Science - 16.08.2019

respectively, might also counteract this inexora-
ble mutation accumulation in somatic cells.

Quality control processes to cope with
mitochondrial burdens

Of the originala-proteobacterial genes, most of
those that survived migrated to the nucleus over
time. Of the thousand or so mitochondrial pro-
teins in mammals, only 13 remain encoded in
the mtDNA today. Perhaps one driver for gene
migration from the mitochondrial genome to
the nucleus is to coordinate protein expression
transcriptionally and minimize proteotoxic dispro-
portionality among proteins working together in
the same pathway. Alternatively, gene transfer to
the nucleus could leave less mtDNA vulnerable
to Muller’s ratchet ( 10 ). The 13 mtDNA protein-
coding genes remaining in humans encode sub-
units of four large multisubunit protein complexes
(named I, III, IV, and V) embedded in the inner
mitochondrial membrane that are involved in
oxidative phosphorylation (Ox/Phos). Why these
few genes remain encoded in mtDNA is not clear;
hypotheses center around challenges of trans-
ferring hydrophobic membrane proteins through
the hydrophilic channelsof the translocator of the
outer membrane (TOM) and translocator of the
inner membrane (TIM) protein import channels
(Fig. 1), or mechanisms to insert hydrophobic
proteins central to large protein complexes in the
inner membrane ( 11 ). All the soluble metabolic
and tricarboxylic acid (TCA) cycle enzymes located
in the mitochondrial matrix are encoded in the
nucleus, where their expression is coordinated.
Recent work shows that mtDNA-encoded Ox/Phos
subunit expression is indeed coordinated with
nuclear encoded Ox/Phos protein expression
and is regulated mainly at the translational level
( 2 , 12 ), and that mtDNA protein expression is
tuned unidirectionally based on expression levels
of nuclear encoded mitochondrial proteins ( 13 ).
How mtDNA-encoded protein translation is linked
to nuclear encoded protein complex assembly is
becoming more clear ( 14 ).
Beyond regulation of RNA transcription and
protein translation, backup processes on the de-
gradation side of protein homeostasis deal with
ensuing proteotoxic stress in several different com-
partments: the cytosol, the mitochondrial matrix,
and in the two mitochondrial membranes (Fig. 1).
Proteolysis in the mitochondrial matrix largely
rebalances protein complex subunit stoichiome-
try by eliminating excess proteins imported from
cytosolic translation of nuclear genes or trans-
lated in the matrix from mtDNA-encoded genes
that misfold in the absence of interacting partners
from the alternate genome ( 15 ). Piecemeal au-
tophagy of mitochondrialsubregions or fragments
(Fig. 2A) may also play a role in extreme cases of
protein misfolding, and mitochondria-derived
vesicles may directly target outer mitochondrial
membrane proteins to lysosomes ( 16 – 19 ).
Aspects of mitochondrial protein quality control
have been known for many years. The proteases
Lon and ClpX/P in the matrix, Yme1 anchored
to the mitochondrial inner membrane facing the
intermembrane space, and AFG3L2/SPG7 an-

chored to the mitochondrial inner membrane

facing the matrix are at the center of protein

quality control proteolysis ( 15 ). They are all ATP-

dependent, AAA adenosinetriphosphatase (ATPase)

proteases with unfoldase activity that degrade

misfolded and superfluous proteins. These AAA

ATPases are all conserved in bacteria and represent

primordial quality control mechanisms ( 20 ).

A recent series of studies has revealed other

pathways that deal with unfolded or misfolded

matrix proteins and mitochondrial import de-

fects. Transcription of certain nuclear encoded

mitochondrial proteins is regulated by mito-

chondrial proteotoxic stress, leading to increased

expression of mitochondrial chaperones that help

fold proteins and proteases that degrade mis-

folded proteins. The original mammalian model

to induce a mitochondrial unfolded protein re-

sponse used overexpression of a deletion mutant

of a mitochondrial protein, ornithine transcar-

bamylase (DOTC), which becomes insoluble in

the matrix ( 21 ).DOTC expression in mammalian

cells activates expression of the HSP60 chap-

eronin and protease ClpP in mitochondria ( 21 ).

Chemical inhibition of Lon protease or the Hsp90

chaperone in mammalian cells also induces HSP60

expression ( 22 ). Autophagy can also eliminate mis-

foldedDOTC selectively relative to other mito-

chondrial proteins ( 23 ). This would be consistent

with a piecemeal or bit-by-bit mitophagy of mito-

chondrial subdomains (Fig. 2A) ( 18 , 24 ).

InCaenorhabditis elegans, mechanistic under-

standing of how the mitochondrial unfolded pro-

tein response activates transcription has been

delineated ( 25 ). A transcription factor, ATFS-1,

has both a mitochondrial import signal and a

nuclear localization signal and is normally im-

ported into mitochondria, degraded, and thereby

repressed ( 26 ). Upon proteotoxic stress or other

stresses that impair mitochondrial protein im-

port, such as loss of mitochondrial membrane

potential, ATFS-1 escapes elimination through

mitochondrial import andtraffics to the nucleus to

induce transcription of avariety of mitochondrial

genes, including the chaperonin HSP60 (Fig. 3).

As mitochondria recover from proteotoxic stress,

they proceed to down-regulate ATFS-1 through

import and degradation. Atf4 and Atf5 have roles

in mitochondrial stress maintenance and appear

to function as mammalian orthologs of ATFS-

1( 22 , 27 , 28 ). In mammals, mammalian target of

rapamycin complex 1 (mTORC1) orchestrates a

transcriptional response to myopathy caused by

mtDNA deletions. Atf4 and Atf5, one-carbon metab-

olism leading to tetrahydrofolate formylation,

and the metabolic cytokine FGF21 are all induced

by this form of mitochondrial stress ( 29 ).

Using yeast, a series of recent studies explored

the consequences of mitochondrial protein import

blockade or mitochondrial membrane protein mis-

folding.Adecreaseincytosolic protein translation

occurs upon mitochondrial proteotoxic stress as

well as improved proteasome subunit assembly,

which is required for cells to cope with the pro-

teotoxic stress ( 30 , 31 ). When hydrophobic inner

mitochondrial membrane proteins are over-

expressed,theymayclogtheTOM/TIMimportchan-

nels.Cis1andMsp1bindtotheTOMcomplexand

clear excess import imtermediates (Fig. 1) ( 32 ). Msp1

in yeast and the ortholog ATAD1 in mammals also

Youle,Science 365 , eaaw9855 (2019) 16 August 2019 2of7

Phagophore

Phagophore

Protein aggregates

Membrane

depolarization

A

B

Piecemeal mitophagy

Wholesale mitophagy

Pink1

Ulk1

Parkin

OPTN, NDP52

Fig. 2. Selective autophagy of mitochondrial proteins is a quality control process.

(A) Piecemeal, also called bit by bit, mitophagy removes mitochondrial subdomains, which can

selectively eliminate protein aggregates in the matrix. (B) Wholesale mitophagy of damaged

and depolarized mitochondria mediated by PINK1/Parkin is suggested to mediate quality control

and elimination of mitochondrial DAMPs to avoid inflammation.

RESEARCH | REVIEW