During micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital for cell survival during starvation

Abeliovich

Dawaliby

Deretic

Dikic

Fulvio Reggiori

Galluzzi

Mochida

Mostofa

Park

Pauline Verlhac

Rahman

Roberts

Rubinsztein

Verlhac, Pauline

Reggiori, Fulvio

University of Groningen Research Database

  
 University of Groningen
Sorting the trash
Verlhac, Pauline; Reggiori, Fulvio
Published in:
The Journal of Cell Biology
DOI:
10.1083/jcb.201806127
IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite from
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Verlhac, P., & Reggiori, F. (2018). Sorting the trash: Micronucleophagy gets selective. The Journal of Cell
Biology, 217(8), 2605-2607. https://doi.org/10.1083/jcb.201806127
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SPOTLIGHT
https://doi.org/10.1083/jcb.201806127 1
J. Cell Biol. 2018
Rockefeller University Press
During micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are 
recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal 
that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital 
for cell survival during starvation.
Sorting the trash: Micronucleophagy gets selective
Pauline Verlhac and Fulvio Reggiori
Autophagy is a catabolic process leading to the lysosomal/vac-
uolar degradation of unwanted cellular components including 
aggregated proteins, damaged or superfluous organelles, and 
even pathogens (Galluzzi et al., 2017). This pathway, which is con-
served from yeast to mammals, is crucial to maintain cell homeo-
stasis and has numerous physiological implications relevant to 
human health (Deretic et al., 2013). Mitochondria, peroxisomes, 
the endoplasmic reticulum, and even portions of the nucleus can 
be targeted and degraded by autophagy under the orchestrated 
action of autophagy-related (Atg) proteins (Dikic and Elazar, 
2018). Autophagic turnover of nuclear material is termed nucle-
ophagy and has been described in two forms in yeast: macronuc-
leophagy and micronucleophagy. Macronucleophagy involves the 
sequestration of a portion of the nucleus into autophagosomes 
and requires the autophagy receptor Atg39 (Mochida et al., 2015). 
The targeted nuclear material is subsequently delivered and 
eliminated in the vacuole upon autophagosome fusion with this 
organelle. During micronucleophagy, a portion of the nucleus is 
directly engulfed by the vacuole at the nuclear vacuole junction 
(NVJ), i.e., the NVJ invaginates and pinches off into the vacuolar 
lumen, leading to a subvacuolar vesicle that is consumed by res-
ident hydrolases (Roberts et al., 2003). Both micro- and macro-
nucleophagy sequester only a portion of the nucleus, indicating 
a specificity similar to the one observed in other selective types 
of autophagy such as mitophagy or pexophagy (Galluzzi et al., 
2017). In particular, DNA is not degraded by these two processes, 
but how this is accomplished remained unknown.
Mostofa et al. describe a mechanism allowing the separation 
of DNA from proteins during micronucleophagy induced by star-
vation conditions in yeast (Fig. 1). They focused on the nucleolus, 
which has previously been shown to be targeted by micronucleo-
phagy (Dawaliby and Mayer, 2010; Mochida et al., 2015). They re-
veal that although nucleolar proteins are brought to the NVJ and 
delivered into the vacuole for turnover, ribosomal DNA (rDNA) 
is spared from degradation and kept in the nucleus (Fig. 1). This 
mechanism of separation requires the components of the two in-
teracting nuclear complexes, chromosome linkage inner nuclear 
membrane protein (CLIP) and cohibin, which are composed by 
Heh1-Nur1 and Csm1-Lrs4, respectively. In cells lacking CLIP or 
cohibin subunits, rDNA and nucleolar proteins remain associ-
ated, and although micronucleophagy is still functional, nucleolar 
proteins are not degraded. Interestingly, the absence of the CLIP 
or cohibin complex does not result in the aberrant degradation 
of rDNA. Thus, the CLIP and cohibin complexes are involved in 
repositioning of the rDNA away from nucleolar proteins but not 
in protection of rDNA or degradation of the micronucleophagic 
cargos per se (Fig. 1). Mostofa et al. (2018) also studied the spatio-
temporal dynamics of micronucleophagy during starvation and 
observed that separation and repositioning of rDNA and nucleolar 
proteins occurs before the beginning of micronucleophagy. They 
also observed that these events depend on micronucleophagy as 
cells defective in this process but not NVJ formation did not show 
separation of nucleolar proteins and rDNA. Taken together, these 
findings indicate that separation and repositioning of nucleolar 
components and subsequent micronucleophagy are coordinated 
processes. This coordination is similar to the one observed be-
tween the fission and Atg machineries during mitophagy and 
pexophagy (Mao et al., 2013, 2014) and could be essential to avoid 
rDNA degradation, which would be lethal for the cell. Finally, they 
found that cells lacking one of the subunits of the CLIP or cohibin 
complexes have reduced survival during starvation, highlighting 
that this parting between rDNA and nucleolar proteins could be 
necessary for cell survival under particular stresses.
Very little is known about the mechanisms underlying micro-
nucleophagy, and the study by Mostofa et al. (2018) is pioneering 
as it provides the crucial groundwork and specific assays for fu-
ture investigations aimed at understanding this pathway and its 
relevance for the cell physiology under stress conditions and be-
yond. By focusing on nucleolar DNA and proteins, they succeeded 
in answering the lingering question of how rDNA is protected 
© 2018 Verlhac and Reggiori This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after 
the publication date (see http:// www .rupress .org/ terms/ ). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 
International license, as described at https:// creativecommons .org/ licenses/ by -nc -sa/ 4 .0/ ).
Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.
Correspondence to Fulvio Reggiori: f.m.reggiori@ umcg .nl. 
on July 19, 2018jcb.rupress.org Downloaded from 
http://doi.org/10.1083/jcb.201806127Published Online: 13 July, 2018 | Supp Info: 
Verlhac and Reggiori 
Micronucleophagy gets selective
Journal of Cell Biology
https://doi.org/10.1083/jcb.201806127
2
during micronucleophagy. Their work demonstrates that cargo 
selection and sequestration are key features of nucleophagy as 
in other forms of selective autophagy. Therefore, this study re-
inforces the paradigm that autophagic recycling is a meticulous 
process guarded by fail-safe mechanisms.
It would be of high interest to decipher the precise physio-
logical relevance of this repositioning of rDNA and nucleolar 
proteins. Although Mostofa et al. (2018) elegantly demonstrated 
the importance of the CLIP and cohibin complexes during micro-
nucleophagy, they did so using knockout strains. Thus, it cannot 
be excluded a priori that the relevance of these complexes for cell 
survival during starvation observed by Mostofa et al. (2018) could 
be due to one or more other functions of these two complexes. It 
would therefore be important to generate and use point mutants 
or possibly ablate known binding partners of the CLIP and co-
hibin complexes such as Sir2, Cdc14, Net1, Tof2, and rDNA-bind-
ing Fob1 to more specifically address this physiological aspect.
Specific mutants will also be key to address some aspects of 
the molecular mechanism of micronucleophagy. For example, 
how is DNA directed away and protected from degradation? Al-
though the CLIP–cohibin system is required for rDNA separation, 
it appears to be unnecessary for its protection from degradation 
as rDNA is not turned over in the absence of these factors, al-
though micronucleophagy still occurs. This suggests the exis-
tence of a different mechanism to avoid delivery of rDNA, and 
possibly chromosomes in general, to the vacuole during both 
micro- and macronucleophagy.
Furthermore, an aspect that will probably attract further re-
search is the identification of the pathway that conveys TORC1 
signaling into the nucleus to communicate both the reposition-
ing of rDNA and the targeting to degradation of nucleolar pro-
teins. TORC1 is a cytosolic complex that allows cells to adapt to 
environmental changes through an integrated orchestration of 
anabolic and catabolic pathways including micronucleophagy. 
