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Protein aggregates have a strong correlation with the pathogenesis of multiple human pathologies represented by neurodegenerative diseases. One type of selective autophagy, known as aggrephagy, can selectively degrade protein aggregates. A recent study from Ge lab reported the TRiC subunit CCT2 (chaperonin containing TCP1 subunit 2) as the first identified specific aggrephagy receptor in mammals. The switch of CCT2's role from a chaperonin to a specific aggrephagy receptor is achieved by CCT2 monomer formation. CCT2 functions independently of ubiquitin and the TRiC complex to facilitate the autophagic clearance of solid protein aggregates. This study provides the intriguing possibility that CCT2, as a specific aggrephagy receptor, might be an important target for the treatment of various diseases associated with protein aggregation.

STX17 (syntaxin 17) mediates autophagosome-lysosome fusion, and the translocation of STX17 to autophagosomes is characteristic of this process. STX17 arrives at autophagosomes when they are closed, stays there for approximately 10 min to promote fusion with lysosomes, and leaves when the autolysosomes are mature. However, the mechanism of this transient visit remains largely unknown. Here, we summarize the current knowledge about this phenomenon, including a recently discovered retrieval mechanism, and discuss remaining questions. Abbreviations: MAM: mitochondria-associated membrane; SNX: sorting nexin; STX17: syntaxin 17.

In the preceding months, the novel SARS-CoV-2 pandemic has devastated global communities. The need for safe and effective prophylactic and therapeutic treatments to combat COVID-19 – the human disease resulting from SARS-CoV-2 infection – is clear. Here, we present recent developments in the effort to combat COVID-19 and consider whether SARS-CoV-2 may potentially interact with the host autophagy pathway. Abbreviations: ACE2, angiotensin converting enzyme II; βCoV, betacoronavirus; COVID-19, Coronavirus Disease 2019; CQ, chloroquine; DMV, double-membrane vesicle; GI, gastrointestinal; HCQ, hydroxychloroquine; IL, interleukin; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MEFs, mouse embryonic fibroblasts; MERS-CoV, Middle East respiratory syndrome coronavirus; MHV, murine hepatitis virus; PE, phosphatidylethanolamine; SARS-CoV, severe acute respiratory syndrome coronavirus; SARS-CoV-2, severe acute respiratory syndrome coronavirus 2; TMPRSS2, transmembrane serine protease 2; TNF, tumor necrosis factor; WHO, World Health Organization

The autophagy receptor for selective reticulophagy, RETREG1/FAM134B is essential for ER maintenance, and its dysfunction is associated with neuronal disorders, vascular dementia, or viral infections. The protein consists of the reticulon-homology domain (RHD) that is flanked at the N- and C-termini by an intrinsically disordered protein region (IDPR), where the C terminal IDPR carries the indispensable LC3-interacting region (LIR) motif for the interaction with LC3. The RHD of RETREG1 is presumed to play a role in membrane remodeling, but the absence of a known 3D structure of this domain so far prevented researchers from gaining mechanistic insights into how the RETREG1 RHD curves membranes, and thereby facilities reticulophagy. The recent study by Bhaskara et al., which is described in this editor’s corner article, used molecular dynamics (MD) simulations to create a structural model of the RETREG1 RHD. MD simulations along with in vitro liposome remodeling experiments reveal how the RHD domain acts on the ER membrane and, in concert with the C terminal IDPR, executes the function of RETREG1 in selective reticulophagy. Abbreviations: ER, endoplasmic reticulum; IDPR, intrinsically disordered protein region; LIR, LC3-interacting region; MD, molecular dynamics; RHD, reticulon-homology domain; TM, transmembrane

The unique cellular organization and metabolic demands of neurons pose a challenge in the maintenance of neuronal homeostasis. A critical element in maintaining neuronal health and homeostasis is mitochondrial quality control via replacement and rejuvenation at the axon. Dysregulation of mitochondrial quality control mechanisms such as mitophagy has been implicated in neurodegenerative diseases including Parkinson disease and amyotrophic lateral sclerosis. To sustain mitophagy at the axon, a continuous supply of PINK1 is required; however, how do neurons maintain a steady supply of this protein at the distal axons? In the study highlighted here, Harbauer et al. show that axonal mitophagy is supported by local translation of Pink1 mRNA that is co-transported with mitochondria to the distal ends of the neuron. This neuronal-specific pathway provides a continuous supply of PINK1 to sustain mitophagy.

