Table Of ContentSPRINGER BRIEFS IN CELL BIOLOGY
Eleftherios Karanasios
Nicholas T. Ktistakis
Autophagy at the
Cell, Tissue and
Organismal Level
123
SpringerBriefs in Cell Biology
More information about this series at http://www.springer.com/series/10708
Eleftherios Karanasios Nicholas T. Ktistakis
(cid:129)
Autophagy at the Cell, Tissue
and Organismal Level
123
Eleftherios Karanasios NicholasT. Ktistakis
Babraham Institute Babraham Institute
Babraham, Cambridge Babraham, Cambridge
UK UK
SpringerBriefs inCell Biology
ISBN978-3-319-33143-0 ISBN978-3-319-33145-4 (eBook)
DOI 10.1007/978-3-319-33145-4
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Contents
1 Autophagy (Autophagia) from 1860 to 1963 . . . . . . . . . . . . . . . . . . 1
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 5
2 History of Autophagy After 1963 . . . . . . . . . . . . . . . . . . . . . . . . . . 7
2.1 The First Morphological Studies . . . . . . . . . . . . . . . . . . . . . . . 7
2.2 The First Functional Studies . . . . . . . . . . . . . . . . . . . . . . . . . . 9
2.3 Difficulties in the Study of Autophagy . . . . . . . . . . . . . . . . . . . 9
2.4 Molecular Era—Identification of Autophagy Genes in Yeast. . . . 10
2.5 Identification of Autophagy Genes in Mammals. . . . . . . . . . . . . 12
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 13
3 Signalling in Autophagy. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 17
3.1 Basal Versus Induced Autophagy. . . . . . . . . . . . . . . . . . . . . . . 17
3.2 Provenance of Autophagy Signals and Their Function . . . . . . . . 19
3.3 mTORC1 is the Major Signalling Hub for Autophagy
Regulation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 22
3.4 Signalling via AMPK. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 26
3.5 Autophagy Signals Independent of mTORC1 . . . . . . . . . . . . . . 26
3.6 Signals that Terminate Autophagy. . . . . . . . . . . . . . . . . . . . . . 27
3.7 Signalling to Autophagy Versus Apoptosis/Cell Death . . . . . . . . 29
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 30
4 Autophagosome Formation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
4.1 Types of Autophagy . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 35
4.2 Steps of Autophagosome Formation. . . . . . . . . . . . . . . . . . . . . 36
4.3 ULK Complex . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 38
4.4 VPS34 Complex and PI3P Effectors. . . . . . . . . . . . . . . . . . . . . 39
4.5 LC3 Lipidation Machinery . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.6 ATG9 . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 40
4.7 Receptor Proteins. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 41
v
vi Contents
4.8 Structural Studies of the Autophagy Machinery. . . . . . . . . . . . . 42
4.9 Membrane Source . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 43
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 45
5 Physiological Role of Autophagy and Implications in Disease. . . . . . 51
5.1 Transgenic Mice . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 51
5.2 Autophagy in Development. . . . . . . . . . . . . . . . . . . . . . . . . . . 52
5.3 Autophagy in Cell Differentiation . . . . . . . . . . . . . . . . . . . . . . 53
5.3.1 Erythrocytes and Lymphocytes . . . . . . . . . . . . . . . . . . 53
5.3.2 Adipocytes . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 53
5.4 Autophagy in Immunity . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 54
5.5 Defending the Cytosol: Autophagy as a Primitive Immune
Response Against Pathogens. . . . . . . . . . . . . . . . . . . . . . . . . . 55
5.6 Autophagy and the Inflammatory Response. . . . . . . . . . . . . . . . 58
5.7 Autophagy and Unconventional Secretion of Cytokines . . . . . . . 60
5.8 Autophagy Involvement in Antigen Processing
and Presentation . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 60
5.8.1 Autophagy has a Role in the Development
and Function of T and B Cells . . . . . . . . . . . . . . . . . . 61
5.9 Autophagy in Disease . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
5.10 Autophagy in Ageing. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 62
5.11 Autophagy in Neurodegeneration. . . . . . . . . . . . . . . . . . . . . . . 64
5.11.1 Alzheimer’s Disease. . . . . . . . . . . . . . . . . . . . . . . . . . 64
5.11.2 Parkinson’s Disease. . . . . . . . . . . . . . . . . . . . . . . . . . 64
5.11.3 Huntington’s Disease . . . . . . . . . . . . . . . . . . . . . . . . . 65
5.11.4 Amyotrophic Lateral Sclerosis. . . . . . . . . . . . . . . . . . . 66
5.11.5 Therapeutic Strategies. . . . . . . . . . . . . . . . . . . . . . . . . 66
5.12 Autophagy in Cancer. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 67
References. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 68
6 Studying Autophagy: List of Useful Antibodies Produced
via a Community Effort. . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . . 81
Chapter 1
Autophagy(Autophagia)from1860to1963
Abstract This chapter provides a historical perspective on the term autophagy
before its first coinage by Christian de Duve in 1963 to signify its current usage.
