Abstract
The prompt for this thematic issue came from a burst of nearly simultaneous publications on the role of autophagic adaptors and molecular earmarks on targets for selective autophagy. This included a range of autophagic cargo from protein aggregates to whole organelles and even intracellular microbes. The continuing motivation emanating from this initial prompt was to distill the points of convergence and common principles and extract the less immediately obvious functional, physiological and evolutionary connections. Another core purpose was to give a side-by-side update and follow-up analysis by the major protagonists of this recent growth, and in some cases provide a forum for bringing up potential controversies. The result is a comprehensive compendium of reviews, addenda and puncta that should give the reader in one place a summary, an update, and an insider glimpse into the ongoing and future studies in this important area of how autophagy accomplishes the goal of finding its targets, and what consequence that has on cellular function.
The prompt for this thematic issue came from a burst of nearly simultaneous publications on the role of autophagic adaptors and molecular earmarks on targets for selective autophagy. This included a range of autophagic cargo from protein aggregates to whole organelles and even intracellular microbes. The continuing motivation emanating from this initial prompt was to distill the points of convergence and common principles and extract the less immediately obvious functional, physiological and evolutionary connections. Another core purpose was to give a side-by-side update and follow-up analysis by the major protagonists of this recent growth, and in some cases provide a forum for bringing up potential controversies. The result is a comprehensive compendium of reviews, addenda and puncta that should give the reader in one place a summary, an update and an insider glimpse into the ongoing and future studies in this important area of how autophagy accomplishes the goal of finding its targets, and what consequence that has on cellular function.
Key Theme and Subplots
The key leitmotif that even a reader unfamiliar with the topic will find as an exciting advance in the field is the identification of both the molecular tags on autophagic targets and the receptors/adaptors that recognize them and help assemble autophagosomal machinery and membranes to engulf the material intended for autophagic delivery and/or disposal. There are also several subplots that may be worth emphasizing: (i) Both the microbial pathogens and mitochondria share in principle at least some aspects of molecular tags and receptors/adapters for autophagic elimination, possibly reflecting mitochondiral evolutionary ancestry from bacteria, the intracellular Rickettsia-like α-proteobacteria that evolved into the endosymbiont and present-day mitochondria. This point is clearly emphasized in an excellent review by Wang and Klionsky; additional published considerations along that theme can be found in the following link: http://f1000.com/reports/b/2/45/. (ii) A crosstalk theme between proteasomal and autophagic degradation of ubiquitinated cargo is another significant undercurrent. This is to be expected, given that ubiquitin tags are shared by the two degradative systems. To illustrate this point, I will extract here a vignette from the comprehensive review by Johansen and Lamark. These authors, among other key points, discuss the report that Hsp70/Hsc70-co-chaperones BAG1 and BAG3 (the latter can be found in complexes with p62) direct the preference between proteasomal versus autophagic degradation of misfolded proteins targeted by autophagic adaptors. A small heat shock protein HspB8 (induced when the proteasome is inhibited) in association with BAG3 affects aberrant huntingtin and autophagy in muscles. In addition, this crosstalk is highlighted in the punctum by Gao and Chen in the context of Wnt signaling, whereby they discuss their published findings that dishevelled, a spontaneously aggregating protein that works as a transmitter of Wnt signaling, is not only a substrate for the proteasomal system, but is modulated by autophagic degradation as well. (iii) An intriguing role of p62 and its bigger (but younger, in terms of arrival on the scientific scene) brother Alfy, is that both are involved not only in autophagy of cytopalsmic targets, but may be found in the nucleus within PML bodies proposed to be the sites for proteasomal degradation of misfolded proteins in the nucleus. These points, and the observation that Alfy and p62 shuttle between the nucleus and cytoplasm, are addressed in the articles by Johansen and Lamark, and Yamamoto and Simonsen and emphasize both the current limits of our knowledge and prospects for expanding our understanding, to how nuclear aggregates are cleared or set off signaling triggers.