It would be quite convenient if every protein had one distinct function, one distinct role in just a single cellular process. In the field of macroautophagy/autophagy, however, we are increasingly finding that this is not the case; several autophagy proteins have two or more roles within the process of autophagy and many even "moonlight" as functional members of entirely different cellular processes. This is perhaps best exemplified by the Atg8-family proteins. These dynamic proteins have already been reported to serve several functions both within autophagy (membrane tethering, membrane fusion, binding to cargo receptors, binding to autophagy machinery) and beyond (LC3-associated phagocytosis, formation of EDEMosomes, immune signaling) but as Maruyama and colleagues suggest in their recent report, this list of functions may not yet be complete.

Time-restricted feeding (TRF) has recently gained interest as a potential anti-aging treatment for organisms from Drosophila to humans.(1–5) TRF restricts food intake to specific hours of the day. Because TRF controls the timing of feeding, not nutrient or caloric content, TRF has been hypothesized to depend on circadian-regulated functions; the underlying molecular mechanisms remain unclear. To exploit the genetic tools and well-characterized aging markers of Drosophila, we developed an intermittent TRF (iTRF) dietary regimen that robustly extended fly lifespan and delayed onset of aging markers in muscles and gut. We found that iTRF enhanced circadian-regulated transcription and that iTRF-mediated lifespan extension required both circadian regulation and autophagy, a conserved longevity pathway. Night-specific induction of autophagy was both necessary and sufficient to extend lifespan on ad lib diet and also prevented further iTRF-mediated lifespan extension. In contrast, day-specific induction of autophagy did not extend lifespan. Thus, these results identify circadian-regulated autophagy as a critical contributor to iTRF-mediated health benefits in Drosophila. Because both circadian regulation and autophagy are highly conserved processes in human aging, this work highlights the possibility that behavioral or pharmaceutical interventions stimulating circadian-regulated autophagy may provide people with similar health benefits such as delayed aging and lifespan extension.

In eukaryotes, ATG4/Atg4 is a critical regulator of macroautophagy/autophagy. The protease activity of Atg4/ATG4, involved in conjugation and deconjugation of Atg8-family proteins, was so far regarded as its sole functional contribution. However, the role of individual ATG4-family proteins during mammalian autophagy had previously not been examined in vivo. During their recent investigation, Nguyen et al. discovered a hitherto unexplored role for mammalian ATG4s during mitophagy - the recruitment of ATG9A-containing vesicles. Their article, highlighted here, discusses the finding, which uses a novel artificial intelligence (AI)-directed analysis technique for focused ion beam-scanning electron microscopy (FIB-SEM) imaging to demonstrate the role of ATG4s in promoting phagophore growth and establishing phagophore-ER contacts.

Glucose deprivation induces macroautophagy/autophagy primarily through AMPK activation. However, little is known about the exact mechanism of this signaling. A recent study from Dr. David C. Rubinsztein's lab showed that ULK1 is activated by AMPK upon glucose starvation, resulting in the phosphorylation of the lipid kinase PIKFYVE on S1548. The activated PIKFYVE consequently enhances the formation of phosphatidylinositol-5-phosphate (PtdIns5P)-containing autophagosomes, and therefore drives autophagy upregulation. The novel discovery of how ULK1 regulates the non-canonical autophagy signaling (PtdIns5P-dependent autophagy), not only expands our knowledge of autophagy, but also sheds light on therapeutic strategies for curing human disorders, where glucose-induced starvation can play an important role.

It has been well established that Atg11 plays a critical role in selective macroautophagy/autophagy, but not in nonselective autophagy in the budding yeast Saccharomyces cerevisiae. However, its mammalian ortholog RB1CC1/FIP200 is indispensable for both types of autophagy, and the molecular mechanism behind its function is a mystery. Recently, Pan et al. showed that in the fission yeast Schizosaccharomyces pombe, Atg11 could also promote nonselective autophagy via activation of Atg1 kinase. These results prompt an interesting idea that Atg11 might have gained an additional ability to mediate nonselective autophagy through evolution.

Reticulophagy, a type of selective autophagy that specifically targets and degrades parts of the endoplasmic reticulum (ER) network (sheets or tubules), plays a crucial role in the responses to ER stress. The selectivity of the ER cargo recognition relies on the unique reticulophagy receptors, which tether and deliver cargos to phagophores, the precursors to autophagosomes. Various integral membrane proteins have been well characterized as reticulophagy receptors, including Atg39, Atg40, RETREG1/FAM134B, SEC62, RTN3L, CCPG1, TEX264, and ATL3, in both yeast and mammals in the past five years. In a recent paper, Zhao et al. discovered in fission yeast a novel reticulophagy receptor, Epr1, which bridges the ER and phagophore by binding to Atg8 and VAPs, a mechanism different from the aforementioned reticulophagy receptors.