Identifying the signaling axis that regulates micronucleophagy 
in the nucleus will help to understand intracellular communi-
cation and the potential crosstalk of micronucleophagy with 
other processes and possibly cell death, a crosstalk suggested by 
the survival defect of cells lacking nucleophagy. An interesting 
candidate signaling axis could be the newly identified Nem1/
Spo7-Pah1 cascade, which has been implicated in micro- and 
macronucleophagy induction notably through positioning of 
Atg39 and Nvj1, a SNA RE-mediating NVJ establishment (Rahman 
et al., 2018). Other lingering questions include determining 
whether a similar rDNA-sorting mechanism takes place during 
macronucleophagy and whether macronucleophagic cargoes are 
different from those of micronucleophagy.
The findings from Mostofa et al. (2018) also provide fascinating 
new perspectives for the study of the precise physiological role(s) 
of micronucleophagy. First, the observation that micronucleoph-
agy still occurs while the retargeting of rDNA and nucleolar pro-
teins is impaired suggests that other nuclear components might be 
degraded through this pathway. Identifying such cargos would be 
crucial to better understand the cellular implications of an even-
tual defect in micronucleophagy. Moreover, Mostofa et al. (2018) 
observed a reduced survival under starvation in cells where the 
repositioning is impaired but nucleophagy is still functional, in 
line with previous observations that nucleophagy is necessary for 
cell survival under stress. Nevertheless, the fact that impairing 
the repositioning alone is enough to induce a survival defect also 
suggests that either degradation of nucleolar proteins is capital or 
other cargos need to be degraded for cells to survive starvation.
Intriguingly, the segregation mechanism described by 
Mostofa et al. (2018) shares some conceptual aspects with what 
was shown for mitophagy in yeast, where specific proteins are 
protected from degradation by forming intramitochondrial 
aggregates while others are preferentially turned over via seg-
regation into the subdomains of the mitochondria targeted by 
mitophagy (Abeliovich et al., 2013). A similar phenomenon might 
be taking place during micro- and possibly macronucleophagy, 
where specific nuclear proteins are preferentially degraded and 
thus concentrated at the site of nucleophagy in a CLIP–cohibin 
system-dependent manner, whereas others could be protected 
by another system through, for example, a retention and/or ex-
clusion mechanism. If some proteins are protected from micro-
nucleophagy, it would be interesting to demonstrate whether the 
mechanism is similar to the one protecting rDNA. Conversely, it 
would be interesting to explore whether mitochondrial DNA is 
protected during mitophagy.
Finally, although autophagy is highly conserved among eu-
karyotes, the same cannot currently be said for nucleophagy. 
Nucleophagy has rarely been observed in mammalian cells and 
exclusively in pathological contexts (Park et al., 2009). The find-
ings of Mostofa et al. (2018) provide the framework that could 
Figure 1. The role of CLIP and cohibin com-
plexes in micronucleophagy. Nucleolar 
proteins, rDNA, and the cohibin complex are 
associated at nucleoli under growing conditions, 
while the CLIP complex is distributed over the 
entire inner side of the nuclear membrane. TORC1 
inactivation triggers the association of nucleolar 
proteins with part of the CLIP complexes and 
their subsequent targeting to the NVJ, where 
they are included into the forming intravacuo-
lar invagination. The pinch-off of this protrusion 
leads to the vacuolar turnover of both nucleolar 
proteins and the CLIP complex. In contrast, rDNA 
and cohibin remain associated and get separated 
from the nucleolar proteins to remain protected 
from micronucleophagic degradation.
Verlhac and Reggiori 
Micronucleophagy gets selective
Journal of Cell Biology
https://doi.org/10.1083/jcb.201806127
3
help elucidating whether micronucleophagy occurs in mamma-
lian cells by studying for example the mammalian counterpart(s) 
of the CLIP and cohibin complexes. As Mostofa et al. (2018) stated 
in their study, it is also possible that the mechanisms of nucleo-
phagy differ greatly between yeast and mammals. The answer 
could lie in the fact that key mammalian ATG components such 
as LC3 proteins, the homologues of yeast Atg8, are also present 
in the nucleus, but a role has not been assigned to this pool yet. 
Defects in selective types of autophagy like mitophagy, reticu-
lophagy, and aggrephagy have been associated to severe human 
pathologies, and therefore, the modulation of these specific 
processes rather than the one of bulk autophagy has great ther-
apeutic potential (Rubinsztein et al., 2012). It is thus crucial to 
determine the molecular mechanism and physiological functions 
of micronucleophagy in mammalian cells, and more in general, 
those of nucleophagy, as this could be relevant for human health.
Acknowledgments
We thank Dr. Mario Mauthe for his critical reading 
of the manuscript. 
F. Reggiori is supported by ZonMW VICI (016.130.606), the 
Netherlands Organization for Scientific Research ALW Open 
Program (ALW OP.310), and the European Commission’s Marie 
Skłodowska-Curie Cofund (713660) and Marie Skłodowska-Curie 
Innovative Training Networks (765912) grants.
The authors declare no competing financial interests.
References
Abeliovich, H., M. Zarei, K.T.G. Rigbolt, R.J. Youle, and J. Dengjel. 2013. In-
volvement of mitochondrial dynamics in the segregation of mitochon-
drial matrix proteins during stationary phase mitophagy. Nat. Commun. 
4:2789. https:// doi .org/ 10 .1038/ ncomms3789
Dawaliby, R., and A. Mayer. 2010. Microautophagy of the nucleus coincides 
with a vacuolar diffusion barrier at nuclear-vacuolar junctions. Mol. 
Biol. Cell. 21:4173–4183. https:// doi .org/ 10 .1091/ mbc .e09 -09 -0782
Deretic, V., T. Saitoh, and S. Akira. 2013. Autophagy in infection, inflammation 
and immunity. Nat. Rev. Immunol. 13:722–737. https:// doi .org/ 10 .1038/ 
nri3532
Dikic, I., and Z. Elazar. 2018. Mechanism and medical implications of mam-
malian autophagy. Nat. Rev. Mol. Cell Biol. 19:349–364. https:// doi .org/ 10 
.1038/ s41580 -018 -0003 -4
Galluzzi, L., E.H. Baehrecke, A. Ballabio, P. Boya, J.M. Bravo-San Pedro, F. Cec-
coni, A.M. Choi, C.T. Chu, P. Codogno, M.I. Colombo, et al. 2017. Molecu-
lar definitions of autophagy and related processes. EMBO J. 36:1811–1836. 
https:// doi .org/ 10 .15252/ embj .201796697
Mao, K., K. Wang, X. Liu, and D.J. Klionsky. 2013. The scaffold protein Atg11 
recruits fission machinery to drive selective mitochondria degradation 
by autophagy. Dev. Cell. 26:9–18. https:// doi .org/ 10 .1016/ j .devcel .2013 
.05 .024
Mao, K., X. Liu, Y. Feng, and D.J. Klionsky. 2014. The progression of peroxi-
somal degradation through autophagy requires peroxisomal division. 
Autophagy. 10:652–661. https:// doi .org/ 10 .4161/ auto .27852
Mochida, K., Y. Oikawa, Y. Kimura, H. Kirisako, H. Hirano, Y. Ohsumi, and 
H. Nakatogawa. 2015. Receptor-mediated selective autophagy degrades 
the endoplasmic reticulum and the nucleus. Nature. 522:359–362. 
https:// doi .org/ 10 .1038/ nature14506
Mostofa, G.M., M.A. Rahman, N. Koike, A.M.S.T. Yeasmin, N. Islam, T.M. Wa-
liullah, S. Hosoyamada, M. Shimobayashi, T. Kobayashi, M.N. Hall, et al. 
2018. CLIP and cohibin separate rDNA from nucleolar proteins destined 
for degradation by nucleophagy. J. Cell Biol. https:// doi .org/ 10 .1083/ jcb 
.201706164
Park, Y.E., Y.K. Hayashi, G. Bonne, T. Arimura, S. Noguchi, I. Nonaka, and I. 
Nishino. 2009. Autophagic degradation of nuclear components in mam-
malian cells. Autophagy. 5:795–804. https:// doi .org/ 10 .4161/ auto .8901
Rahman, M.A., M.G. Mostofa, and T. Ushimaru. 2018. The Nem1/Spo7-Pah1/
lipin axis is required for autophagy induction after TORC1 inactivation. 
FEBS J. 285:1840–1860. https:// doi .org/ 10 .1111/ febs .14448
Roberts, P., S. Moshitch-Moshkovitz, E. Kvam, E. O’Toole, M. Winey, and D.S. 
Goldfarb. 2003. Piecemeal microautophagy of nucleus in Saccharomy-
ces cerevisiae. Mol. Biol. Cell. 14:129–141. https:// doi .org/ 10 .1091/ mbc 
.e02 -08 -0483
Rubinsztein, D.C., P. Codogno, and B. Levine. 2012. Autophagy modulation as 
a potential therapeutic target for diverse diseases. Nat. Rev. Drug Discov. 
11:709–730. https:// doi .org/ 10 .1038/ nrd3802


