Papers by DanielJ Klionsky
Autophagy
Over the past several years, I have been interacting with an increasing number of Iranian scienti... more Over the past several years, I have been interacting with an increasing number of Iranian scientists, including those currently living in Iran as well as others who are being educated elsewhere or have independent positions outside of that country. In all circumstances, the resulting collaborations have extended my own knowledge and allowed me to contribute to papers on a variety of topics that are outside my specific area of expertise, including xenophagy, nanoparticles, cardiac disease and cancer. As the editor-in-chief of this journal, one of my goals is to be as inclusive as possible, encouraging scientists from around the world to engage in autophagy-related research, and to heighten awareness of this work with an aim toward a more complete understanding of the basic process, and to aid in progress toward the modulation of autophagy for medical applications. For this reason, I have been extremely dismayed by the actions of the current government in Iran, which have led to attacks on scientists and students, and in particular to policies that encourage the repression of women. Although we still have not achieved full equality for women in the United States of America, I think we are slowly moving in a positive direction. It is my sincere hope that the lives and aspirations of women around the world can continue to improve so that this half of our population can fully contribute to the scientific enterprise.
Autophagy, 2006
With its relevance to our understanding of eukaryotic cell function in the normal and disease sta... more With its relevance to our understanding of eukaryotic cell function in the normal and disease state, autophagy is an important topic in modern cell biology; yet, few textbooks discuss autophagy beyond a two-or three-sentence summary. Here, we report an undergraduate/graduate class lesson for the in-depth presentation of autophagy using an active learning approach. By our method, students will work in small groups to solve problems and interpret an actual data set describing genes involved in autophagy. The problem-solving exercises and data set analysis will instill within the students a much greater understanding of the autophagy pathway than can be achieved by simple rote memorization of lecture materials; furthermore, the students will gain a general appreciation of the process by which data are interpreted and eventually formed into an understanding of a given pathway. As the data sets used in these class lessons are largely genomic and complementary in content, students will also understand first-hand the advantage of an integrative or systems biology study: No single data set can be used to define the pathway in full-the information from multiple complementary studies must be integrated in order to recapitulate our present understanding of the pathways mediating autophagy. In total, our teaching methodology offers an effective presentation of autophagy as well as a general template for the discussion of nearly any signaling pathway within the eukaryotic kingdom.
Cardiology Plus
Heart failure (HF) refers to a progressive pathological condition when cardiac muscles fail to pu... more Heart failure (HF) refers to a progressive pathological condition when cardiac muscles fail to pump adequate blood supply (cardiac output) to meet the metabolic demand of the body. Among various cellular and molecular mechanisms identified for the onset and progression of HF, autophagy dysregulation is increasingly getting recognized. Autophagy is a natural cellular process that is observed in almost all eukaryotic cells. Autophagy removes damaged/long-lived organelles, protein aggregates, and unwanted cellular compomemts via forming autophagosomes then fusing with lysosomes. Although mild-to-moderate induction of autophagy is deemed cytoprotective and adaptive, excessive or unchecked induction of autophagy can be detrimental and maladaptive. Both adaptive and maladaptive autophagy play a vital role in the pathophysiology of HF. In the current review, we provide an overview of autophagy regulation in HF and possible strategies targeting autophagy for the management of HF.
Circulation Research, 2015
Autophagy is a catabolic recycling pathway triggered by various intra-or extracellular stimuli th... more Autophagy is a catabolic recycling pathway triggered by various intra-or extracellular stimuli that is conserved from yeast to mammals. During autophagy, diverse cytosolic constituents are enveloped by double-membrane vesicles, autophagosomes, which later fuse with lysosomes or the vacuole to degrade their cargo. Dysregulation in autophagy is associated with a diverse range of pathologies including cardiovascular disease, the leading cause of death in the world. Accordingly, there is tremendous interest in modulating autophagy for therapeutic purposes. One complexity with regard to cardiovascular homeostasis, however, is that the timing of autophagic activity appears to be critical; for example, cardiomyocyte autophagy during ischemia/reperfusion can be either beneficial or harmful. Here, we review the molecular mechanisms that govern autophagosome formation and analyze the link between autophagy and cardiovascular disease.