Several studies have provided insight into the unique intracellular localization, dynamic trafficking and diverse repertoire of binding partners of Atg9/ATG9, but structural details of the protein have remained elusive. Guardia and colleagues now report the structure of human ATG9A to a resolution of 2.9 A, revealing, among other features, an elaborate system of tunnels permeating the ATG9A protein complex.

A key feature of macroautophagy (hereafter autophagy) is the formation of the phagophore, a double-membrane compartment sequestering cargos and finally maturing into a vesicle termed an autophagosome; however, where these membranes originate from is not clear. In a previous study, researchers from the Rubinsztein lab proposed a model in which the autophagosome can evolve from the RAB11A-positive recycling endosome. In their recent paper, they determine that DNM2 (dynamin 2) functions in scission of the recycling endosome, and the release of the autophagosome precursor. These findings explain how the centronuclear myopathy (CNM) mutation in DNM2 results in the accumulation of immature autophagic structures.

Classical macroautophagy/autophagy functions to maintain cell health during stressful conditions by targeting cytosolic components for degradation and recycling through the lysosomal pathway. In contrast, nondegradative secretory autophagy functions as an alternative autophagy mechanism to mediate extracellular secretion. A recent study published in Nature Cell Biology from the laboratory of Jayanta Debnath has identified components of the LC3-conjugation machinery as mediators in the selection of cargo for nonclassical secretion. Termed LC3-dependent extracellular vesicle loading and secretion (LDELS), this mechanism provides an additional link between secretory autophagy and the release of extracellular vesicles. ABBREVIATIONS: ATG, autophagy-related; BioID, proximity-dependent biotinylation; CM, conditioned medium; EV, extracellular vesicle; HNRNPK, heterogeneous nuclear ribonuclear protein K; ILVs, intralumenal vesicles; LDELS, LC3-dependent EV loading and secretion; LIR, LC3-interacting region; MAP1LC3/LC3, microtubule associated protein 1 light chain 3; MS, mass spectrometry; MVBs, multivesicular bodies; ncRNA, non-coding RNA; NSMAF/FAN, neutral sphingomyelinase activation associated factor; P-bodies, processing bodies; PE, phosphatidylethanolamine; RB1CC1/FIP200, RB1 inducible coiled-coil 1; RBP, RNA-binding protein; RNA-seq, RNA sequencing; SAFB, scaffold-attachment factor B; SILAC, stable isotope labeling of amino acids in cell culture; SMPD3/nSMase2, sphingomyelin phosphodiesterase 3; TEM, transmission electron microscopy; TMT, tandem mass tagging

In a recent issue of this journal I attempted to explain the purpose of macroautophagy/autophagy to a non-specialist audience through the use of cartoons. In the present article, I am continuing this approach by considering the topic of autophagy regulation-why does the cell need to modulate the autophagic response, and what are the basic morphological mechanisms that can be used to attain different levels of autophagy activity?

In my role as an instructor I am constantly looking for ways to more effectively convey information to my audience, which is typically the students in my class. However, the same concerns apply to most of the people who attend a seminar. The approach you take to making the material easier to understand is likely to be influenced by the course you teach. That is, the same instructor may use different examples when teaching an upper division vs. a lower division course. I teach introductory biology, and my students may have little familiarity with cell biology, let alone autophagy. Accordingly, I have tried to consider how to illustrate the importance of autophagy in a way that can be comprehended by people who may not even be familiar with the term.

Dear Colleagues,The UT Southwestern community continues to mourn the loss of Dr. Beth Levine – a renowned physician-scientist, dedicated and caring educator, mentor, respected colleague and friend....

Macroautophagy/autophagy is a complex process that involves over 40 proteins in Saccharomyces cerevisiae. How these proteins are organized, and their activities orchestrated to facilitate an efficient autophagic mechanism remain elusive. Sawa-Makarsha et al. reconstitute the initial steps of autophagosome biogenesis during selective autophagy using autophagy factors purified from yeast. Their results show that Atg9 vesicles serve as platforms for the recruitment of the autophagy machinery, and establish membrane contact sites to initiate lipid transfer for autophagosome biogenesis. Abbreviations: GUV, giant unilamellar vesicles; PAS, phagophore assembly site; PL, proteolipisomes.

