Cell Cycle
ISSN: 1538-4101 (Print) 1551-4005 (Online) Journal homepage: http://www.tandfonline.com/loi/kccy20
Appetite for ER/nucleus destruction Keisuke Mochida & Hitoshi Nakatogawa To cite this article: Keisuke Mochida & Hitoshi Nakatogawa (2015) Appetite for ER/nucleus destruction, Cell Cycle, 14:20, 3209-3210, DOI: 10.1080/15384101.2015.1084206 To link to this article: http://dx.doi.org/10.1080/15384101.2015.1084206
Published online: 30 Oct 2015.
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Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=kccy20 Download by: [180.172.240.99]
Date: 18 January 2016, At: 23:35
EDITORIALS: CELL CYCLE FEATURES Cell Cycle 14:20, 3209--3210; October 15, 2015; © 2015 Taylor & Francis Group, LLC
Appetite for ER/nucleus destruction Keisuke Mochida1 and Hitoshi Nakatogawa1,2,* Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama, Japan; 2CREST; Japan Science and Technology Agency; Saitama, Japan
Downloaded by [180.172.240.99] at 23:35 18 January 2016
1
Eukaryotic cells have developed various organelles, and therein separated subsets of reactions, to perform diverse cellular functions in an organized manner. They have also been equipped with elaborate mechanisms to strictly control quality and quantity of organelles, and deficiencies in these mechanisms can lead to diseases in humans. Autophagy, an intracellular degradation pathway, proceeds through the following steps: (1) a double-membraned vesicle called the autophagosome is formed in the cytoplasm to sequester degradation targets, (2) the autophagosome fuses with the lysosomal or vacuolar membrane, and (3) the sequestered material is degraded by hydrolases in lysosomes/ vacuoles.1 While autophagy randomly degrades cytoplasmic constituents under nutrient-limiting conditions, it can also selectively degrade certain molecules or structures via landmark proteins called autophagy receptors.2 These proteins localize to specific targets, and also bind to Atg8-family proteins on expanding autophagosomal membranes, leading to the sequestration of the targets by autophagosomes. Previous studies have shown that receptor-mediated selective autophagy largely contributes to degradation of some organelles, including mitochondria and peroxisomes, as well as protein aggregates and invading pathogens.2 However, how extensively selective autophagy is involved in organelle homeostasis and regulation remained to be investigated. In a recent study, we have revealed that when starved, yeast cells actively degrade their own endoplasmic reticulum (ER) and nucleus via selective autophagy, which involves 2 novel receptors.3
We hypothesized that novel autophagic receptors would be identified among Atg8-binding proteins, and thus performed mass spectrometry of immunoprecipitates of Atg8 in the budding yeast Saccharomyces cerevisiae. Among proteins detected, we focused on 2 proteins of unknown function, and named them Atg39 and Atg40. These proteins had no homology to each other, but both possessed putative transmembrane domains and the Atg8-family interacting motif, which is shared by autophagy receptors. We found that both Atg39 and Atg40 localized to the ER. A previous study reported that ER fragments are frequently incorporated into autophagosomes and degraded in the vacuole under starvation conditions,4 but the molecular mechanism underlying this pathway, which should be called ‘ER-phagy’, remained unknown. Nitrogen starvation dramatically induced expression of Atg39 and Atg40, followed by activation of ER-phagy. We speculated that Atg39 and Atg40 might be receptors for ER-phagy. Indeed, deletion of either ATG39 or ATG40 partially decreased ERphagy, and the double deletion almost completely abolished the activity. We also showed that the interactions of Atg39 and Atg40 with Atg8 were important for ERphagy, and that overexpression of Atg39 or Atg40 promoted ER-phagy. Taken together, we concluded that Atg39 and Atg40 are both ER-phagy receptors. In yeast cells, the ER is composed of perinuclear, cytoplasmic, and cortical subdomains, which are connected to each other.5 Interestingly, Atg39 and Atg40 were differently distributed to these ER subdomains. Whereas Atg39 specifically