Sorting the trash:Micronucleophagy gets selective

NARCIS 

Sorting the trash: Micronucleophagy gets selective

Crossref

During micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital for cell survival during starvation.</p

ARTS repository - University of Groningen

   University of GroningenSorting the trashVerlhac, Pauline; Reggiori, FulvioPublished in:The Journal of Cell BiologyDOI:10.1083/jcb.201806127IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2018Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Verlhac, P., & Reggiori, F. (2018). Sorting the trash: Micronucleophagy gets selective. The Journal of CellBiology, 217(8), 2605-2607. https://doi.org/10.1083/jcb.201806127CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 31-10-2023SPOTLIGHThttps://doi.org/10.1083/jcb.201806127 1J. Cell Biol. 2018Rockefeller University PressDuring micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital for cell survival during starvation.Sorting the trash: Micronucleophagy gets selectivePauline Verlhac and Fulvio ReggioriAutophagy is a catabolic process leading to the lysosomal/vac-uolar degradation of unwanted cellular components including aggregated proteins, damaged or superfluous organelles, and even pathogens (Galluzzi et al., 2017). This pathway, which is con-served from yeast to mammals, is crucial to maintain cell homeo-stasis and has numerous physiological implications relevant to human health (Deretic et al., 2013). Mitochondria, peroxisomes, the endoplasmic reticulum, and even portions of the nucleus can be targeted and degraded by autophagy under the orchestrated action of autophagy-related (Atg) proteins (Dikic and Elazar, 2018). Autophagic turnover of nuclear material is termed nucle-ophagy and has been described in two forms in yeast: macronuc-leophagy and micronucleophagy. Macronucleophagy involves the sequestration of a portion of the nucleus into autophagosomes and requires the autophagy receptor Atg39 (Mochida et al., 2015). The targeted nuclear material is subsequently delivered and eliminated in the vacuole upon autophagosome fusion with this organelle. During micronucleophagy, a portion of the nucleus is directly engulfed by the vacuole at the nuclear vacuole junction (NVJ), i.e., the NVJ invaginates and pinches off into the vacuolar lumen, leading to a subvacuolar vesicle that is consumed by res-ident hydrolases (Roberts et al., 2003). Both micro- and macro-nucleophagy sequester only a portion of the nucleus, indicating a specificity similar to the one observed in other selective types of autophagy such as mitophagy or pexophagy (Galluzzi et al., 2017). In particular, DNA is not degraded by these two processes, but how this is accomplished remained unknown.Mostofa et al. describe a mechanism allowing the separation of DNA from proteins during micronucleophagy induced by star-vation conditions in yeast (Fig. 1). They focused on the nucleolus, which has previously been shown to be targeted by micronucleo-phagy (Dawaliby and Mayer, 2010; Mochida et al., 2015). They re-veal that although nucleolar proteins are brought to the NVJ and delivered into the vacuole for turnover, ribosomal DNA (rDNA) is spared from degradation and kept in the nucleus (Fig. 1). This mechanism of separation requires the components of the two in-teracting nuclear complexes, chromosome linkage inner nuclear membrane protein (CLIP) and cohibin, which are composed by Heh1-Nur1 and Csm1-Lrs4, respectively. In cells lacking CLIP or cohibin subunits, rDNA and nucleolar proteins remain associ-ated, and although micronucleophagy is still functional, nucleolar proteins are not degraded. Interestingly, the absence of the CLIP or cohibin complex does not result in the aberrant degradation of rDNA. Thus, the CLIP and cohibin complexes are involved in repositioning of the rDNA away from nucleolar proteins but not in protection of rDNA or degradation of the micronucleophagic cargos per se (Fig. 1). Mostofa et al. (2018) also studied the spatio-temporal dynamics of micronucleophagy during starvation and observed that separation and repositioning of rDNA and nucleolar proteins occurs before the beginning of micronucleophagy. They also observed that these events depend on micronucleophagy as cells defective in this process but not NVJ formation did not show separation of nucleolar proteins and rDNA. Taken together, these findings indicate that separation and repositioning of nucleolar components and subsequent micronucleophagy are coordinated processes. This coordination is similar to the one observed be-tween the fission and Atg machineries during mitophagy and pexophagy (Mao et al., 2013, 2014) and could be essential to avoid rDNA degradation, which would be lethal for the cell. Finally, they found that cells lacking one of the subunits of the CLIP or cohibin complexes have reduced survival during starvation, highlighting that this parting between rDNA and nucleolar proteins could be necessary for cell survival under particular stresses.Very little is known about the mechanisms underlying micro-nucleophagy, and the study by Mostofa et al. (2018) is pioneering as it provides the crucial groundwork and specific assays for fu-ture investigations aimed at understanding this pathway and its relevance for the cell physiology under stress conditions and be-yond. By focusing on nucleolar DNA and proteins, they succeeded in answering the lingering question of how rDNA is protected © 2018 Verlhac and Reggiori This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http:// www .rupress .org/ terms/ ). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https:// creativecommons .org/ licenses/ by -nc -sa/ 4 .0/ ).Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.Correspondence to Fulvio Reggiori: f.m.reggiori@ umcg .nl. on July 19, 2018jcb.rupress.org Downloaded from http://doi.org/10.1083/jcb.201806127Published Online: 13 July, 2018 | Supp Info: Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061272during micronucleophagy. Their work demonstrates that cargo selection and sequestration are key features of nucleophagy as in other forms of selective autophagy. Therefore, this study re-inforces the paradigm that autophagic recycling is a meticulous process guarded by fail-safe mechanisms.It would be of high interest to decipher the precise physio-logical relevance of this repositioning of rDNA and nucleolar proteins. Although Mostofa et al. (2018) elegantly demonstrated the importance of the CLIP and cohibin complexes during micro-nucleophagy, they did so using knockout strains. Thus, it cannot be excluded a priori that the relevance of these complexes for cell survival during starvation observed by Mostofa et al. (2018) could be due to one or more other functions of these two complexes. It would therefore be important to generate and use point mutants or possibly ablate known binding partners of the CLIP and co-hibin complexes such as Sir2, Cdc14, Net1, Tof2, and rDNA-bind-ing Fob1 to more specifically address this physiological aspect.Specific mutants will also be key to address some aspects of the molecular mechanism of micronucleophagy. For example, how is DNA directed away and protected from degradation? Al-though the CLIP–cohibin system is required for rDNA separation, it appears to be unnecessary for its protection from degradation as rDNA is not turned over in the absence of these factors, al-though micronucleophagy still occurs. This suggests the exis-tence of a different mechanism to avoid delivery of rDNA, and possibly chromosomes in general, to the vacuole during both micro- and macronucleophagy.Furthermore, an aspect that will probably attract further re-search is the identification of the pathway that conveys TORC1 signaling into the nucleus to communicate both the reposition-ing of rDNA and the targeting to degradation of nucleolar pro-teins. TORC1 is a cytosolic complex that allows cells to adapt to environmental changes through an integrated orchestration of anabolic and catabolic pathways including micronucleophagy. Identifying the signaling