Selective autophagy is critical for the regulation of cellular homeostasis in organisms from yeast to humans. This process is a specific degradation pathway for a wide variety of substrates including unwanted cytosolic components, such as protein aggregates, damaged and/or superfluous organelles, and pathogens. However, it has been less clear as to whether a protein complex or substructure of an organelle can be targeted for removal by selective autophagy. One example of such a substrate is the nuclear pore complex (NPC), a large macromolecular assembly that is present throughout the nuclear envelope. Here, we highlight two recent studies that demonstrate for the first time that NPCs are targeted for vacuolar degradation through selective autophagy. ABBREVIATIONS: AIM: Atg8-interacting motif; NE: nuclear envelope; NPC: nuclear pore complex; Nup: nucleoporin; PMN/micronucleophagy: piecemeal microautophagy of the nucleus

There is a type of noncanonical autophagy, which is independent of ATG5 (autophagy related 5), also referred to as alternative autophagy. Both canonical and ATG5-independent alternative autophagy require the initiator ULK1 (unc-51 like kinase 1), but how ULK1 regulates these two types of autophagy differently remains unclear. A recent paper from Torii et al. demonstrates that phosphorylation of ULK1 at Ser746 by RIPK3 (receptor interacting serine/threonine kinase 3) is the key difference between these two types of autophagy; this phosphorylation is exclusively found during alternative autophagy.

AMPK is one of the main regulators of energy homeostasis in the cell, achieving this role in part by upregulating autophagy in times of nutrient deprivation. Previous reports have described several AMPK substrates involved in autophagy regulation; however, there are still undiscovered AMPK downstream effectors that could play an important role in autophagy. In a new article, Dohmen et al. discovered that the CCNY-CDK16 complex is a novel AMPK substrate involved in autophagy activation.

In 2013, Dr. Lora Hooper and colleagues described the induction of antibacterial macroautophagy/autophagy in intestinal epithelial cells as a cytoprotective host defense mechanism against invading Salmonella enterica serovar Typhimurium (S. Typhimurium). Canonical autophagy functions in a primarily degradative capacity to safeguard cells and ensure survival during stress conditions, including pathogen infection. In contrast, secretory autophagy has emerged as an alternative nondegradative mechanism for cellular trafficking and unconventional protein secretion. More recently, a study by Bel et al. from Dr. Hooper's lab describes how intestinal Paneth cells exploit the endoplasmic reticulum (ER) stress response to release antibacterial lysozyme through secretory autophagy in response to S. Typhimurium infection.

I am writing this editorial for two purposes. First, the plan is to start sending out invitations to prospective authors this month. If you have not heard from me by October 1, you would like to be...

The actin regulator JMY creates filament networks that move membranes during autophagy. Hu and Mullins find that JMY is normally inhibited by interaction with the STRAP protein, but upon starvation, JMY is recruited away from STRAP and activated by LC3., During autophagy, actin filament networks move and remodel cellular membranes to form autophagosomes that enclose and metabolize cytoplasmic contents. Two actin regulators, WHAMM and JMY, participate in autophagosome formation, but the signals linking autophagy to actin assembly are poorly understood. We show that, in nonstarved cells, cytoplasmic JMY colocalizes with STRAP, a regulator of JMY’s nuclear functions, on nonmotile vesicles with no associated actin networks. Upon starvation, JMY shifts to motile, LC3-containing membranes that move on actin comet tails. LC3 enhances JMY’s de novo actin nucleation activity via a cryptic actin-binding sequence near JMY’s N terminus, and STRAP inhibits JMY’s ability to nucleate actin and activate the Arp2/3 complex. Cytoplasmic STRAP negatively regulates autophagy. Finally, we use purified proteins to reconstitute LC3- and JMY-dependent actin network formation on membranes and inhibition of network formation by STRAP. We conclude that LC3 and STRAP regulate JMY’s actin assembly activities in trans during autophagy.

A Google search for the combined terms "de Duve, autophagy, 1963" will reveal over 45,000 hits, most of them referring to the idea that the term autophagy was coined by the brilliant Christian de Duve on the sidelines of a symposium on lysosomes that took place in 1963. However, the first use of the term "autophagy" actually took place a century earlier.

Mitophagy is a conserved and highly regulated process of selective degradation crucial in maintaining normal cellular physiology. Genetic defects and cellular aberrations affecting mitophagy have been associated with the development of Parkinson disease. In their recently published article (highlighted in a punctum in this issue of the journal) Hsieh et al. present a putative mitophagy marker, which serves as a mechanistic link between sporadic and familial Parkinson disease.