Modification of target molecules by ubiquitin or ubiquitin-like (Ubl) proteins is generally rever... more Modification of target molecules by ubiquitin or ubiquitin-like (Ubl) proteins is generally reversible. Little is known, however, about the physiological function of the reverse reaction, deconjugation. Atg8 is a unique Ubl protein whose conjugation target is the lipid phosphatidylethanolamine (PE). Atg8 functions in the formation of double-membrane autophagosomes, a central step in the well-conserved intracellular degradation pathway of macroautophagy (hereafter autophagy). Here we show that the deconjugation of Atg82PE by the cysteine protease Atg4 plays dual roles in the formation of autophagosomes. During the early stage of autophagosome formation, deconjugation releases Atg8 from non-autophagosomal membranes to maintain a proper supply of Atg8. At a later stage, the release of Atg8 from intermediate autophagosomal membranes facilitates the maturation of these structures into fusion-capable autophagosomes. These results provide new insights into the functions of Atg82PE and its deconjugation.
Modification of target molecules by ubiquitin or ubiquitin-like (Ubl) proteins is generally rever... more Modification of target molecules by ubiquitin or ubiquitin-like (Ubl) proteins is generally reversible. Little is known, however, about the physiological function of the reverse reaction, deconjugation. Atg8 is a unique Ubl protein whose conjugation target is the lipid phosphatidylethanolamine (PE). Atg8 functions in the formation of double-membrane autophagosomes, a central step in the well-conserved intracellular degradation pathway of macroautophagy (hereafter autophagy). Here we show that the deconjugation of Atg82PE by the cysteine protease Atg4 plays dual roles in the formation of autophagosomes. During the early stage of autophagosome formation, deconjugation releases Atg8 from non-autophagosomal membranes to maintain a proper supply of Atg8. At a later stage, the release of Atg8 from intermediate autophagosomal membranes facilitates the maturation of these structures into fusion-capable autophagosomes. These results provide new insights into the functions of Atg82PE and its deconjugation.
Cells must regulate both biosynthesis and degradation to ensure proper homeostasis of cellular or... more Cells must regulate both biosynthesis and degradation to ensure proper homeostasis of cellular organelles and proteins. This balance is demonstrated in a unique way in the yeast Saccharomyces cerevisiae, which possesses two distinct, yet mechanistically related trafficking routes mediating the delivery of proteins from the cytoplasm to the vacuole: the biosynthetic cytoplasm to vacuole targeting (Cvt) and the degradative autophagy pathways. Several components employed by these two transport routes have been identified, but their mechanistic interactions remain largely unknown. Here we report a novel gene involved in these pathways, which we have named ATG23. Atg23 localizes to the pre-autophagosomal structure but also to other cytosolic punctate compartments. Our characterization of the Atg23 protein indicates that it is required for the Cvt pathway and efficient autophagy but not pexophagy. In the absence of Atg23, cargo molecules such as prApe1 are correctly recruited to a pre-autophagosomal structure that is unable to give rise to Cvt vesicles. We also demonstrate that Atg23 is a peripheral membrane protein that requires the presence of Atg9/Apg9 to be specifically targeted to lipid bilayers. Atg9 transiently interacts with Atg23 suggesting that it participates in the recruitment of this protein.