axis that regulates micronucleophagy in the nucleus will help to understand intracellular communi-cation and the potential crosstalk of micronucleophagy with other processes and possibly cell death, a crosstalk suggested by the survival defect of cells lacking nucleophagy. An interesting candidate signaling axis could be the newly identified Nem1/Spo7-Pah1 cascade, which has been implicated in micro- and macronucleophagy induction notably through positioning of Atg39 and Nvj1, a SNA RE-mediating NVJ establishment (Rahman et al., 2018). Other lingering questions include determining whether a similar rDNA-sorting mechanism takes place during macronucleophagy and whether macronucleophagic cargoes are different from those of micronucleophagy.The findings from Mostofa et al. (2018) also provide fascinating new perspectives for the study of the precise physiological role(s) of micronucleophagy. First, the observation that micronucleoph-agy still occurs while the retargeting of rDNA and nucleolar pro-teins is impaired suggests that other nuclear components might be degraded through this pathway. Identifying such cargos would be crucial to better understand the cellular implications of an even-tual defect in micronucleophagy. Moreover, Mostofa et al. (2018) observed a reduced survival under starvation in cells where the repositioning is impaired but nucleophagy is still functional, in line with previous observations that nucleophagy is necessary for cell survival under stress. Nevertheless, the fact that impairing the repositioning alone is enough to induce a survival defect also suggests that either degradation of nucleolar proteins is capital or other cargos need to be degraded for cells to survive starvation.Intriguingly, the segregation mechanism described by Mostofa et al. (2018) shares some conceptual aspects with what was shown for mitophagy in yeast, where specific proteins are protected from degradation by forming intramitochondrial aggregates while others are preferentially turned over via seg-regation into the subdomains of the mitochondria targeted by mitophagy (Abeliovich et al., 2013). A similar phenomenon might be taking place during micro- and possibly macronucleophagy, where specific nuclear proteins are preferentially degraded and thus concentrated at the site of nucleophagy in a CLIP–cohibin system-dependent manner, whereas others could be protected by another system through, for example, a retention and/or ex-clusion mechanism. If some proteins are protected from micro-nucleophagy, it would be interesting to demonstrate whether the mechanism is similar to the one protecting rDNA. Conversely, it would be interesting to explore whether mitochondrial DNA is protected during mitophagy.Finally, although autophagy is highly conserved among eu-karyotes, the same cannot currently be said for nucleophagy. Nucleophagy has rarely been observed in mammalian cells and exclusively in pathological contexts (Park et al., 2009). The find-ings of Mostofa et al. (2018) provide the framework that could Figure 1. The role of CLIP and cohibin com-plexes in micronucleophagy. Nucleolar proteins, rDNA, and the cohibin complex are associated at nucleoli under growing conditions, while the CLIP complex is distributed over the entire inner side of the nuclear membrane. TORC1 inactivation triggers the association of nucleolar proteins with part of the CLIP complexes and their subsequent targeting to the NVJ, where they are included into the forming intravacuo-lar invagination. The pinch-off of this protrusion leads to the vacuolar turnover of both nucleolar proteins and the CLIP complex. In contrast, rDNA and cohibin remain associated and get separated from the nucleolar proteins to remain protected from micronucleophagic degradation.Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061273help elucidating whether micronucleophagy occurs in mamma-lian cells by studying for example the mammalian counterpart(s) of the CLIP and cohibin complexes. As Mostofa et al. (2018) stated in their study, it is also possible that the mechanisms of nucleo-phagy differ greatly between yeast and mammals. The answer could lie in the fact that key mammalian ATG components such as LC3 proteins, the homologues of yeast Atg8, are also present in the nucleus, but a role has not been assigned to this pool yet. Defects in selective types of autophagy like mitophagy, reticu-lophagy, and aggrephagy have been associated to severe human pathologies, and therefore, the modulation of these specific processes rather than the one of bulk autophagy has great ther-apeutic potential (Rubinsztein et al., 2012). It is thus crucial to determine the molecular mechanism and physiological functions of micronucleophagy in mammalian cells, and more in general, those of nucleophagy, as this could be relevant for human health.AcknowledgmentsWe thank Dr. Mario Mauthe for his critical reading of the manuscript. F. Reggiori is supported by ZonMW VICI (016.130.606), the Netherlands Organization for Scientific Research ALW Open Program (ALW OP.310), and the European Commission’s Marie Skłodowska-Curie Cofund (713660) and Marie Skłodowska-Curie Innovative Training Networks (765912) grants.The authors declare no competing financial interests.ReferencesAbeliovich, H., M. Zarei, K.T.G. Rigbolt, R.J. Youle, and J. Dengjel. 2013. In-volvement of mitochondrial dynamics in the segregation of mitochon-drial matrix proteins during stationary phase mitophagy. Nat. Commun. 4:2789. https:// doi .org/ 10 .1038/ ncomms3789Dawaliby, R., and A. Mayer. 2010. Microautophagy of the nucleus coincides with a vacuolar diffusion barrier at nuclear-vacuolar junctions. Mol. Biol. Cell. 21:4173–4183. https:// doi .org/ 10 .1091/ mbc .e09 -09 -0782Deretic, V., T. Saitoh, and S. Akira. 2013. Autophagy in infection, inflammation and immunity. Nat. Rev. Immunol. 13:722–737. https:// doi .org/ 10 .1038/ nri3532Dikic, I., and Z. Elazar. 2018. Mechanism and medical implications of mam-malian autophagy. Nat. Rev. Mol. Cell Biol. 19:349–364. https:// doi .org/ 10 .1038/ s41580 -018 -0003 -4Galluzzi, L., E.H. Baehrecke, A. Ballabio, P. Boya, J.M. Bravo-San Pedro, F. Cec-coni, A.M. Choi, C.T. Chu, P. Codogno, M.I. Colombo, et al. 2017. Molecu-lar definitions of autophagy and related processes. EMBO J. 36:1811–1836. https:// doi .org/ 10 .15252/ embj .201796697Mao, K., K. Wang, X. Liu, and D.J. Klionsky. 2013. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev. Cell. 26:9–18. https:// doi .org/ 10 .1016/ j .devcel .2013 .05 .024Mao, K., X. Liu, Y. Feng, and D.J. Klionsky. 2014. The progression of peroxi-somal degradation through autophagy requires peroxisomal division. Autophagy. 10:652–661. https:// doi .org/ 10 .4161/ auto .27852Mochida, K., Y. Oikawa, Y. Kimura, H. Kirisako, H. Hirano, Y. Ohsumi, and H. Nakatogawa. 2015. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature. 522:359–362. https:// doi .org/ 10 .1038/ nature14506Mostofa, G.M., M.A. Rahman, N. Koike, A.M.S.T. Yeasmin, N. Islam, T.M. Wa-liullah, S. Hosoyamada, M. Shimobayashi, T. Kobayashi, M.N. Hall, et al. 2018. CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy. J. Cell Biol. https:// doi .org/ 10 .1083/ jcb .201706164Park, Y.E., Y.K. Hayashi, G. Bonne, T. Arimura, S. Noguchi, I. Nonaka, and I. Nishino. 2009. Autophagic degradation of nuclear components in mam-malian cells. Autophagy. 5:795–804. https:// doi .org/ 10 .4161/ auto .8901Rahman, M.A., M.G. Mostofa, and T. Ushimaru. 2018. The Nem1/Spo7-Pah1/lipin axis is required for autophagy induction after TORC1 inactivation. FEBS J. 285:1840–1860. https:// doi .org/ 10 .1111/ febs .14448Roberts, P., S. Moshitch-Moshkovitz, E. Kvam, E. O’Toole, M. Winey, and D.S. Goldfarb. 2003. Piecemeal microautophagy of nucleus in Saccharomy-ces cerevisiae. Mol. Biol. Cell. 14:129–141. https:// doi .org/ 10 .1091/ mbc .e02 -08 -0483Rubinsztein, D.C., P. Codogno, and B. Levine. 2012. Autophagy modulation as a potential therapeutic target for diverse diseases. Nat. Rev. Drug Discov. 11:709–730. https:// doi .org/ 10 .1038/ nrd3802