localized to the perinuclear ER, Atg40 was mainly observed in the cytoplasmic and cortical ER. Consistent with its localization, Atg39 was required for autophagic degradation of the perinuclear ER but not for that of the cytoplasmic/cortical ER. By contrast, Atg40 was essential for degradation of the cytoplasmic/cortical ER, but less important for perinuclear ER degradation than Atg39. Our analysis further revealed that Atg39 induces the sequestration of double-membraned vesicles derived from the perinuclear ER by autophagosomes, whereas Atg40 acts to load the cytoplasmic/cortical ER as folded tubules/sheets into autophagosomes (Fig. 1). Thus, Atg39 and Atg40 were shown to mediate selective autophagy of different ER subdomains. Because the perinuclear ER is equivalent to the nuclear envelope in yeast, we hypothesized that double-membraned vesicles derived from the perinuclear ER contain nuclear components. Indeed, immunoelectron microscopy detected signals of a nucleolar protein inside the vesicles. In addition to this nucleolar protein, an inner nuclear membrane protein was also degraded in an Atg39-dependent manner, similar to a protein localized to the outer nuclear membrane. These results suggested that double-membraned vesicles can be regarded as part of the nucleus. Therefore, Atg39-mediated selective autophagy should also be referred to as ‘nucleophagy’. ATG39 mutants exhibited abnormal nuclear morphology and died earlier than wild-type cells in nitrogen starvation conditions, suggesting that Atg39-mediated perinuclear ER-phagy/nucleophagy is
*Correspondence to: Hitoshi Nakatogawa; Email: [email protected] Submitted: 07/15/2015; Accepted: 08/08/2015 http://dx.doi.org/10.1080/15384101.2015.1084206 Comment on: Mochida K, et al. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature 2015; 522(7556):359-62; PMID: 26040717; http://dx.doi.org/10.1038/nature14506
www.tandfonline.com
Cell Cycle
3209
Downloaded by [180.172.240.99] at 23:35 18 January 2016
Figure 1. Atg39 and Atg40 are autophagy receptors for the perinuclear ER/nucleus and the cytoplasmic/cortical ER, respectively. Atg39 localizes to the perinuclear ER membrane/nuclear envelope, and causes the autophagosomal sequestration of double-membraned vesicles, which are generated from these membranes and contain intranuclear components. Atg40 primarily localizes to the cytoplasmic/cortical ER, and loads part of these ER subdomains as folded tubules/sheets into autophagosomes. In these processes, Atg39 and Atg40 bind to Atg8 on growing autophagosomal membranes to facilitate the sequestration of the corresponding ER/nucleus fragments. Autophagosomes fuse with the vacuole, and vacuolar hydrolases degrade the sequestered fragments.
important for cell survival in these conditions. On the other hand, ATG40 knockout cells displayed densely-reticulated
References 1. NakatogawaH, et al. Nat Rev Mol Cell Biol 2009; 10:458-67; PMID:19491929; http://dx.doi.org/ 10.1038/nrm2708 2. Stolz A, et al. Nat Cell Biol 2014; 16:495-501; PMID:24875736; http://dx.doi.org/10.1038/ ncb2979
3210
cortical ER under the same conditions, although their viability was indistinguishable from with wild-type cells. Under star-
3. Mochida K, et al. Nature 2015; 522:359-62; PMID:26040717; http://dx.doi.org/10.1038/nature14506 4. Hamasaki M, et al. Traffic 2005; 6:56-65; PMID:15569245; http://dx.doi.org/10.1111/j.1600-0854.2004.00245.x 5. Friedman JR, et al. Trends Cell Biol 2011; 21:709-17; PMID:21900009; http://dx.doi.org/10.1016/j. tcb.2011.07.004
Cell Cycle
vation conditions, ER-phagy/nucleophagy may play crucial roles in nutrient recycling by catabolizing ER/nucleus components and/or in elimination of deleterious materials accumulated in these organelles. In an accompanying paper, Khaminets et al. reported that FAM134B is an ERphagy receptor in mammals, and loss of FAM134B causes sensory neuropathy.6 Although FAM134B and Atg40 do not share amino acid sequence homology, these proteins were similar in their domain organization and intracellular localization, suggesting that FAM134B is a functional homolog of Atg40 in mammalian cells. Functional counterparts of Atg39 may also exist in higher eukaryotes, including mammals, in which autophagic degradation of the nucleus has been observed.7 Our results demonstrated the existence of receptor-mediated ER-phagy and nucleophagy. However, their molecular mechanisms and physiological roles still remain largely unknown. We believe that identification of Atg39 and Atg40 will be a breakthrough in the research on these new autophagy pathways not only in yeast but also in other organisms.