Cells must regulate both biosynthesis and degradation to ensure proper homeostasis of cellular or... more Cells must regulate both biosynthesis and degradation to ensure proper homeostasis of cellular organelles and proteins. This balance is demonstrated in a unique way in the yeast Saccharomyces cerevisiae, which possesses two distinct, yet mechanistically related trafficking routes mediating the delivery of proteins from the cytoplasm to the vacuole: the biosynthetic cytoplasm to vacuole targeting (Cvt) and the degradative autophagy pathways. Several components employed by these two transport routes have been identified, but their mechanistic interactions remain largely unknown. Here we report a novel gene involved in these pathways, which we have named ATG23. Atg23 localizes to the pre-autophagosomal structure but also to other cytosolic punctate compartments. Our characterization of the Atg23 protein indicates that it is required for the Cvt pathway and efficient autophagy but not pexophagy. In the absence of Atg23, cargo molecules such as prApe1 are correctly recruited to a pre-autophagosomal structure that is unable to give rise to Cvt vesicles. We also demonstrate that Atg23 is a peripheral membrane protein that requires the presence of Atg9/Apg9 to be specifically targeted to lipid bilayers. Atg9 transiently interacts with Atg23 suggesting that it participates in the recruitment of this protein.
Autophagy, pexophagy, and the Cvt pathway are processes that deliver hydrolytic enzymes and subst... more Autophagy, pexophagy, and the Cvt pathway are processes that deliver hydrolytic enzymes and substrates to the yeast vacuole/lysosome via double-membrane cytosolic vesicles. Whereas these pathways operate under different nutritional conditions, they all employ common machinery with only a few specific factors assisting in the choice of the delivery program and the membrane source for the sequestering vesicle. We found that the YKR020w gene product is essential for Cvt vesicle formation but not for pexophagy or induction of autophagy. Autophagosomes in the ykr020wΔ mutant, however, have a reduced size. We demonstrate that Ykr020 is a subunit of the Vps fiftythree tethering complex, composed of Vps52, Vps53, and Vps54, which is required for retrograde traffic from the early endosome back to the late Golgi, and for this reason we named it Vps51. This complex participates in a fusion event together with Tlg1 and Tlg2, two SNAREs also shown to be necessary for Cvt vesicle assembly. In particular, those factors are essential to correctly target the prApe1-Cvt19-Cvt9 complex to the preautophagosomal structure, the site of Cvt vesicle formation. Autophagy is a catabolic process conserved among yeast, plants, and animal cells that permits the cell to eliminate unwanted or unnecessary proteins and organelles and to recycle the components for reuse (1,2). The organellar turnover is exclusively accomplished in the lysosome/vacuole lumen by a wide range of hydrolases capable of breaking down all cellular constituents (1,2). Autophagy plays an essential role during normal physiological processes such as starvation, cellular differentiation, cell death, and aging, but also in preventing some types of cellular dysfunction including cancer (2).
Autophagy, pexophagy, and the Cvt pathway are processes that deliver hydrolytic enzymes and subst... more Autophagy, pexophagy, and the Cvt pathway are processes that deliver hydrolytic enzymes and substrates to the yeast vacuole/lysosome via double-membrane cytosolic vesicles. Whereas these pathways operate under different nutritional conditions, they all employ common machinery with only a few specific factors assisting in the choice of the delivery program and the membrane source for the sequestering vesicle. We found that the YKR020w gene product is essential for Cvt vesicle formation but not for pexophagy or induction of autophagy. Autophagosomes in the ykr020wΔ mutant, however, have a reduced size. We demonstrate that Ykr020 is a subunit of the Vps fiftythree tethering complex, composed of Vps52, Vps53, and Vps54, which is required for retrograde traffic from the early endosome back to the late Golgi, and for this reason we named it Vps51. This complex participates in a fusion event together with Tlg1 and Tlg2, two SNAREs also shown to be necessary for Cvt vesicle assembly. In particular, those factors are essential to correctly target the prApe1-Cvt19-Cvt9 complex to the preautophagosomal structure, the site of Cvt vesicle formation. Autophagy is a catabolic process conserved among yeast, plants, and animal cells that permits the cell to eliminate unwanted or unnecessary proteins and organelles and to recycle the components for reuse (1,2). The organellar turnover is exclusively accomplished in the lysosome/vacuole lumen by a wide range of hydrolases capable of breaking down all cellular constituents (1,2). Autophagy plays an essential role during normal physiological processes such as starvation, cellular differentiation, cell death, and aging, but also in preventing some types of cellular dysfunction including cancer (2).