English

   University of GroningenSorting the trashVerlhac, Pauline; Reggiori, FulvioPublished in:The Journal of Cell BiologyDOI:10.1083/jcb.201806127IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2018Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Verlhac, P., & Reggiori, F. (2018). Sorting the trash: Micronucleophagy gets selective. The Journal of CellBiology, 217(8), 2605-2607. https://doi.org/10.1083/jcb.201806127CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 13-02-2023SPOTLIGHThttps://doi.org/10.1083/jcb.201806127 1J. Cell Biol. 2018Rockefeller University PressDuring micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital for cell survival during starvation.Sorting the trash: Micronucleophagy gets selectivePauline Verlhac and Fulvio ReggioriAutophagy is a catabolic process leading to the lysosomal/vac-uolar degradation of unwanted cellular components including aggregated proteins, damaged or superfluous organelles, and even pathogens (Galluzzi et al., 2017). This pathway, which is con-served from yeast to mammals, is crucial to maintain cell homeo-stasis and has numerous physiological implications relevant to human health (Deretic et al., 2013). Mitochondria, peroxisomes, the endoplasmic reticulum, and even portions of the nucleus can be targeted and degraded by autophagy under the orchestrated action of autophagy-related (Atg) proteins (Dikic and Elazar, 2018). Autophagic turnover of nuclear material is termed nucle-ophagy and has been described in two forms in yeast: macronuc-leophagy and micronucleophagy. Macronucleophagy involves the sequestration of a portion of the nucleus into autophagosomes and requires the autophagy receptor Atg39 (Mochida et al., 2015). The targeted nuclear material is subsequently delivered and eliminated in the vacuole upon autophagosome fusion with this organelle. During micronucleophagy, a portion of the nucleus is directly engulfed by the vacuole at the nuclear vacuole junction (NVJ), i.e., the NVJ invaginates and pinches off into the vacuolar lumen, leading to a subvacuolar vesicle that is consumed by res-ident hydrolases (Roberts et al., 2003). Both micro- and macro-nucleophagy sequester only a portion of the nucleus, indicating a specificity similar to the one observed in other selective types of autophagy such as mitophagy or pexophagy (Galluzzi et al., 2017). In particular, DNA is not degraded by these two processes, but how this is accomplished remained unknown.Mostofa et al. describe a mechanism allowing the separation of DNA from proteins during micronucleophagy induced by star-vation conditions in yeast (Fig. 1). They focused on the nucleolus, which has previously been shown to be targeted by micronucleo-phagy (Dawaliby and Mayer, 2010; Mochida et al., 2015). They re-veal that although nucleolar proteins are brought to the NVJ and delivered into the vacuole for turnover, ribosomal DNA (rDNA) is spared from degradation and kept in the nucleus (Fig. 1). This mechanism of separation requires the components of the two in-teracting nuclear complexes, chromosome linkage inner nuclear membrane protein (CLIP) and cohibin, which are composed by Heh1-Nur1 and Csm1-Lrs4, respectively. In cells lacking CLIP or cohibin subunits, rDNA and nucleolar proteins remain associ-ated, and although micronucleophagy is still functional, nucleolar proteins are not degraded. Interestingly, the absence of the CLIP or cohibin complex does not result in the aberrant degradation of rDNA. Thus, the CLIP and cohibin complexes are involved in repositioning of the rDNA away from nucleolar proteins but not in protection of rDNA or degradation of the micronucleophagic cargos per se (Fig. 1). Mostofa et al. (2018) also studied the spatio-temporal dynamics of micronucleophagy during starvation and observed that separation and repositioning of rDNA and nucleolar proteins occurs before the beginning of micronucleophagy. They also observed that these events depend on micronucleophagy as cells defective in this process but not NVJ formation did not show separation of nucleolar proteins and rDNA. Taken together, these findings indicate that separation and repositioning of nucleolar components and subsequent micronucleophagy are coordinated processes. This coordination is similar to the one observed be-tween the fission and Atg machineries during mitophagy and pexophagy (Mao et al., 2013, 2014) and could be essential to avoid rDNA degradation, which would be lethal for the cell. Finally, they found that cells lacking one of the subunits of the CLIP or cohibin complexes have reduced survival during starvation, highlighting that this parting between rDNA and nucleolar proteins could be necessary for cell survival under particular stresses.Very little is known about the mechanisms underlying micro-nucleophagy, and the study by Mostofa et al. (2018) is pioneering as it provides the crucial groundwork and specific assays for fu-ture investigations aimed at understanding this pathway and its relevance for the cell physiology under stress conditions and be-yond. By focusing on nucleolar DNA and proteins, they succeeded in answering the lingering question of how rDNA is protected © 2018 Verlhac and Reggiori This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http:// www .rupress .org/ terms/ ). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https:// creativecommons .org/ licenses/ by -nc -sa/ 4 .0/ ).Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.Correspondence to Fulvio Reggiori: f.m.reggiori@ umcg .nl. on July 19, 2018jcb.rupress.org Downloaded from http://doi.org/10.1083/jcb.201806127Published Online: 13 July, 2018 | Supp Info: Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061272during micronucleophagy. Their work demonstrates that cargo selection and sequestration are key features of nucleophagy as in other forms of selective autophagy. Therefore, this study re-inforces the paradigm that autophagic recycling is a meticulous process guarded by fail-safe mechanisms.It would be of high interest to decipher the precise physio-logical relevance of this repositioning of rDNA and nucleolar proteins. Although Mostofa et al. (2018) elegantly demonstrated the importance of the CLIP and cohibin complexes during micro-nucleophagy, they did so using knockout strains. Thus, it cannot be excluded a priori that the relevance of these complexes for cell survival during starvation observed by Mostofa et al. (2018) could be due to one or more other functions of these two complexes. It would therefore be important to generate and use point mutants or possibly ablate known binding partners of the CLIP and co-hibin complexes such as Sir2, Cdc14, Net1, Tof2, and rDNA-bind-ing Fob1 to more specifically address this physiological aspect.Specific mutants will also be key to address some aspects of the molecular mechanism of micronucleophagy. For example, how is DNA directed away and protected from degradation? Al-though the CLIP–cohibin system is required for rDNA separation, it appears to be unnecessary for its protection from degradation as rDNA is not turned over in the absence of these factors, al-though micronucleophagy still occurs. This suggests the exis-tence of a different mechanism to avoid delivery of rDNA, and possibly chromosomes in general, to the vacuole during both micro- and macronucleophagy.Furthermore, an aspect that will probably attract further re-search is the identification of the pathway that conveys TORC1 signaling into the nucleus to communicate both the reposition-ing of rDNA and the targeting to degradation of nucleolar pro-teins. TORC1 is a cytosolic complex that allows cells to adapt to environmental changes through an integrated orchestration of anabolic and catabolic pathways including micronucleophagy. Identifying the signaling axis that regulates micronucleophagy in the nucleus will help to understand intracellular communi-cation and the potential crosstalk of micronucleophagy with other processes and possibly cell death, a crosstalk suggested by the survival defect of cells lacking nucleophagy. An interesting candidate signaling axis could be the newly identified Nem1/Spo7-Pah1 cascade, which has been implicated in micro- and macronucleophagy induction notably through positioning of Atg39 and Nvj1, a SNA RE-mediating NVJ establishment (Rahman et al., 2018). Other lingering questions include determining whether a similar rDNA-sorting mechanism takes place during macronucleophagy and whether macronucleophagic cargoes are different from those of micronucleophagy.The findings from Mostofa et al. (2018) also provide fascinating new perspectives for the study of the precise physiological role(s) of micronucleophagy. First, the observation that micronucleoph-agy still occurs while the retargeting of rDNA and nucleolar pro-teins is impaired suggests that other nuclear components might be degraded through this pathway. Identifying such cargos would be crucial to better understand the cellular implications of an even-tual defect in micronucleophagy. Moreover, Mostofa et al. (2018) observed a reduced survival under starvation in cells where the repositioning is impaired but nucleophagy is still functional, in line with previous observations that nucleophagy is necessary for cell survival under stress. Nevertheless, the fact that impairing the repositioning alone is enough to induce a survival defect also suggests that either degradation of nucleolar proteins is capital or other cargos need to be degraded for cells to survive starvation.Intriguingly, the segregation mechanism described by Mostofa et al. (2018) shares some conceptual aspects with what was shown for mitophagy in yeast, where specific proteins are protected from degradation by forming intramitochondrial aggregates while others are preferentially turned over via seg-regation into the subdomains of the mitochondria targeted by mitophagy (Abeliovich et al., 2013). A similar phenomenon might be taking place during micro- and possibly macronucleophagy, where specific nuclear proteins are preferentially degraded and thus concentrated at the site of nucleophagy in a CLIP–cohibin system-dependent manner, whereas others could be protected by another system through, for example, a retention and/or ex-clusion mechanism. If some proteins are protected from micro-nucleophagy, it would be interesting to demonstrate whether the mechanism is similar to the one protecting rDNA. Conversely, it would be interesting to explore whether mitochondrial DNA is protected during mitophagy.Finally, although autophagy is highly conserved among eu-karyotes, the same cannot currently be said for nucleophagy. Nucleophagy has rarely been observed in mammalian cells and exclusively in pathological contexts (Park et al., 2009). The find-ings of Mostofa et al. (2018) provide the framework that could Figure 1. The role of CLIP and cohibin com-plexes in micronucleophagy. Nucleolar proteins, rDNA, and the cohibin complex are associated at nucleoli under growing conditions, while the CLIP complex is distributed over the entire inner side of the nuclear membrane. TORC1 inactivation triggers the association of nucleolar proteins with part of the CLIP complexes and their subsequent targeting to the NVJ, where they are included into the forming intravacuo-lar invagination. The pinch-off of this protrusion leads to the vacuolar turnover of both nucleolar proteins and the CLIP complex. In contrast, rDNA and cohibin remain associated and get separated from the nucleolar proteins to remain protected from micronucleophagic degradation.Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061273help elucidating whether micronucleophagy occurs in mamma-lian cells by studying for example the mammalian counterpart(s) of the CLIP and cohibin complexes. As Mostofa et al. (2018) stated in their study, it is also possible that the mechanisms of nucleo-phagy differ greatly between yeast and mammals. The answer could lie in the fact that key mammalian ATG components such as LC3 proteins, the homologues of yeast Atg8, are also present in the nucleus, but a role has not been assigned to this pool yet. Defects in selective types of autophagy like mitophagy, reticu-lophagy, and aggrephagy have been associated to severe human pathologies, and therefore, the modulation of these specific processes rather than the one of bulk autophagy has great ther-apeutic potential (Rubinsztein et al., 2012). It is thus crucial to determine the molecular mechanism and physiological functions of micronucleophagy in mammalian cells, and more in general, those of nucleophagy, as this could be relevant for human health.AcknowledgmentsWe thank Dr. Mario Mauthe for his critical reading of the manuscript. F. Reggiori is supported by ZonMW VICI (016.130.606), the Netherlands Organization for Scientific Research ALW Open Program (ALW OP.310), and the European Commission’s Marie Skłodowska-Curie Cofund (713660) and Marie Skłodowska-Curie Innovative Training Networks (765912) grants.The authors declare no competing financial interests.ReferencesAbeliovich, H., M. Zarei, K.T.G. Rigbolt, R.J. Youle, and J. Dengjel. 2013. In-volvement of mitochondrial dynamics in the segregation of mitochon-drial matrix proteins during stationary phase mitophagy. Nat. Commun. 4:2789. https:// doi .org/ 10 .1038/ ncomms3789Dawaliby, R., and A. Mayer. 2010. Microautophagy of the nucleus coincides with a vacuolar diffusion barrier at nuclear-vacuolar junctions. Mol. Biol. Cell. 21:4173–4183. https:// doi .org/ 10 .1091/ mbc .e09 -09 -0782Deretic, V., T. Saitoh, and S. Akira. 2013. Autophagy in infection, inflammation and immunity. Nat. Rev. Immunol. 13:722–737. https:// doi .org/ 10 .1038/ nri3532Dikic, I., and Z. Elazar. 2018. Mechanism and medical implications of mam-malian autophagy. Nat. Rev. Mol. Cell Biol. 19:349–364. https:// doi .org/ 10 .1038/ s41580 -018 -0003 -4Galluzzi, L., E.H. Baehrecke, A. Ballabio, P. Boya, J.M. Bravo-San Pedro, F. Cec-coni, A.M. Choi, C.T. Chu, P. Codogno, M.I. Colombo, et al. 2017. Molecu-lar definitions of autophagy and related processes. EMBO J. 36:1811–1836. https:// doi .org/ 10 .15252/ embj .201796697Mao, K., K. Wang, X. Liu, and D.J. Klionsky. 2013. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev. Cell. 26:9–18. https:// doi .org/ 10 .1016/ j .devcel .2013 .05 .024Mao, K., X. Liu, Y. Feng, and D.J. Klionsky. 2014. The progression of peroxi-somal degradation through autophagy requires peroxisomal division. Autophagy. 10:652–661. https:// doi .org/ 10 .4161/ auto .27852Mochida, K., Y. Oikawa, Y. Kimura, H. Kirisako, H. Hirano, Y. Ohsumi, and H. Nakatogawa. 2015. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature. 522:359–362. https:// doi .org/ 10 .1038/ nature14506Mostofa, G.M., M.A. Rahman, N. Koike, A.M.S.T. Yeasmin, N. Islam, T.M. Wa-liullah, S. Hosoyamada, M. Shimobayashi, T. Kobayashi, M.N. Hall, et al. 2018. CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy. J. Cell Biol. https:// doi .org/ 10 .1083/ jcb .201706164Park, Y.E., Y.K. Hayashi, G. Bonne, T. Arimura, S. Noguchi, I. Nonaka, and I. Nishino. 2009. Autophagic degradation of nuclear components in mam-malian cells. Autophagy. 5:795–804. https:// doi .org/ 10 .4161/ auto .8901Rahman, M.A., M.G. Mostofa, and T. Ushimaru. 2018. The Nem1/Spo7-Pah1/lipin axis is required for autophagy induction after TORC1 inactivation. FEBS J. 285:1840–1860. https:// doi .org/ 10 .1111/ febs .14448Roberts, P., S. Moshitch-Moshkovitz, E. Kvam, E. O’Toole, M. Winey, and D.S. Goldfarb. 2003. Piecemeal microautophagy of nucleus in Saccharomy-ces cerevisiae. Mol. Biol. Cell. 14:129–141. https:// doi .org/ 10 .1091/ mbc .e02 -08 -0483Rubinsztein, D.C., P. Codogno, and B. Levine. 2012. Autophagy modulation as a potential therapeutic target for diverse diseases. Nat. Rev. Drug Discov. 11:709–730. https:// doi .org/ 10 .1038/ nrd3802