Incidences of congenital syndrome associated with maternal zika virus (ZIKV) infection during pregnancy are well documented; however, the cellular and molecular mechanisms by which ZIKV infection causes these devastating fetal pathologies are still under active investigation. ZIKV is a member of the flavivirus family and is mainly transmitted to human hosts through Aedes mosquito vectors. However, in vivo models for the neurological tropism of the virus and the arthropod vector have been lacking. A recent study published in Cell Host & Microbe from Dr. Sara Cherry's lab investigates both of these key aspects of the ZIKV infectious life cycle. Liu et al. demonstrate how inflammatory activated Sting/dSTING-dependent antiviral macroautophagy/autophagy is sufficient to restrict ZIKV infection in the Drosophila melanogaster brain. Additionally, this study provides further evidence for the ancestral function of autophagy in protecting host cells from viral invaders. Abbreviations: AGO2: Argonaute 2; ATG: autophagy-related; Dcr-2: Dicer-2; DptA/Dipt: Diptericin A; Drs: Drosomycin; DCV: Drosophila C virus; IMD: immune-deficiency; qRT-PCR: quantitative real-time PCR; Rel/NF-κB: Relish; RNAi: RNA interference; ZIKV: zika virus.

Recently, NIH has funded a center for autophagy research named the Autophagy, Inflammation, and Metabolism (AIM) Center of Biomedical Research Excellence, located at the University of New Mexico Health Science Center (UNM HSC), with aspirations to promote autophagy research locally, nationally, and internationally. The center has 3 major missions: (i) to support junior faculty in their endeavors to develop investigations in this area and obtain independent funding; (ii) to develop and provide technological platforms to advance autophagy research with emphasis on cellular approaches for high quality reproducible research; and (iii) to foster international collaborations through the formation of an International Council of Affiliate Members and through hosting national and international workshops and symposia. Scientifically, the AIM center is focused on autophagy and its intersections with other processes, with emphasis on both fundamental discoveries and applied translational research.

Xenophagy, a unique type of selective macroautophagy/autophagy, targets invading pathogens as part of the host immune response. In order to survive within the host, bacteria have established various self-defense mechanisms. In a recent paper from Feng Shao’s lab, the Salmonella effector protein SopF has been demonstrated to block xenophagy by interrupting the vacuolar type H(+)-translocating (v-) ATPase-ATG16L1 axis, which is important for antibacterial autophagy initiation. SopF can specifically ADP-ribosylate Gln124 on ATP6V0C, a v-ATPase component, thus influencing recruitment of ATG16L1 onto the bacteria-containing vacuole within the host cytosol. Abbreviations: ATG: autophagy-related; S. Typhimurium: Salmonella enterica serovar Typhimurium; T3SS: type III secretion system

ULK1 and ATG13 assemble with RB1CC1/FIP200 and ATG101 to form a macroautophagy (hereafter autophagy) induction (ULK1) complex in higher eukaryotes. The yeast counterpart, the Atg1 complex, is comprised of Atg1 and Atg13 (ULK1 and ATG13 homologs), Atg17 (a proposed functional homolog of RB1CC1), and either the Atg101 subunit (in Schizosaccharomyces pombe) or the Atg29-Atg31 heterodimer (in Saccharomyces cerevisiae). With mutual exclusivity of, and no detectable homology between, the Atg29-Atg31 dimer and Atg101, knowledge about the roles of these proteins in autophagy induction is an important piece in the puzzle of understanding the molecular mechanism of autophagy initiation. A recent study reporting the structure of the S. pombe homolog Atg101 bound to the Atg13HORMA domain is a notable contribution to this knowledge (see the punctum in this issue of the journal).

When it comes to cancer initiation and progression, macroautophagy/autophagy seemingly acts in a contradictory fashion, serving either as a suppressive factor that functions to protect against tumor formation or as a support mechanism that sustains the disease itself through its cytoprotective functions. In tumor suppression, autophagy assists by restricting oxidative stress and curbing genomic instability that could possibly cause oncogenic mutations. However, in certain circumstances, autophagy can also promote cancer by providing nourishment and by limiting stress-response pathways, leading to cancer cell survival and rapid proliferation. Thus, autophagy's role in oncogenesis is highly context-dependent and varies from one cancer type to another. As a consequence, identifying the mechanisms that alter and rewire autophagic regulation and flux is extremely crucial to target autophagy as a possible avenue for anticancer treatment. In a recent study, Qian et al. endeavored to identify one such key regulatory pathway in hypoxia- and glutamine deprivation-induced autophagy in tumorigenic cells. In this pathway, phosphatidylinositol 3-phosphate (PtdIns3P) production by the class III phosphatidylinositol 3-kinase (PtdIns3K) complex is greatly improved through a cascade of posttranslational modifications that culminates in the phosphorylation of the scaffolding protein BECN1 by the glycolytic pathway kinase PGK1.