6. Khaminets A, et al. Nature 2015; 522:354-8; PMID:26040720; http://dx.doi.org/10.1038/ nature14498 7. Mijaljica D, et al. J Cell Sci 2013; 126:4325-30; PMID:24013549; http://dx.doi.org/10.1242/ jcs.133090
Volume 14 Issue 20
ISSN: 1538-4101 (Print) 1551-4005 (Online) Journal homepage: http://www.tandfonline.com/loi/kccy20
Appetite for ER/nucleus destruction Keisuke Mochida & Hitoshi Nakatogawa To cite this article: Keisuke Mochida & Hitoshi Nakatogawa (2015) Appetite for ER/nucleus destruction, Cell Cycle, 14:20, 3209-3210, DOI: 10.1080/15384101.2015.1084206 To link to this article: http://dx.doi.org/10.1080/15384101.2015.1084206
Published online: 30 Oct 2015.
Submit your article to this journal
Article views: 84
View related articles
View Crossmark data
Full Terms & Conditions of access and use can be found at http://www.tandfonline.com/action/journalInformation?journalCode=kccy20 Download by: [180.172.240.99]
Date: 18 January 2016, At: 23:35
EDITORIALS: CELL CYCLE FEATURES Cell Cycle 14:20, 3209--3210; October 15, 2015; © 2015 Taylor & Francis Group, LLC
Appetite for ER/nucleus destruction Keisuke Mochida1 and Hitoshi Nakatogawa1,2,* Graduate School of Bioscience and Biotechnology; Tokyo Institute of Technology; Yokohama, Japan; 2CREST; Japan Science and Technology Agency; Saitama, Japan
Downloaded by [180.172.240.99] at 23:35 18 January 2016
1
Eukaryotic cells have developed various organelles, and therein separated subsets of reactions, to perform diverse cellular functions in an organized manner. They have also been equipped with elaborate mechanisms to strictly control quality and quantity of organelles, and deficiencies in these mechanisms can lead to diseases in humans. Autophagy, an intracellular degradation pathway, proceeds through the following steps: (1) a double-membraned vesicle called the autophagosome is formed in the cytoplasm to sequester degradation targets, (2) the autophagosome fuses with the lysosomal or vacuolar membrane, and (3) the sequestered material is degraded by hydrolases in lysosomes/ vacuoles.1 While autophagy randomly degrades cytoplasmic constituents under nutrient-limiting conditions, it can also selectively degrade certain molecules or structures via landmark proteins called autophagy receptors.2 These proteins localize to specific targets, and also bind to Atg8-family proteins on expanding autophagosomal membranes, leading to the sequestration of the targets by autophagosomes. Previous studies have shown that receptor-mediated selective autophagy largely contributes to degradation of some organelles, including mitochondria and peroxisomes, as well as protein aggregates and invading pathogens.2 However, how extensively selective autophagy is involved in organelle homeostasis and regulation remained to be investigated. In a recent study, we have revealed that when starved, yeast cells actively degrade their own endoplasmic reticulum (ER) and nucleus via selective autophagy, which involves 2 novel receptors.3
We hypothesized that novel autophagic receptors would be identified among Atg8-binding proteins, and thus performed mass spectrometry of immunoprecipitates of Atg8 in the budding yeast Saccharomyces cerevisiae. Among proteins detected, we focused on 2 proteins of unknown function, and named them Atg39 and Atg40. These proteins had no homology to each other, but both possessed putative transmembrane domains and the Atg8-family interacting motif, which is shared by autophagy receptors. We found that both Atg39 and Atg40 localized to the ER. A previous study reported that ER fragments are frequently incorporated into autophagosomes and degraded in the vacuole under starvation conditions,4 but the molecular mechanism underlying this pathway, which should be called ‘ER-phagy’, remained unknown. Nitrogen starvation dramatically induced expression of Atg39 and Atg40, followed by activation of ER-phagy. We speculated that Atg39 and Atg40 might be receptors for ER-phagy. Indeed, deletion of either ATG39 or ATG40 partially decreased ERphagy, and the double deletion almost completely abolished the activity. We also showed that the interactions of Atg39 and Atg40 with Atg8 were important for ERphagy, and that overexpression of Atg39 or Atg40 promoted ER-phagy. Taken together, we concluded that Atg39 and Atg40 are both ER-phagy receptors. In yeast cells, the ER is composed of perinuclear, cytoplasmic, and cortical subdomains, which are connected to each other.5 Interestingly, Atg39 and Atg40 were differently distributed to these ER subdomains. Whereas Atg39 specifically