University of Groningen

   University of GroningenSorting the trashVerlhac, Pauline; Reggiori, FulvioPublished in:The Journal of Cell BiologyDOI:10.1083/jcb.201806127IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2018Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Verlhac, P., & Reggiori, F. (2018). Sorting the trash: Micronucleophagy gets selective. The Journal of CellBiology, 217(8), 2605-2607. https://doi.org/10.1083/jcb.201806127CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 12-11-2019SPOTLIGHThttps://doi.org/10.1083/jcb.201806127 1J. Cell Biol. 2018Rockefeller University PressDuring micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital for cell survival during starvation.Sorting the trash: Micronucleophagy gets selectivePauline Verlhac and Fulvio ReggioriAutophagy is a catabolic process leading to the lysosomal/vac-uolar degradation of unwanted cellular components including aggregated proteins, damaged or superfluous organelles, and even pathogens (Galluzzi et al., 2017). This pathway, which is con-served from yeast to mammals, is crucial to maintain cell homeo-stasis and has numerous physiological implications relevant to human health (Deretic et al., 2013). Mitochondria, peroxisomes, the endoplasmic reticulum, and even portions of the nucleus can be targeted and degraded by autophagy under the orchestrated action of autophagy-related (Atg) proteins (Dikic and Elazar, 2018). Autophagic turnover of nuclear material is termed nucle-ophagy and has been described in two forms in yeast: macronuc-leophagy and micronucleophagy. Macronucleophagy involves the sequestration of a portion of the nucleus into autophagosomes and requires the autophagy receptor Atg39 (Mochida et al., 2015). The targeted nuclear material is subsequently delivered and eliminated in the vacuole upon autophagosome fusion with this organelle. During micronucleophagy, a portion of the nucleus is directly engulfed by the vacuole at the nuclear vacuole junction (NVJ), i.e., the NVJ invaginates and pinches off into the vacuolar lumen, leading to a subvacuolar vesicle that is consumed by res-ident hydrolases (Roberts et al., 2003). Both micro- and macro-nucleophagy sequester only a portion of the nucleus, indicating a specificity similar to the one observed in other selective types of autophagy such as mitophagy or pexophagy (Galluzzi et al., 2017). In particular, DNA is not degraded by these two processes, but how this is accomplished remained unknown.Mostofa et al. describe a mechanism allowing the separation of DNA from proteins during micronucleophagy induced by star-vation conditions in yeast (Fig. 1). They focused on the nucleolus, which has previously been shown to be targeted by micronucleo-phagy (Dawaliby and Mayer, 2010; Mochida et al., 2015). They re-veal that although nucleolar proteins are brought to the NVJ and delivered into the vacuole for turnover, ribosomal DNA (rDNA) is spared from degradation and kept in the nucleus (Fig. 1). This mechanism of separation requires the components of the two in-teracting nuclear complexes, chromosome linkage inner nuclear membrane protein (CLIP) and cohibin, which are composed by Heh1-Nur1 and Csm1-Lrs4, respectively. In cells lacking CLIP or cohibin subunits, rDNA and nucleolar proteins remain associ-ated, and although micronucleophagy is still functional, nucleolar proteins are not degraded. Interestingly, the absence of the CLIP or cohibin complex does not result in the aberrant degradation of rDNA. Thus, the CLIP and cohibin complexes are involved in repositioning of the rDNA away from nucleolar proteins but not in protection of rDNA or degradation of the micronucleophagic cargos per se (Fig. 1). Mostofa et al. (2018) also studied the spatio-temporal dynamics of micronucleophagy during starvation and observed that separation and repositioning of rDNA and nucleolar proteins occurs before the beginning of micronucleophagy. They also observed that these events depend on micronucleophagy as cells defective in this process but not NVJ formation did not show separation of nucleolar proteins and rDNA. Taken together, these findings indicate that separation and repositioning of nucleolar components and subsequent micronucleophagy are coordinated processes. This coordination is similar to the one observed be-tween the fission and Atg machineries during mitophagy and pexophagy (Mao et al., 2013, 2014) and could be essential to avoid rDNA degradation, which would be lethal for the cell. Finally, they found that cells lacking one of the subunits of the CLIP or cohibin complexes have reduced survival during starvation, highlighting that this parting between rDNA and nucleolar proteins could be necessary for cell survival under particular stresses.Very little is known about the mechanisms underlying micro-nucleophagy, and the study by Mostofa et al. (2018) is pioneering as it provides the crucial groundwork and specific assays for fu-ture investigations aimed at understanding this pathway and its relevance for the cell physiology under stress conditions and be-yond. By focusing on nucleolar DNA and proteins, they succeeded in answering the lingering question of how rDNA is protected © 2018 Verlhac and Reggiori This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http:// www .rupress .org/ terms/ ). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https:// creativecommons .org/ licenses/ by -nc -sa/ 4 .0/ ).Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.Correspondence to Fulvio Reggiori: f.m.reggiori@ umcg .nl. on July 19, 2018jcb.rupress.org Downloaded from http://doi.org/10.1083/jcb.201806127Published Online: 13 July, 2018 | Supp Info: Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061272during micronucleophagy. Their work demonstrates that cargo selection and sequestration are key features of nucleophagy as in other forms of selective autophagy. Therefore, this study re-inforces the paradigm that autophagic recycling is a meticulous process guarded by fail-safe mechanisms.It would be of high interest to decipher the precise physio-logical relevance of this repositioning of rDNA and nucleolar proteins. Although Mostofa et al. (2018) elegantly demonstrated the importance of the CLIP and cohibin complexes during micro-nucleophagy, they did so using knockout strains. Thus, it cannot be excluded a priori that the relevance of these complexes for cell survival during starvation observed by Mostofa et al. (2018) could be due to one or more other functions of these two complexes. It would therefore be important to generate and use point mutants or possibly ablate known binding partners of the CLIP and co-hibin complexes such as Sir2, Cdc14, Net1, Tof2, and rDNA-bind-ing Fob1 to more specifically address this physiological aspect.Specific mutants will also be key to address some aspects of the molecular mechanism of micronucleophagy. For example, how is DNA directed away and protected from degradation? Al-though the CLIP–cohibin system is required for rDNA separation, it appears to be unnecessary for its protection from degradation as rDNA is not turned over in the absence of these factors, al-though micronucleophagy still occurs. This suggests the exis-tence of a different mechanism to avoid delivery of rDNA, and possibly chromosomes in general, to the vacuole during both micro- and macronucleophagy.Furthermore, an aspect that will probably attract further re-search is the identification of the pathway that conveys TORC1 signaling into the nucleus to communicate both the reposition-ing of rDNA and the targeting to degradation of nucleolar pro-teins. TORC1 is a cytosolic complex that allows cells to adapt to environmental changes through an integrated orchestration of anabolic and catabolic pathways including micronucleophagy. Identifying the signaling axis that regulates micronucleophagy in the nucleus will help to understand intracellular communi-cation and the potential crosstalk of micronucleophagy with other processes and possibly cell death, a crosstalk suggested by the survival defect of cells lacking nucleophagy. An interesting candidate signaling axis could be the newly identified Nem1/Spo7-Pah1 cascade, which has been implicated in micro- and macronucleophagy induction notably through positioning of Atg39 and Nvj1, a SNA RE-mediating NVJ establishment (Rahman et al., 2018). Other lingering questions include determining whether a similar rDNA-sorting mechanism takes place during macronucleophagy and whether macronucleophagic cargoes are different from those of micronucleophagy.The findings from Mostofa et al. (2018) also provide fascinating new perspectives for the study of the precise physiological role(s) of micronucleophagy. First, the observation that micronucleoph-agy still occurs while the retargeting of rDNA and nucleolar pro-teins is impaired suggests that other nuclear components might be degraded through this pathway. Identifying such cargos would be crucial to better understand the cellular implications of an even-tual defect in micronucleophagy. Moreover, Mostofa et al. (2018) observed a reduced survival under starvation in cells where the repositioning is impaired but nucleophagy is still functional, in line with previous observations that nucleophagy is necessary for cell survival under stress. Nevertheless, the fact that impairing the repositioning alone is enough to induce a survival defect also suggests that either degradation of nucleolar proteins is capital or other cargos need to be degraded for cells to survive starvation.Intriguingly, the segregation mechanism described by Mostofa et al. (2018) shares some conceptual aspects with what was shown for mitophagy in yeast, where specific proteins are protected from degradation by forming intramitochondrial aggregates while others are preferentially turned over via seg-regation into the subdomains of the mitochondria targeted by mitophagy (Abeliovich et al., 2013). A similar phenomenon might be taking place during micro- and possibly macronucleophagy, where specific nuclear proteins are preferentially degraded and thus concentrated at the site of nucleophagy in a CLIP–cohibin system-dependent manner, whereas others could be protected by another system through, for example, a retention and/or ex-clusion mechanism. If some proteins are protected from micro-nucleophagy, it would be interesting to demonstrate whether the mechanism is similar to the one protecting rDNA. Conversely, it would be interesting to explore whether mitochondrial DNA is protected during mitophagy.Finally, although autophagy is highly conserved among eu-karyotes, the same cannot currently be said for nucleophagy. Nucleophagy has rarely been observed in mammalian cells and exclusively in pathological contexts (Park et al., 2009). The find-ings of Mostofa et al. (2018) provide the framework that could Figure 1. The role of CLIP and cohibin com-plexes in micronucleophagy. Nucleolar proteins, rDNA, and the cohibin complex are associated at nucleoli under growing conditions, while the CLIP complex is distributed over the entire inner side of the nuclear membrane. TORC1 inactivation triggers the association of nucleolar proteins with part of the CLIP complexes and their subsequent targeting to the NVJ, where they are included into the forming intravacuo-lar invagination. The pinch-off of this protrusion leads to the vacuolar turnover of both nucleolar proteins and the CLIP complex. In contrast, rDNA and cohibin remain associated and get separated from the nucleolar proteins to remain protected from micronucleophagic degradation.Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061273help elucidating whether micronucleophagy occurs in mamma-lian cells by studying for example the mammalian counterpart(s) of the CLIP and cohibin complexes. As Mostofa et al. (2018) stated in their study, it is also possible that the mechanisms of nucleo-phagy differ greatly between yeast and mammals. The answer could lie in the fact that key mammalian ATG components such as LC3 proteins, the homologues of yeast Atg8, are also present in the nucleus, but a role has not been assigned to this pool yet. Defects in selective types of autophagy like mitophagy, reticu-lophagy, and aggrephagy have been associated to severe human pathologies, and therefore, the modulation of these specific processes rather than the one of bulk autophagy has great ther-apeutic potential (Rubinsztein et al., 2012). It is thus crucial to determine the molecular mechanism and physiological functions of micronucleophagy in mammalian cells, and more in general, those of nucleophagy, as this could be relevant for human health.AcknowledgmentsWe thank Dr. Mario Mauthe for his critical reading of the manuscript. F. Reggiori is supported by ZonMW VICI (016.130.606), the Netherlands Organization for Scientific Research ALW Open Program (ALW OP.310), and the European Commission’s Marie Skłodowska-Curie Cofund (713660) and Marie Skłodowska-Curie Innovative Training Networks (765912) grants.The authors declare no competing financial interests.ReferencesAbeliovich, H., M. Zarei, K.T.G. Rigbolt, R.J. Youle, and J. Dengjel. 2013. In-volvement of mitochondrial dynamics in the segregation of mitochon-drial matrix proteins during stationary phase mitophagy. Nat. Commun. 4:2789. https:// doi .org/ 10 .1038/ ncomms3789Dawaliby, R., and A. Mayer. 2010. Microautophagy of the nucleus coincides with a vacuolar diffusion barrier at nuclear-vacuolar junctions. Mol. Biol. Cell. 21:4173–4183. https:// doi .org/ 10 .1091/ mbc .e09 -09 -0782Deretic, V., T. Saitoh, and S. Akira. 2013. Autophagy in infection, inflammation and immunity. Nat. Rev. Immunol. 13:722–737. https:// doi .org/ 10 .1038/ nri3532Dikic, I., and Z. Elazar. 2018. Mechanism and medical implications of mam-malian autophagy. Nat. Rev. Mol. Cell Biol. 19:349–364. https:// doi .org/ 10 .1038/ s41580 -018 -0003 -4Galluzzi, L., E.H. Baehrecke, A. Ballabio, P. Boya, J.M. Bravo-San Pedro, F. Cec-coni, A.M. Choi, C.T. Chu, P. Codogno, M.I. Colombo, et al. 2017. Molecu-lar definitions of autophagy and related processes. EMBO J. 36:1811–1836. https:// doi .org/ 10 .15252/ embj .201796697Mao, K., K. Wang, X. Liu, and D.J. Klionsky. 2013. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev. Cell. 26:9–18. https:// doi .org/ 10 .1016/ j .devcel .2013 .05 .024Mao, K., X. Liu, Y. Feng, and D.J. Klionsky. 2014. The progression of peroxi-somal degradation through autophagy requires peroxisomal division. Autophagy. 10:652–661. https:// doi .org/ 10 .4161/ auto .27852Mochida, K., Y. Oikawa, Y. Kimura, H. Kirisako, H. Hirano, Y. Ohsumi, and H. Nakatogawa. 2015. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature. 522:359–362. https:// doi .org/ 10 .1038/ nature14506Mostofa, G.M., M.A. Rahman, N. Koike, A.M.S.T. Yeasmin, N. Islam, T.M. Wa-liullah, S. Hosoyamada, M. Shimobayashi, T. Kobayashi, M.N. Hall, et al. 2018. CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy. J. Cell Biol. https:// doi .org/ 10 .1083/ jcb .201706164Park, Y.E., Y.K. Hayashi, G. Bonne, T. Arimura, S. Noguchi, I. Nonaka, and I. Nishino. 2009. Autophagic degradation of nuclear components in mam-malian cells. Autophagy. 5:795–804. https:// doi .org/ 10 .4161/ auto .8901Rahman, M.A., M.G. Mostofa, and T. Ushimaru. 2018. The Nem1/Spo7-Pah1/lipin axis is required for autophagy induction after TORC1 inactivation. FEBS J. 285:1840–1860. https:// doi .org/ 10 .1111/ febs .14448Roberts, P., S. Moshitch-Moshkovitz, E. Kvam, E. O’Toole, M. Winey, and D.S. Goldfarb. 2003. Piecemeal microautophagy of nucleus in Saccharomy-ces cerevisiae. Mol. Biol. Cell. 14:129–141. https:// doi .org/ 10 .1091/ mbc .e02 -08 -0483Rubinsztein, D.C., P. Codogno, and B. Levine. 2012. Autophagy modulation as a potential therapeutic target for diverse diseases. Nat. Rev. Drug Discov. 11:709–730. https:// doi .org/ 10 .1038/ nrd3802

