fission and autophagic degradation could possibly be interconnected in one bipartite reaction sequence. Mitochondrial fission is crucial for mitophagy and enables the removal of damaged sections of mitochondria or the limitation of organelle size for a more efficient engulfment by autophagosomal membranes (11). Therefore, both processes can be functionally interconnected. Interestingly, it has been shown that fission also precedes pexophagy in yeast cells (12), which are thought to use organelle-specific adaptors instead of ubiquitin as a degradation tag. However, these observations suggest that MARCH5 might coordinate peroxisomal fission with pexophagy even in mammalian peroxisomes.In summary, the Zheng et al. study not only identifies a central mechanistic module required for the turnover of mammalian peroxisomes (1) but also raises many interesting questions that will result in further studies dealing with the interplay of the peroxisomal ubiquitination factors, the crosstalk between mitochondria and peroxisomes, and the organization and regulation of the peroxisomal fission machinery as well as the convergence of peroxisomal fission and pexophagy pathways.     

Phospholipase D1 regulates autophagic flux and clearance of α-synuclein aggregates

Many neurodegenerative diseases, such as Alzheimer''s disease and Parkinson''s disease, are characterized by abnormal accumulations of aggregated proteins. Brains in these diseases also show accumulation of autophagic vesicles in the neuronal cytoplasm, suggesting impairment of the autophagic process. As autophagy involves de novo membrane production and vesicle fusion, extensive changes in lipid molecules are necessary. However, the involvement of signaling lipid-modifying enzymes in autophagy and their roles in neurodegenerative diseases are not clear. Using specific inhibitor, we show that loss of phospholipase D1 (PLD1) activity resulted in an accumulation of microtubule-associated protein light chain 3 (LC3), p62, and polyubiquitinated proteins, signs representing malfunction in autophagic flux. Fluorescence and electron microscopic analyses demonstrated impaired fusion of autophagosomes with lysosomes, resulting in accumulation of autophagosomes. Within the cells with impaired autophagic flux, α-synuclein aggregates accumulated in autophagosomes. Knockdown of PLD1 expression using small interfering RNA also resulted in impaired autophagic flux and accumulation of α-synuclein aggregates in autophagosomes. Neuronal toxicity caused by α-synuclein accumulation was rescued by overexpression of PLD1; however, expression of activity-deficient mutant, PLD1-KRM, showed reduced rescue effects. Finally, we demonstrated that both PLD activity and expression levels were reduced in brain tissues of dementia with Lewy bodies (DLB) patients, whereas the amounts of α-synuclein and p62 were increased in the same tissue samples. Collectively, these results suggest that insufficient PLD activity, and therefore, the changes in phospholipid compositions within membranes, might be an important contributor to impaired autophagic process and protein accumulation in Lewy body diseases.Macroautophagy is the best-characterized autophagy pathway that mediates the lysosomal degradation of the cytoplasmic organelles and proteins.¹ In this paper, macroautophagy will be simply referred to as autophagy. Autophagy may be characterized by nonspecific sequestration and degradation of the bulk cytoplasm, a process that recycles essential building blocks for production of macromolecules under conditions where nutrients are limited. Autophagy may also occur to selectively degrade polyubiquitinated targets, and this is often referred to as the quality control autophagy.² Many long-lived proteins and perhaps protein aggregates may be the substrates of the quality control autophagy.As being an essential process for macromolecular metabolism, perturbation of autophagy has been linked to various human diseases, such as neurodegenerative diseases, cancer, and infectious diseases.³ Autophagic dysfunction in neurons, in particular, causes accumulation of aggregation-prone proteins and neurodegeneration that are associated with various neurodegenerative diseases, including Alzheimer''s disease (AD), Parkinson''s disease (PD), and Huntington''s disease (HD).⁴ Recently, genetic mutations that are linked to some of the major neurodegenerative diseases have turned out to reside in the genes that are involved in multiple steps in the autophagic pathways,⁴ implicating the therapeutic potential of controlling autophagy.Autophagy involves sequestration of cytoplasmic substrates by a double-membraned compartment known as the autophagosome (AP).¹ Autophagy process initiates with the formation of a distinct structure referred to as the phagophore that extends its ends and seals in circle to form the AP. APs can fuse with various endosomal vesicles, forming amphisomes, and eventually fuse with lysosomes to form autolysosomes, where degradation of contents takes place. Autophagy involves a wide range of changes in membrane structures, such as de novo membrane biogenesis and membrane fusion. Therefore, lipid molecules and lipid-metabolizing enzymes must play essential roles in the autophagic process. A well-characterized such lipid enzyme is the class III phosphatidylinositol-3 kinase (PI3K), Vps34, that is essential for biogenesis of APs through interactions with various proteins.⁵ Other than Vps34, little has been known about the roles of lipid enzymes in autophagic process.In the current study, we explored the role of phospholipase D1 (PLD1) in autophagy and clearance of α-synuclein aggregates, suspected culprit of PD.⁶ PLD1 generates phosphatidic acid (PA) from phosphatidylcholine and has been known to be involved in intracellular vesicle trafficking.⁷ Our results suggest that PLD1 is an important player for maintaining autophagic flux via regulating autolysosome formation. We also showed that enzymatic inhibition and reduction in expression of PLD1 resulted in impaired clearance of α-synuclein aggregates. Finally, our data showed that reduced expression, and thus activity, of PLD1 was associated with Lewy body diseases.     

A Fission-Fusion Origin for Life

To develop a comprehensive cells-first approach to the origin of life, we propose that protocells form spontaneously and that the fission and fusion of these protocells drives the dynamics of their evolution. The fitness criterion for this evolution is taken to be the the stability (conservation) of domains in the protocellular membrane as determined by non-covalent molecular associations between the amphiphiles of the membrane and a subset of the macromolecules in the protocell. In the presence of a source of free energy the macromolecular content of the protocell (co-)evolves as the result of (domain-dependent) membrane-catalysed polymerisation of the prebiotic constituents delivered to the protocell by fusion. The metabolism of the cell therefore (co-)evolves on a rugged fitness landscape. We indicate how domain evolution with the same fitness criterion can potentially give rise to coding. Membrane domains may therefore provide the link between protocells and the RNA/DNA-world.