From Cell Signaling to Aggrephagy and Mitophagy
Servicing all of the above, this thematic issue begins with an extensive review by Johansen and Lamark covering autophagic adaptors and their roles. This article is a comprehensive, state-of-the-art coverage of autophagic adaptors in both broad strokes and fine details. It also outlines discrepancies and expands into an important area of overlap between autophagic adaptors and cell signaling.
As mentioned above, Gao and Chen highlight how autophagy and p62/sequestosome 1 adapter-LC3 work together in Wnt signaling, of significance for embryogenesis, tissue homeostasis and possibly in proper stem cell deployment and tissue renewal. A major relay in Wnt signaling is Dvl. It turns out, as Gao and Chen discuss, that autophagy modulates this key pathway by removing Dvl, which has a spontaneous tendency to form aggregates (and thus represents an obvious target for autophagy) via its DIX domain. The Dvl aggregate elimination process depends on ubiquitination and p62, which is one of the leitmotifs of this thematic issue, albeit the authors also find an LC3-interacting region (LIR)-like motif (WLKI) directly in Dvl, and make a suggestion that a canonical target-ubiquitin-adaptor-LC3 combination is not an absolute requirement. It is also reasonable to assume that starvation induced by the absence of growth factors (possibly equivalent to some of the inherent features of the loss of Wnt signals), hypoxia and other stress triggers employ autophagy in Wnt signaling to modulate cell survival and adult tissue maintenance, and perhaps contribute to protection against human degenerative diseases and cancer.
Another important advance covered in this issue is the competition between different adaptor/receptor systems, addressed by Yamamoto and Simonsen in their addendum on Alfy function. Alfy is a giant protein that binds to p62 (also to PtdIns(3)P and Atg5), is expressed highly in the brain (where aggregate protein removal is key) while it is present at much lower levels in the liver (which is an organ where autophagy converts cytoplasm into nutrients when needed to feed the rest of the body), and helps clear large protein aggregates such as polyQ expansion proteins associated with Huntington disease. In their addendum, Yamamoto and Simonsen provide data that show a competition between aggrephagy (aggregate removal) and nutritional autophagy (when cells convert long-lived proteins into amino acids) by simply overexpressing Alfy and showing that it can redirect autophagy away from the latter process of starvation-induced autophagy.
Springer and Kahle provide a comprehensive review of the role of Pink1 and Parkin in mitochondrial clearance, and the latest connections to the autophagy pathway. This is given against the health significance backdrop of Parkinson disease (PD) summarizing a long journey that it took to begin to explain the mechanism of action of the genetic factors in PD. The authors dissect in exquisite detail the emerging literature with lots of new important findings published in 2010 and outline key pathway steps in the following series: mitochondrial depolarization Pink1-Parkin—ubiquitination of mitochondrial targets (VDAC1 and Mfn)—HDAC6- and microtubule motor-driven collection and clustering of faulty mitochondria in a perinuclear mito-aggresome. They highlight p62 and other autophagic adaptors plus mammalian Atg8 (LC3) facilitating autophagy of clustered mitochondria, and the potential role of HDAC6, cortactin and actin in lysosomal fusion and maturation into autolysosomes. Complementing this insightful and comprehensive text, Johansen and Lamark discuss in their review some of the competing recent views on the exact role of p62 in mitochondrial aggregation versus mitophagy. Novak and Dikic discuss the role of Nix in autophagy of mitochondria, and indicate that in addition to Nix (BNIP3L), Bnip3 has a LIR motif and both may play a role in mitochondrial clearance under hypoxic conditions, of significance both for metabolic adjustments and cell survival.
Wang and Klionsky cover mitophagy with an emphasis on yeast as a model system. In this review the reader can also find an update on how many ATG genes there are currently in yeast, and comparisons between different selective autophagy pathways (Cvt, pexophagy, mitophagy) and their convergence on Atg11. They also pose an interesting question as to whether ribophagy in yeast, which is associated with ubiquitination/deubiquitination (implicated in metazoans as a tag recognized by adaptor proteins) is more Atg11-like or mammalian-like, i.e., employing ubiquitin + adapter. In this review, the roles and features of adaptor proteins are cast in an evolutionary comparative manner analyzing the specifics in yeast, C. elegans and mammalian systems.