localized to the perinuclear ER, Atg40 was mainly observed in the cytoplasmic and cortical ER. Consistent with its localization, Atg39 was required for autophagic degradation of the perinuclear ER but not for that of the cytoplasmic/cortical ER. By contrast, Atg40 was essential for degradation of the cytoplasmic/cortical ER, but less important for perinuclear ER degradation than Atg39. Our analysis further revealed that Atg39 induces the sequestration of double-membraned vesicles derived from the perinuclear ER by autophagosomes, whereas Atg40 acts to load the cytoplasmic/cortical ER as folded tubules/sheets into autophagosomes (Fig. 1). Thus, Atg39 and Atg40 were shown to mediate selective autophagy of different ER subdomains. Because the perinuclear ER is equivalent to the nuclear envelope in yeast, we hypothesized that double-membraned vesicles derived from the perinuclear ER contain nuclear components. Indeed, immunoelectron microscopy detected signals of a nucleolar protein inside the vesicles. In addition to this nucleolar protein, an inner nuclear membrane protein was also degraded in an Atg39-dependent manner, similar to a protein localized to the outer nuclear membrane. These results suggested that double-membraned vesicles can be regarded as part of the nucleus. Therefore, Atg39-mediated selective autophagy should also be referred to as ‘nucleophagy’. ATG39 mutants exhibited abnormal nuclear morphology and died earlier than wild-type cells in nitrogen starvation conditions, suggesting that Atg39-mediated perinuclear ER-phagy/nucleophagy is
*Correspondence to: Hitoshi Nakatogawa; Email: [email protected] Submitted: 07/15/2015; Accepted: 08/08/2015 http://dx.doi.org/10.1080/15384101.2015.1084206 Comment on: Mochida K, et al. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature 2015; 522(7556):359-62; PMID: 26040717; http://dx.doi.org/10.1038/nature14506
www.tandfonline.com
Cell Cycle
3209
Downloaded by [180.172.240.99] at 23:35 18 January 2016
Figure 1. Atg39 and Atg40 are autophagy receptors for the perinuclear ER/nucleus and the cytoplasmic/cortical ER, respectively. Atg39 localizes to the perinuclear ER membrane/nuclear envelope, and causes the autophagosomal sequestration of double-membraned vesicles, which are generated from these membranes and contain intranuclear components. Atg40 primarily localizes to the cytoplasmic/cortical ER, and loads part of these ER subdomains as folded tubules/sheets into autophagosomes. In these processes, Atg39 and Atg40 bind to Atg8 on growing autophagosomal membranes to facilitate the sequestration of the corresponding ER/nucleus fragments. Autophagosomes fuse with the vacuole, and vacuolar hydrolases degrade the sequestered fragments.
important for cell survival in these conditions. On the other hand, ATG40 knockout cells displayed densely-reticulated
References 1. NakatogawaH, et al. Nat Rev Mol Cell Biol 2009; 10:458-67; PMID:19491929; http://dx.doi.org/ 10.1038/nrm2708 2. Stolz A, et al. Nat Cell Biol 2014; 16:495-501; PMID:24875736; http://dx.doi.org/10.1038/ ncb2979
3210
cortical ER under the same conditions, although their viability was indistinguishable from with wild-type cells. Under star-
3. Mochida K, et al. Nature 2015; 522:359-62; PMID:26040717; http://dx.doi.org/10.1038/nature14506 4. Hamasaki M, et al. Traffic 2005; 6:56-65; PMID:15569245; http://dx.doi.org/10.1111/j.1600-0854.2004.00245.x 5. Friedman JR, et al. Trends Cell Biol 2011; 21:709-17; PMID:21900009; http://dx.doi.org/10.1016/j. tcb.2011.07.004
Cell Cycle
vation conditions, ER-phagy/nucleophagy may play crucial roles in nutrient recycling by catabolizing ER/nucleus components and/or in elimination of deleterious materials accumulated in these organelles. In an accompanying paper, Khaminets et al. reported that FAM134B is an ERphagy receptor in mammals, and loss of FAM134B causes sensory neuropathy.6 Although FAM134B and Atg40 do not share amino acid sequence homology, these proteins were similar in their domain organization and intracellular localization, suggesting that FAM134B is a functional homolog of Atg40 in mammalian cells. Functional counterparts of Atg39 may also exist in higher eukaryotes, including mammals, in which autophagic degradation of the nucleus has been observed.7 Our results demonstrated the existence of receptor-mediated ER-phagy and nucleophagy. However, their molecular mechanisms and physiological roles still remain largely unknown. We believe that identification of Atg39 and Atg40 will be a breakthrough in the research on these new autophagy pathways not only in yeast but also in other organisms.
6. Khaminets A, et al. Nature 2015; 522:354-8; PMID:26040720; http://dx.doi.org/10.1038/ nature14498 7. Mijaljica D, et al. J Cell Sci 2013; 126:4325-30; PMID:24013549; http://dx.doi.org/10.1242/ jcs.133090
Volume 14 Issue 20