The mechanism regulating Atg1 kinase activity for the initiation of selective macroautophagy (hereafter autophagy) under nutrient-rich conditions has been a long-standing question. Canonically in yeast, nutrient starvation or rapamycin treatment repress TOR complex 1 and stimulate the Atg1 complex (including at least Atg1, Atg13, Atg17, Atg29 and Atg31), which allows the recruitment of downstream autophagy-related (Atg) components to the phagophore assembly site (PAS), culminating in phagophore formation, and, subsequently, autophagosome biogenesis. Atg1 also functions under conditions promoting selective autophagy that do not necessarily require nutrient deprivation for induction. However, there has been some debate as to whether Atg1 catalytic activity plays a more important role under conditions of nutrient starvation-induced autophagy (i.e., bulk autophagy) vs. selective autophagy (e.g., the cytoplasm-to-vacuole targeting [Cvt] pathway). A recent paper by Kamber and colleagues investigates the mechanism regulating Atg1 activity during selective autophagy.

The formation and maturation of the autophagosome, a morphological hallmark of macroautophagy/autophagy, is tightly controlled with regard to location, timing and intensity. Various proteins have been characterized to be essential in regulating autophagosome biogenesis, whereas little is known about the roles of specific lipids and their metabolizing enzymes in this process. In a recent paper, Holland et al. identified the phosphoinositide-binding protein HS1BP3 as a novel negative regulator of autophagosome formation. HS1BP3 is proposed to act by inhibiting PLD1 (phospholipase D1) activity and localization to ATG16L1 and TFRC (transferrin receptor)-positive vesicles thereby modulating the phosphatidic acid (PA) levels and lipid composition of autophagosome precursor membranes.

The treatment of L929 fibrosarcoma cells with zVAD has been shown to induce necroptosis. However, whether autophagy is involved or not in this event remains controversial. In this study, we re-examined the role of autophagy in zVAD-induced cell death in L929 cells and further elucidated the signaling pathways triggered by caspase inhibition and contributing to autophagic death. First, we found that zVAD can stimulate LC3-II formation, autophagosome and autolysosome formation, and ROS accumulation. Antioxidants, beclin 1 or Atg5 silencing, and class III PtdIns3K inhibitors all effectively blocked ROS production and cell death, suggesting ROS accumulation downstream of autophagy contributes to cell necrosis. zVAD also stimulated PARP activation, and the PARP inhibitor DPQ can reduce zVAD-induced cell death, but did not affect ROS production, suggesting the increased ROS leads to PARP activation and cell death. Notably, our data also indicated the involvement of Src-dependent JNK and ERK in zVAD-induced ROS production and autophagic death. We found caspase 8 is associated with c-Src at the resting state, and upon zVAD treatment this association was decreased and accompanied by c-Src activation. In conclusion, we confirm the autophagic death in zVAD-treated L929 cells, and define a new molecular pathway in which Src-dependent ERK and JNK activation can link a signal from caspase inhibition to autophagy, which in turn induce ROS production and PARP activation, eventually leading to necroptosis. Thus, in addition to initiating proteolytic activity for cell apoptosis, inactivated caspase 8 also functions as a signaling molecule for autophagic death.

In eukaryotes, xenophagy is defined as a type of selective macroautophagy/autophagy that is used for eliminating invading pathogens. In contrast to other types of selective autophagy, such as mitophagy, pexophagy and ribophagy, xenophagy is used by eukaryotes for targeting microbes-hence the prefix "xeno" meaning "other" or "foreign"-that have infected a host cell, leading to their lysosomal degradation. This unique characteristic links xenophagy to antibacterial and antiviral defenses, as well as the immune response. Furthermore, recent studies suggest a complicated role of xenophagy in cancer, through either suppressing tumorigenesis or promoting survival of established tumors. In this issue, Sui et al. summarize previous and current studies of xenophagy and consider them in the context of anticancer treatment.

Edwin M. Southern is a professor emeritus at the University of Oxford. He is perhaps best known for development of the “Southern blot” (Dr. Southern was at the University of Edinburgh when he wrote his landmark paper). The Southern blot provided a scientific breakthrough by allowing scientists to detect a particular DNA sequence without first purifying it from the rest of the genome; the basic method involves the transfer of the DNA to a membrane, followed by detection with a specific probe. Although few people perform Southern blots as originally carried out by Southern, due in part to the more recent technique of the polymerase chain reaction, the basic concept continues to play an important role in molecular biology.

The morphometric examination of autophagic bodies provides useful information about the mechanism and magnitude of macroautophagy, and yeast researchers frequently utilize various measurements of these structures as part of their quantification of the process. The utility of this approach, however, has led to the common misconception that autophagic bodies can be found in the mammalian lysosome, which is generally not correct.