Bacterial Clearance and Autophagic Adaptors
As announced in the introduction, a significant number of articles in this thematic issue are dedicated to the growing role of autophagic adapters in elimination of intracellular microbes (“xenophagy”). These include articles by Sumpter and Levine on p62 and Sindbis virus, two papers from John Brumell's group (Shahnazari et al. on the role of diacylglycerol in addition to ubiquitin as a targeting signal, and Cemma et al. on the interplay between p62 and NDP52 in targeting Salmonella for autophagy), an article by Ogawa et al. on p62 and antiautophagic action by Listeria, a piece by Felix Randow on the role of NDP52 in xenophagy of Salmonella, and a punctum by Ponpuak and Deretic on the role of p62 and autophagy in generating neoantimicrobial peptides.
The review by Felix Randow treats us to an elegant overview of autophagy's role in the removal of intracellular microbes, and to a very fitting new term—“cytosolic immunity.” It covers the role of NDP52 as an autophagic adaptor against Salmonella and how it links with TBK1 signaling, known to play a role in type I interferon and anti-viral immunity. There is also a discussion on whether bacteria targeted by autophagic adaptors are themselves ubiquitinated, or rather host proteins associated with bacteria are tagged with ubiquitin; an example of M. marinum is given where urea treatment was not able to remove the ubiquitin tags suggesting modification of bacteria themselves, or of a tightly associated cellular material. The article from Sasakawa's group reviews in depth the infectious and intracellular life cycle of Listeria monocytogenes, one of the classical model microbes for studying immunology and cell biology of intracellular pathogens along with the latest findings on how cytosolic Listeria is recognized for autophagy by p62, and how this is countered by the Listerial factor ActA. The addendum from the Brumell group shows interesting new data regarding p62 and NDP52 and also provides a key indication that ubiquitin may not be the only signal for selective autophagy of bacteria (and possibly broader), and that an important membrane signaling lipid, diacylglycerol, and its effectors play a role in modulating autophagic targeting. Complementary to this notion is one of the issues discussed in the review by Sumpter and Levine, where the authors emphasize that p62 could potentially recognize targets that are not ubiquitinated.
Pathology of Viral and Bacterial Infections and Autophagic Adapter Proteins—A Couple of Surprises
In the review by Sumpter and Levine, the authors link two major pathways of cell-autonomous protection against viruses, by proposing a link between the double-stranded RNA-activated kinase PKR with autophagy, in defense against Sindbis virus. The PKR link adds a new dimension to the budding understanding of the interactions between autophagy and viral nucleic acids pattern recognition receptors. This article also takes a broad view connecting viral infection, autophagy and certain illnesses such as Paget disease, the latter also being addressed elsewhere in this thematic issue. The reader will find out through this article that, most surprisingly, autophagy seems not to limit Sindbis viral titers (although Sindbis virus capsid was clearly targeted by p62 for autophagy), but nevertheless has protective effects against Sindbis-induced pathology. One of the interesting effects discussed is that infected cells that accumulate p62 (when it is not consumed by autophagy) and protein aggregates may increase inflammation or protein aggregate toxicity to neurons. The authors propose a very relevant idea that p62 and autophagy are likely involved in clearing viral debris from cells, given that viral infections are exceptionally common. This goes well with notions in the field considering p62 action as proinflammatory per se, as seen in the literature in the contexts of cancer, bacterial infections and possibly neurodegeneration. Complementing the points made by Sumpter and Levine on what happens with viral neuropathology when p62 is not used up or used properly by autophagy, the punctum by Ponpuak and Deretic shows the extended protective side of p62's role when autophagy is allowed to proceed to completion by scavenging cytoplasmic proteins and converting them within autophagic organelles into neo-antimicrobial peptides that can then in turn kill the causative agent of tuberculosis.
In summary, this thematic issue is not just a snapshot of what we know about selective autophagy and targeting, but should be a source of ideas and inspiration to further our understanding of these fascinating processes that provide the molecular underpinnings for autophagy as one of the last key biological paradigms that remain to be unraveled.
Happy reading.