Nihil fit ex nihilo…
(cid:1) (cid:1)
Keywords Autophagy Autophagia History
Despiteitsstatusasawell-acceptedfactinthefield,theterm“autophagy”wasnot
originated (or invented) in 1963 by Christian de Duve.
An article by M. Auselmier in the Journal Progress of Medical Science from
January 28, 1860 states: “Experimental researches made on animals subjected to a
moreorlessabsoluteprivationoffoodhaveshownthatlifemaybemaintainedfora
certain period at the expense of the substance of the organs, as is proved by the
progressive diminution of the weight of the animal suffering from inanition. This
modeofnutritionhaslongbeentermedautophagy…”(M.Auselmier,OnNutrition
by Blood in Starvation, Selections from Foreign Journals, in Progress of Medical
Science p 98, 1860). So “autophagy” was certainly known to the scientific com-
munityataround1860,andperhapsearlier(wehavenotbeenabletofindawritten
reference to the word earlier).
In a book titled “The skim-milk treatment of diabetes and Bright’s disease” by
Arthur Scott Donkin and published in 1871, the author describes symptoms of
diabetesasdescribedbyanotherphysicianthus:“Thetermautophagia,appliedby
Dr. Jaccoud to designate the emaciation produced by the disease, is certainly
objectionable, inasmuch as he uses it to imply the operation of a cause of very
doubtfulexistence,namely:theproductionofdiabeticsugar outofthealbuminous
tissues of the body” (Arhur Scott Donkin, The Skim-Milk Treatment of Diabetes
and Bright’s Disease, p 63, Longmans, Green and Co, London 1871). The
“Dr. Jaccoud” referred to here is Francois Sigismond Jaccoud (1830–1913), a
Swiss-born French-educated physician of “Jaccoud arthropathy” fame who
described and researched several diseases including tuberculosis, rheumatic fever
and diabetes, publishing frequently his work in Dictionnaire de Medecine et de
Chirurgie pratiques. His description of the five stages of diabetes (glycosuria,
©TheAuthor(s)2016 1
E.KaranasiosandN.T.Ktistakis,AutophagyattheCell,Tissue
andOrganismalLevel,SpringerBriefsinCellBiology,
DOI10.1007/978-3-319-33145-4_1
2 1 Autophagy(Autophagia)from1860to1963
polyuria, polydipsia, polyphagia, autophagia) published in 1869 (Sigismond
Jaccoud,NouveauDietdeMM.etdeChirurg.pratiq.torn.xi248,Paris1869),was
influentialinthenineteenthandearlytwentiethcentury,andtheterm“autophagia”
is widely connected with this disease in the literature of the time.
An article by Augusto Bonazzi in the Journal of Bacteriology from 1921 refers
to Azotobacter “autophagy” as a phase of growth whereby an “organism is really
living onitsown reservesandtheby-products ofitsprevious lifeactivities, justas
yeast will continue to live in a fermented mixture at the expense of the glycogen,
glycerol and succinic acid which it formed during the early stages of development
and active fermentation” (Bonazzi 1921). What was being described by Bonazzi
aroseasaresultofaprobleminmetabolicmeasurementsofAzotobacter,whereby
quantities of sugar formed during normal growth were unaccounted for in the
secreted metabolites. At the same time, it was noticed that under normal growth
conditions the cells were filed with granules which, however, disappeared upon
starvation.Thisledtothehypothesisthatduringnormalgrowth,cellswerestoring
excess sugar in some type of granule to be attacked later under conditions of
starvation. Interestingly, several subsequent papers concerned themselves with the
question of whether the granules were alive or dead matter and of their exact
composition[discussedin(Lewis1937)].AsdiscussedbyBonazziandothers,this
concept of re-utilising stored nutrients to prolong life during starvation was in fact
described by the French biologist Jacques Duclaux (the discoverer of enzyme
adaptation and one of Pasteur’s collaborators; http://www.encyclopedia.com/doc/
1G2-2830901240.html) earlier with the almost philosophical term “phènoméne de
vie continuée”.
Other uses of the term autophagy before de Duve are evident in the scientific
literature. The finding that bacterial stabs above a certain size and stored for a few
daystendedtocontainnon-viablecellsattheperipherybutviablecellsatthecentre
was taken to indicate some life-sustaining process—termed “autophagy”—taking
place within the cells of the central region [(Hartsell 1953) quoting Korinek et al.