The midge Belgica antarctica is the only insect endemic to Antarctica and has the southernmost range of any insect. In its natural environment, B. antarctica frequently faces desiccating conditions, as environmental water is frozen for up to 9 months annually. The molecular mechanisms by which B. antarctica tolerates extreme dehydration are poorly understood, but recent work from our laboratory reports genome-wide expression changes in response to extreme dehydration (~40% water loss), the first genome-scale transcriptome reported for an Antarctic animal. Among transcripts differentially regulated during dehydration, there is coordinated upregulation of numerous genes involved in autophagy, including genes responsible for autophagosome synthesis and autophagy-associated transcription factors. Also, several genes and pathways that interact with and regulate autophagy, e.g., sestrins and proteasomal genes, are concurrently upregulated. This suggests that autophagy and related processes are key elements regulating stress tolerance in this extreme environment.

In eukaryotic cells, cell migration is a dynamic and complex process that involves finely tuned orchestration of a multitude of proteins including, for example, those involved in focal adhesions (FAs). Cell migration plays an indispensable role in particular stages of development and its proper regulation is crucial in various biological processes, from wound healing to the immune response. FAs are transmembrane protein complexes that traverse cytoskeletal infrastructures all the way to the extracellular matrix, producing traction at the leading edge of the cell, thus allowing for motility. The assembly of FAs has been extensively studied, whereas disassembly remains poorly understood. Here, we highlight 2 recent studies (see the corresponding puncta in the previous and current issues of the journal) that demonstrate a requirement for macroautophagy/autophagy in FA disassembly. These studies also provide a deeper understanding of how autophagy can contribute to cell migration among multiple cell types.

Autophagy, a cellular self-eating mechanism, is important for maintaining cell survival and tissue homeostasis in various stressed conditions. Although the molecular mechanism of autophagy induction has been well studied, how cells terminate autophagy process remains elusive. Here, we show that ULK1, a serine/threonine kinase critical for autophagy initiation, is a substrate of the Cul3-KLHL20 ubiquitin ligase. Upon autophagy induction, ULK1 autophosphorylation facilitates its recruitment to KLHL20 for ubiquitination and proteolysis. This autophagy-stimulated, KLHL20-dependent ULK1 degradation restrains the amplitude and duration of autophagy. Additionally, KLHL20 governs the degradation of ATG13, VPS34, Beclin-1, and ATG14 in prolonged starvation through a direct or indirect mechanism. Impairment of KLHL20-mediated regulation of autophagy dynamics potentiates starvation-induced cell death and aggravates diabetes-associated muscle atrophy. Our study identifies a key role of KLHL20 in autophagy termination by controlling autophagy-dependent turnover of ULK1 and VPS34 complex subunits and reveals the pathophysiological functions of this autophagy termination mechanism.

The ubiquitin-proteasome system (UPS) and macroautophagy/autophagy are 2 main degradative routes, which are important for cellular homeostasis. In a study conducted by Marshall et al., the authors demonstrated that the UPS and autophagy converge in Arabidopsis (see the punctum in issue #11-10). In particular, they found that the 26S proteasome is degraded by autophagy, either nonselectively (induced by nitrogen starvation) or selectively (induced by proteasome inhibition). The selective phenotype is mediated through the proteasome subunit RPN10, which can bind both ubiquitin and ATG8. This newly identified autophagic degradation of the proteasome is termed "proteaphagy," and the process reveals an interesting relationship between these degradative systems.

Autophagy, a highly regulated cellular degradation and recycling process, can occur constitutively at a basal level, and plays an essential role in many aspects of cell physiology. A recently published study (see the related punctum in Autophagy, Vol. 12, No. 4) suggests that basal autophagy is also important for maintaining the regenerative capacity of muscle stem cells, and that the decline of autophagy with aging is the cause of entry into senescence from quiescence in satellite cells.

As an editor, and in this case I mean as a person who, along with the assistant editor, proofreads the final text of submitted manuscripts to help ensure uniformity, clarity and adherence to a stan...

The third edition of the autophagy guidelines is now published. This turned out to be a major undertaking in part because of the tremendous increase in the number of researchers participating in autophagy studies, and hence in revising the guidelines. First, I cannot emphasize enough that this paper represents a true community effort—it would simply not be possible for one person to generate such an in-depth and up-to-date manuscript covering this diverse range of topics in the autophagy field. Second, it is of critical importance that this paper indeed does not represent the opinions of a single individual, but rather seeks to obtain a consensus opinion regarding the best methods to monitor autophagy and interpret the results of the corresponding experiments. So, thank you to all who have contributed to the latest version.