   University of GroningenSorting the trashVerlhac, Pauline; Reggiori, FulvioPublished in:The Journal of Cell BiologyDOI:10.1083/jcb.201806127IMPORTANT NOTE: You are advised to consult the publisher's version (publisher's PDF) if you wish to cite fromit. Please check the document version below.Document VersionPublisher's PDF, also known as Version of recordPublication date:2018Link to publication in University of Groningen/UMCG research databaseCitation for published version (APA):Verlhac, P., & Reggiori, F. (2018). Sorting the trash: Micronucleophagy gets selective. The Journal of CellBiology, 217(8), 2605-2607. https://doi.org/10.1083/jcb.201806127CopyrightOther than for strictly personal use, it is not permitted to download or to forward/distribute the text or part of it without the consent of theauthor(s) and/or copyright holder(s), unless the work is under an open content license (like Creative Commons).The publication may also be distributed here under the terms of Article 25fa of the Dutch Copyright Act, indicated by the “Taverne” license.More information can be found on the University of Groningen website: https://www.rug.nl/library/open-access/self-archiving-pure/taverne-amendment.Take-down policyIf you believe that this document breaches copyright please contact us providing details, and we will remove access to the work immediatelyand investigate your claim.Downloaded from the University of Groningen/UMCG research database (Pure): http://www.rug.nl/research/portal. For technical reasons thenumber of authors shown on this cover page is limited to 10 maximum.Download date: 28-04-2023SPOTLIGHThttps://doi.org/10.1083/jcb.201806127 1J. Cell Biol. 2018Rockefeller University PressDuring micronucleophagy, the nucleolus is targeted by autophagic degradation, but although nucleolar proteins are recycled, ribosomal DNA is spared. Mostofa et al. (2018. J. Cell Biol. https://doi.org/10.1083/jcb.201706164) reveal that the separation of these two nucleolar components is mediated by the CLIP and cohibin complexes and is vital for cell survival during starvation.Sorting the trash: Micronucleophagy gets selectivePauline Verlhac and Fulvio ReggioriAutophagy is a catabolic process leading to the lysosomal/vac-uolar degradation of unwanted cellular components including aggregated proteins, damaged or superfluous organelles, and even pathogens (Galluzzi et al., 2017). This pathway, which is con-served from yeast to mammals, is crucial to maintain cell homeo-stasis and has numerous physiological implications relevant to human health (Deretic et al., 2013). Mitochondria, peroxisomes, the endoplasmic reticulum, and even portions of the nucleus can be targeted and degraded by autophagy under the orchestrated action of autophagy-related (Atg) proteins (Dikic and Elazar, 2018). Autophagic turnover of nuclear material is termed nucle-ophagy and has been described in two forms in yeast: macronuc-leophagy and micronucleophagy. Macronucleophagy involves the sequestration of a portion of the nucleus into autophagosomes and requires the autophagy receptor Atg39 (Mochida et al., 2015). The targeted nuclear material is subsequently delivered and eliminated in the vacuole upon autophagosome fusion with this organelle. During micronucleophagy, a portion of the nucleus is directly engulfed by the vacuole at the nuclear vacuole junction (NVJ), i.e., the NVJ invaginates and pinches off into the vacuolar lumen, leading to a subvacuolar vesicle that is consumed by res-ident hydrolases (Roberts et al., 2003). Both micro- and macro-nucleophagy sequester only a portion of the nucleus, indicating a specificity similar to the one observed in other selective types of autophagy such as mitophagy or pexophagy (Galluzzi et al., 2017). In particular, DNA is not degraded by these two processes, but how this is accomplished remained unknown.Mostofa et al. describe a mechanism allowing the separation of DNA from proteins during micronucleophagy induced by star-vation conditions in yeast (Fig. 1). They focused on the nucleolus, which has previously been shown to be targeted by micronucleo-phagy (Dawaliby and Mayer, 2010; Mochida et al., 2015). They re-veal that although nucleolar proteins are brought to the NVJ and delivered into the vacuole for turnover, ribosomal DNA (rDNA) is spared from degradation and kept in the nucleus (Fig. 1). This mechanism of separation requires the components of the two in-teracting nuclear complexes, chromosome linkage inner nuclear membrane protein (CLIP) and cohibin, which are composed by Heh1-Nur1 and Csm1-Lrs4, respectively. In cells lacking CLIP or cohibin subunits, rDNA and nucleolar proteins remain associ-ated, and although micronucleophagy is still functional, nucleolar proteins are not degraded. Interestingly, the absence of the CLIP or cohibin complex does not result in the aberrant degradation of rDNA. Thus, the CLIP and cohibin complexes are involved in repositioning of the rDNA away from nucleolar proteins but not in protection of rDNA or degradation of the micronucleophagic cargos per se (Fig. 1). Mostofa et al. (2018) also studied the spatio-temporal dynamics of micronucleophagy during starvation and observed that separation and repositioning of rDNA and nucleolar proteins occurs before the beginning of micronucleophagy. They also observed that these events depend on micronucleophagy as cells defective in this process but not NVJ formation did not show separation of nucleolar proteins and rDNA. Taken together, these findings indicate that separation and repositioning of nucleolar components and subsequent micronucleophagy are coordinated processes. This coordination is similar to the one observed be-tween the fission and Atg machineries during mitophagy and pexophagy (Mao et al., 2013, 2014) and could be essential to avoid rDNA degradation, which would be lethal for the cell. Finally, they found that cells lacking one of the subunits of the CLIP or cohibin complexes have reduced survival during starvation, highlighting that this parting between rDNA and nucleolar proteins could be necessary for cell survival under particular stresses.Very little is known about the mechanisms underlying micro-nucleophagy, and the study by Mostofa et al. (2018) is pioneering as it provides the crucial groundwork and specific assays for fu-ture investigations aimed at understanding this pathway and its relevance for the cell physiology under stress conditions and be-yond. By focusing on nucleolar DNA and proteins, they succeeded in answering the lingering question of how rDNA is protected © 2018 Verlhac and Reggiori This article is distributed under the terms of an Attribution–Noncommercial–Share Alike–No Mirror Sites license for the first six months after the publication date (see http:// www .rupress .org/ terms/ ). After six months it is available under a Creative Commons License (Attribution–Noncommercial–Share Alike 4.0 International license, as described at https:// creativecommons .org/ licenses/ by -nc -sa/ 4 .0/ ).Department of Cell Biology, University of Groningen, University Medical Center Groningen, Groningen, Netherlands.Correspondence to Fulvio Reggiori: f.m.reggiori@ umcg .nl. on July 19, 2018jcb.rupress.org Downloaded from http://doi.org/10.1083/jcb.201806127Published Online: 13 July, 2018 | Supp Info: Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061272during micronucleophagy. Their work demonstrates that cargo selection and sequestration are key features of nucleophagy as in other forms of selective autophagy. Therefore, this study re-inforces the paradigm that autophagic recycling is a meticulous process guarded by fail-safe mechanisms.It would be of high interest to decipher the precise physio-logical relevance of this repositioning of rDNA and nucleolar proteins. Although Mostofa et al. (2018) elegantly demonstrated the importance of the CLIP and cohibin complexes during micro-nucleophagy, they did so using knockout strains. Thus, it cannot be excluded a priori that the relevance of these complexes for cell survival during starvation observed by Mostofa et al. (2018) could be due to one or more other functions of these two complexes. It would therefore be important to generate and use point mutants or possibly ablate known binding partners of the CLIP and co-hibin complexes such as Sir2, Cdc14, Net1, Tof2, and rDNA-bind-ing Fob1 to more specifically address this physiological aspect.Specific mutants will also be key to address some aspects of the molecular mechanism of micronucleophagy. For example, how is DNA directed away and protected from degradation? Al-though the CLIP–cohibin system is required for rDNA separation, it appears to be unnecessary for its protection from degradation as rDNA is not turned over in the absence of these factors, al-though micronucleophagy still occurs. This suggests the exis-tence of a different mechanism to