Autophagy, 2012
Spanel-Borowski, Katharina; Smith, Mark A.; Simone, Cristiano; Simonsen, Anne; Simon, Hans-Uwe; S... more Spanel-Borowski, Katharina; Smith, Mark A.; Simone, Cristiano; Simonsen, Anne; Simon, Hans-Uwe; Silva-Zacarin, Elaine CM; Sibirny, Andrei; Shapiro, Irving M.; Shacka, John J.; Settleman, Jeffrey; Seleverstov, Oleksandr; Seglen, Per O.; Sass, Miklós; Schneider, ...
Autophagy
With its relevance to our understanding of eukaryotic cell function in the normal and disease sta... more With its relevance to our understanding of eukaryotic cell function in the normal and disease state, autophagy is an important topic in modern cell biology; yet, few textbooks discuss autophagy beyond a two- or three-sentence summary. Here, we report an undergraduate/graduate class lesson for the in-depth presentation of autophagy using an active learning approach. By our method, students will work in small groups to solve problems and interpret an actual data set describing genes involved in autophagy. The problem-solving exercises and data set analysis will instill within the students a much greater understanding of the autophagy pathway than can be achieved by simple rote memorization of lecture materials; furthermore, the students will gain a general appreciation of the process by which data are interpreted and eventually formed into an understanding of a given pathway. As the data sets used in these class lessons are largely genomic and complementary in content, students will a...
Autophagy, 2012
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since t... more In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
Autophagy, 2012
In 2008 we published the first set of guidelines for standardizing research in autophagy. Since t... more In 2008 we published the first set of guidelines for standardizing research in autophagy. Since then, research on this topic has continued to accelerate, and many new scientists have entered the field. Our knowledge base and relevant new technologies have also been expanding. Accordingly, it is important to update these guidelines for monitoring autophagy in different organisms. Various reviews have described the range of assays that have been used for this purpose. Nevertheless, there continues to be confusion regarding acceptable methods to measure autophagy, especially in multicellular eukaryotes. A key point that needs to be emphasized is that there is a difference between measurements that monitor the numbers or volume of autophagic elements (e.g., autophagosomes or autolysosomes) at any stage of the autophagic process vs. those that measure flux through the autophagy pathway (i.e., the complete process); thus, a block in macroautophagy that results in autophagosome accumulation needs to be differentiated from stimuli that result in increased autophagic activity, defined as increased autophagy induction coupled with increased delivery to, and degradation within, lysosomes (in most higher eukaryotes and some protists such as Dictyostelium) or the vacuole (in plants and fungi). In other words, it is especially important that investigators new to the field understand that the appearance of more autophagosomes does not necessarily equate with more autophagy. In fact, in many cases, autophagosomes accumulate because of a block in trafficking to lysosomes without a concomitant change in autophagosome biogenesis, whereas an increase in autolysosomes may reflect a reduction in degradative activity. Here, we present a set of guidelines for the selection and interpretation of methods for use by investigators who aim to examine macroautophagy and related processes, as well as for reviewers who need to provide realistic and reasonable critiques of papers that are focused on these processes. These guidelines are not meant to be a formulaic set of rules, because the appropriate assays depend in part on the question being asked and the system being used. In addition, we emphasize that no individual assay is guaranteed to be the most appropriate one in every situation, and we strongly recommend the use of multiple assays to monitor autophagy. In these guidelines, we consider these various methods of assessing autophagy and what information can, or cannot, be obtained from them. Finally, by discussing the merits and limits of particular autophagy assays, we hope to encourage technical innovation in the field.
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Papers by DanielJ Klionsky