This Editor's Corner may sound like the title of a mystery novel, but it actually reflects a question I have about the puncta articles that appear in Autophagy (or rather, the ones that do not appear). In particular, I am surprised by the number of solicitations sent out for puncta that are either ignored, or, less frequently, declined. It is not that I expect the principal investigator (PI) to find the invitation to write a punctum undeniably attractive. Rather, it is the unilateral decision that it is not worthwhile for graduate students or postdocs who performed the work—and likely wrote at least the first draft of the paper—to write the punctum. In fact, time spent drafting a punctum yields considerable benefits: puncta provide more exposure for the lab, offer opportunities for young scientists to gain additional writing experience, and make a nice (albeit small) addition to a curriculum vitae. It is for the latter reason that I find it particularly disappointing that PIs decide to dismiss the opportunity to write a punctum. I fully understand that for many PIs, adding a punctum will not have a significant impact on a curriculum vitae. Yet for a student or a postdoc who might have a relatively small number of publications at this stage of their career, a punctum (even though it is not a full-fledged research article) can have a more meaningful impact on their C.V.

In 2008 we published the first guidelines paper for monitoring autophagy and interpreting the data resulting from the various assays used in our field. The guidelines paper was substantially expanded and updated in 2012. Based on the number of citations, and on comments from many users, I think it is accurate to say that the guidelines have been very useful for many researchers. Because the field continues to undergo rapid development, it is necessary to update the guidelines once again.

In this issue of the journal we are publishing a series of papers that inaugurate a new category—clinical research. We already have a category for translational research, so what is the need for this new category? In part, this question may be answered by first considering the difference between papers submitted as “Basic Science” and “Translational.” Both of these types of papers report findings from standard bench research that most readers of this journal are familiar with; however, research done in most model organisms is at least a few steps away from practical application (that is, being used for therapeutic purposes in a clinical setting), whereas that done with mammalian cell culture or in certain animal models, depending on the topic and the specific experiments, may be directly addressing a health-related question. The former type of research would be considered basic, and the latter is translational. As more specific examples, studies on the role of Atg proteins in yeast are generally basic research, whereas those examining the effect of inhibiting/stimulating autophagy in combination with an anticancer treatment in a mouse tumor model could be translational. In contrast to both of these types of studies, “Clinical” papers report results from actual trials, such as the phase I trials described in this issue or studies in patients pertaining to disease prevention. There are significant differences between these 2 types of studies, clinical and nonclinical, and these are worth considering both for potential reviewers and readers of these and similar papers. Finally, we note that there has been, and will likely continue to be, a move toward the clinical application of findings from basic research that pertain to various pathologies associated with autophagy or defects in this process, including infectious disease, neurodegeneration, diabetes, and others. The phase I trials published in this issue are one example of this, but we anticipate an increasing number of studies on the modulation of autophagy for therapeutic purposes.

How does the phagophore form? Which membrane acts as a platform for its biogenesis? Over the years, extensive use of microscopy techniques have led to the controversial identification of multiple potential membranes as precursors for phagophore nucleation and/or for the supply of lipids to the expanding compartment. Nevertheless, none of these studies has established a direct functional link between membrane sources and autophagosome biogenesis. Addressing this point, in a recent study highlighted by a punctum in this issue, Ge and coworkers developed an in vitro approach to determine the identity of the membranes responsible for the lipidation of LC3, thus identifying the ER-Golgi intermediate compartment (ERGIC) as a potential key determinant of phagophore biogenesis.

LC3 (microtubule-associated protein 1 light chain 3), an essential macroautophagy (hereafter autophagy) protein, localizes in the nucleus in addition to the cytoplasm where it primarily functions. However, little is known about the role of nuclear LC3 in autophagy. In the study conducted by Huang et al., the authors characterize the molecular mechanism through which it regulates autophagosome formation. Upon nutrient deprivation, deacetylation of nuclear LC3 by the deacetylase SIRT1 promotes its association with the nuclear factor TP53INP2/DOR, resulting in the redistribution of nuclear LC3 to the cytoplasm. LC3 is then able to interact with ATG7, a step required for LC3 lipidation and subsequent autophagosome biogenesis.

Posttranslational regulation of macroautophagy (hereafter autophagy), including phosphorylating and dephosphorylating components of the autophagy-related (Atg) core machinery and the corresponding upstream transcriptional factors, is important for the precise modulation of autophagy levels. Several kinases that are involved in phosphorylating autophagy-related proteins have been identified in both yeast and mammalian cells. However, there has been much less research published with regard to the identification of the complementary phosphatases that function in autophagy. A recent study identified PPP3/calcineurin, a calcium-dependent phosphatase, as a regulator of autophagy, and demonstrated that one of the key targets of PPP3/calcineurin is TFEB, a master transcriptional factor that controls autophagy and lysosomal function in mammalian cells.