avoid delivery of rDNA, and possibly chromosomes in general, to the vacuole during both micro- and macronucleophagy.Furthermore, an aspect that will probably attract further re-search is the identification of the pathway that conveys TORC1 signaling into the nucleus to communicate both the reposition-ing of rDNA and the targeting to degradation of nucleolar pro-teins. TORC1 is a cytosolic complex that allows cells to adapt to environmental changes through an integrated orchestration of anabolic and catabolic pathways including micronucleophagy. Identifying the signaling axis that regulates micronucleophagy in the nucleus will help to understand intracellular communi-cation and the potential crosstalk of micronucleophagy with other processes and possibly cell death, a crosstalk suggested by the survival defect of cells lacking nucleophagy. An interesting candidate signaling axis could be the newly identified Nem1/Spo7-Pah1 cascade, which has been implicated in micro- and macronucleophagy induction notably through positioning of Atg39 and Nvj1, a SNA RE-mediating NVJ establishment (Rahman et al., 2018). Other lingering questions include determining whether a similar rDNA-sorting mechanism takes place during macronucleophagy and whether macronucleophagic cargoes are different from those of micronucleophagy.The findings from Mostofa et al. (2018) also provide fascinating new perspectives for the study of the precise physiological role(s) of micronucleophagy. First, the observation that micronucleoph-agy still occurs while the retargeting of rDNA and nucleolar pro-teins is impaired suggests that other nuclear components might be degraded through this pathway. Identifying such cargos would be crucial to better understand the cellular implications of an even-tual defect in micronucleophagy. Moreover, Mostofa et al. (2018) observed a reduced survival under starvation in cells where the repositioning is impaired but nucleophagy is still functional, in line with previous observations that nucleophagy is necessary for cell survival under stress. Nevertheless, the fact that impairing the repositioning alone is enough to induce a survival defect also suggests that either degradation of nucleolar proteins is capital or other cargos need to be degraded for cells to survive starvation.Intriguingly, the segregation mechanism described by Mostofa et al. (2018) shares some conceptual aspects with what was shown for mitophagy in yeast, where specific proteins are protected from degradation by forming intramitochondrial aggregates while others are preferentially turned over via seg-regation into the subdomains of the mitochondria targeted by mitophagy (Abeliovich et al., 2013). A similar phenomenon might be taking place during micro- and possibly macronucleophagy, where specific nuclear proteins are preferentially degraded and thus concentrated at the site of nucleophagy in a CLIP–cohibin system-dependent manner, whereas others could be protected by another system through, for example, a retention and/or ex-clusion mechanism. If some proteins are protected from micro-nucleophagy, it would be interesting to demonstrate whether the mechanism is similar to the one protecting rDNA. Conversely, it would be interesting to explore whether mitochondrial DNA is protected during mitophagy.Finally, although autophagy is highly conserved among eu-karyotes, the same cannot currently be said for nucleophagy. Nucleophagy has rarely been observed in mammalian cells and exclusively in pathological contexts (Park et al., 2009). The find-ings of Mostofa et al. (2018) provide the framework that could Figure 1. The role of CLIP and cohibin com-plexes in micronucleophagy. Nucleolar proteins, rDNA, and the cohibin complex are associated at nucleoli under growing conditions, while the CLIP complex is distributed over the entire inner side of the nuclear membrane. TORC1 inactivation triggers the association of nucleolar proteins with part of the CLIP complexes and their subsequent targeting to the NVJ, where they are included into the forming intravacuo-lar invagination. The pinch-off of this protrusion leads to the vacuolar turnover of both nucleolar proteins and the CLIP complex. In contrast, rDNA and cohibin remain associated and get separated from the nucleolar proteins to remain protected from micronucleophagic degradation.Verlhac and Reggiori Micronucleophagy gets selectiveJournal of Cell Biologyhttps://doi.org/10.1083/jcb.2018061273help elucidating whether micronucleophagy occurs in mamma-lian cells by studying for example the mammalian counterpart(s) of the CLIP and cohibin complexes. As Mostofa et al. (2018) stated in their study, it is also possible that the mechanisms of nucleo-phagy differ greatly between yeast and mammals. The answer could lie in the fact that key mammalian ATG components such as LC3 proteins, the homologues of yeast Atg8, are also present in the nucleus, but a role has not been assigned to this pool yet. Defects in selective types of autophagy like mitophagy, reticu-lophagy, and aggrephagy have been associated to severe human pathologies, and therefore, the modulation of these specific processes rather than the one of bulk autophagy has great ther-apeutic potential (Rubinsztein et al., 2012). It is thus crucial to determine the molecular mechanism and physiological functions of micronucleophagy in mammalian cells, and more in general, those of nucleophagy, as this could be relevant for human health.AcknowledgmentsWe thank Dr. Mario Mauthe for his critical reading of the manuscript. F. Reggiori is supported by ZonMW VICI (016.130.606), the Netherlands Organization for Scientific Research ALW Open Program (ALW OP.310), and the European Commission’s Marie Skłodowska-Curie Cofund (713660) and Marie Skłodowska-Curie Innovative Training Networks (765912) grants.The authors declare no competing financial interests.ReferencesAbeliovich, H., M. Zarei, K.T.G. Rigbolt, R.J. Youle, and J. Dengjel. 2013. In-volvement of mitochondrial dynamics in the segregation of mitochon-drial matrix proteins during stationary phase mitophagy. Nat. Commun. 4:2789. https:// doi .org/ 10 .1038/ ncomms3789Dawaliby, R., and A. Mayer. 2010. Microautophagy of the nucleus coincides with a vacuolar diffusion barrier at nuclear-vacuolar junctions. Mol. Biol. Cell. 21:4173–4183. https:// doi .org/ 10 .1091/ mbc .e09 -09 -0782Deretic, V., T. Saitoh, and S. Akira. 2013. Autophagy in infection, inflammation and immunity. Nat. Rev. Immunol. 13:722–737. https:// doi .org/ 10 .1038/ nri3532Dikic, I., and Z. Elazar. 2018. Mechanism and medical implications of mam-malian autophagy. Nat. Rev. Mol. Cell Biol. 19:349–364. https:// doi .org/ 10 .1038/ s41580 -018 -0003 -4Galluzzi, L., E.H. Baehrecke, A. Ballabio, P. Boya, J.M. Bravo-San Pedro, F. Cec-coni, A.M. Choi, C.T. Chu, P. Codogno, M.I. Colombo, et al. 2017. Molecu-lar definitions of autophagy and related processes. EMBO J. 36:1811–1836. https:// doi .org/ 10 .15252/ embj .201796697Mao, K., K. Wang, X. Liu, and D.J. Klionsky. 2013. The scaffold protein Atg11 recruits fission machinery to drive selective mitochondria degradation by autophagy. Dev. Cell. 26:9–18. https:// doi .org/ 10 .1016/ j .devcel .2013 .05 .024Mao, K., X. Liu, Y. Feng, and D.J. Klionsky. 2014. The progression of peroxi-somal degradation through autophagy requires peroxisomal division. Autophagy. 10:652–661. https:// doi .org/ 10 .4161/ auto .27852Mochida, K., Y. Oikawa, Y. Kimura, H. Kirisako, H. Hirano, Y. Ohsumi, and H. Nakatogawa. 2015. Receptor-mediated selective autophagy degrades the endoplasmic reticulum and the nucleus. Nature. 522:359–362. https:// doi .org/ 10 .1038/ nature14506Mostofa, G.M., M.A. Rahman, N. Koike, A.M.S.T. Yeasmin, N. Islam, T.M. Wa-liullah, S. Hosoyamada, M. Shimobayashi, T. Kobayashi, M.N. Hall, et al. 2018. CLIP and cohibin separate rDNA from nucleolar proteins destined for degradation by nucleophagy. J. Cell Biol. https:// doi .org/ 10 .1083/ jcb .201706164Park, Y.E., Y.K. Hayashi, G. Bonne, T. Arimura, S. Noguchi, I. Nonaka, and I. Nishino. 2009. Autophagic degradation of nuclear components in mam-malian cells. Autophagy. 5:795–804. https:// doi .org/ 10 .4161/ auto .8901Rahman, M.A., M.G. Mostofa, and T. Ushimaru. 2018. The Nem1/Spo7-Pah1/lipin axis is required for autophagy induction after TORC1 inactivation. FEBS J. 285:1840–1860. https:// doi .org/ 10 .1111/ febs .14448Roberts, P., S. Moshitch-Moshkovitz, E. Kvam, E. O’Toole, M. Winey, and D.S. Goldfarb. 2003. Piecemeal microautophagy of nucleus in Saccharomy-ces cerevisiae. Mol. Biol. Cell. 14:129–141. https:// doi .org/ 10 .1091/ mbc .e02 -08 -0483Rubinsztein, D.C., P. Codogno, and B. Levine. 2012. Autophagy modulation as a potential therapeutic target for diverse diseases. Nat. Rev. Drug Discov. 11:709–730. https:// doi .org/ 10 .1038/ nrd3802

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