(Korinek,J.,Jirsak,J.,Jirsakova,A.,Starka,J.Thenutritionofthebacterialcolony
BullInternatl.Cl.Sci.Math.,Nat.etMed.Acad.TchequesSci,50:1–71951.Biol
Abstracts 26: 15475, 1952)]. Perhaps the most literal (and gory!) use of the term
autophagypre-deDuvewasindescriptionsoftheeatinghabitsofvariousspeciesof
insects such as the weta of New Zealand (Richards 1954). Together with many
instancesofcannibalism,especiallyduringthematingseason,exampleswerenoted
by Richards where both male and female specimens kept alone in captivity but in
fedconditionsbrokeoffpartsoftheirownlimbsandatethem.Suchbehaviourwas
wide spread enough to become part of the regular characterization of the feeding
habits of other animals such as lizards [which apparently engaged in cannibalism
but not autophagy, see for example (Lewis 1951)].
A most surprising and prescient use of the term autophagy is found not only in
the scientific literature, but also in an essay by the Italian writer Italo Svevo
(pseudonym of Aron Ettore Schmitz) who is considered as Italy’s first Modernist
andwasgreatlyadmiredbyJamesJoyceamongothers(http://www.famousauthors.
org/italo-svevo). Svevo’s writings are semi-autobiographical and, although
1 Autophagy(Autophagia)from1860to1963 3
seemingly simple, have the ability to engage the reader’s attention and draw them
intotheisolatedworldofthetextnotunliketheworkofProust.Belowisasection
from an essay by Italo Svevo written in 1928 and translated into English in 1952.
We provide both the original text from 1928 as well as the English translation to
show that the word autophagy (autophagia in Italian) was actually used by Svevo
and in a context bearing remarkable similarity to what we currently understand to
be the connection between autophagy and well-being at the organismal level.
Il mio ozio, Italo Svevo (1861–1928), from Corto viaggio sentimentale (1928)
DevoquiconfessarecheilmiodimagrimentolodevoproprioaCarlo.Fuunodei
suoi primi successi curativi. Egli mi propose di saltare uno dei tre miei pasti
quotidianiediorisolsidisacrificarelacenachenoiaTriesteprendiamoalleotto
diseraadifferenzadeglialtriitalianichefannocolazioneamezzodìeprendonoil
pranzo alle sette. In ogni giorno digiuno ininterrottamente per diciott’ore.
Intantodormiimeglio.Sentiisubitocheilcuorenonoccupatopiùdaltravaglio
della digestione poteva dedicare ogni suo battito ad irrorare le vene, ad allon-
tanare I detriti dall’organismo, a nutrire soprattutto i polmoni. Io che avevo già
provato l’orrenda insonnia, l’agitazione enorme di chi anela alla pace e proprio
perciòlasmarrisce,giacevolàinerteadattenderepacificoilcaloreeilsonnoche
arrivava lungo, una vera parentesi nella vita affaticante. Il sonno dopo la lauta
colazione è tutt’altra cosa: Allora il cuore provvede alla sola digestione ed è
esonerato da qualunque altra cura.
Si provò così prima di tutto ch’io ero meglio adatto ad astenermi che a mod-
erarmi. Era più facile non cenare affatto che limitare il cibo a colazione e di
mattina. Qui non c’erano oramai altre limitazioni. Due volte al giorno potevo
mangiare quanto volevo. Ciò non nuoceva perché poi seguivano 18 ore di aut-
ofagia.Inunprimotempolacolazionedipastaasciuttaelegumieracompletatada
alcune uova. Poi abolii anche queste non per volere del Raulli o di Carlo ma in
seguitoaiconsigliassennatidiunfilosofo,ErbertoSpencer,ilqualescoperseuna
certa legge per cui gli organi che—per sovranutrizione –si sviluppano troppo
rapidamente,sonomenofortidiquellicheimpieganomaggiortempoacrescere.Si
trattava di bambini, naturalmente, ma io sono convinto che il ricambio sia
anch’essounosviluppoecheancheunbambinodisettant’annifabeneadamarei
suoi organi piuttosto che sovranutrirli. Poi Carlo fu molto d’accordo col mio
teorema anzi talvolta vorrebbe far credere di averlo inventato lui.
This indolence of mine (Il mio ozio), Italo Svevo, transl by Ben Johnson, The
Hudson Review Vol 4, No. 4 (Winter, 1952)
AndhereImustconfessthatIreallyowemylossofweighttoCarlo.Itwasoneof
hisfirstcurativesuccesses.HeproposedthatIforegooneofmythreedailymeals;
andIresolved tosacrificesupper,whichweTriestinestake ateight intheevening
unlikeotherItalianswhohavelunchatnoonanddinneratseven. EverydayIfast
uninterruptedly for eighteen hours.
First of all, I slept better. I felt at once that my heart, no longer assisting in
digestivework,coulddevoteeverybeattofillingtheveins,tocarryingwastematter
