Role of the AAA protease Yme1 in folding of proteins in the mitochondrial intermembrane space

The vast majority of mitochondrial proteins are encoded in the
nucleus and synthesized as precursor proteins on cytosolic
ribosomes. After translation, these precursor proteins are imported
in a largely, if not completely, unfolded state into one of the
four mitochondrial subcompartments, the outer membrane, the
intermembrane space, the inner membrane or the matrix. Once the
precursor proteins reach their compartment of destination, they can
fold into the functionally active three-dimensional native
structure. Therefore, internal mitochondrial folding systems are
needed in each subcompartment to assist folding of these precursor
proteins upon import. Members of several “classical” chaperone
families are present in the mitochondrial matrix and have been
shown to support import and folding of newly imported polypeptides.
However, folding of proteins in the mitochondrial intermembrane
space is only poorly understood. Recently, a disulfide relay system
in the intermembrane space that mediates import and folding was
described, but this system is limited to proteins that form
disulfide bonds. For the majority of intermembrane proteins,
folding helpers that promote folding have not yet been discovered.
In order to identify general folding helpers of the intermembrane
space, the well studied model substrate mouse dihydrofolate
reductase (DHFR) was targeted to the mitochondrial intermembrane
space of S. cerevisiae and its folding analyzed. DHFR assumes its
mature fold in the intermembrane space and heat shock induces DHFR
aggregation. Interestingly, aggregation is counteracted by an
ATP-dependent process. The i-AAA protease Yme1 that is anchored in
the inner mitochondrial membrane and exposes its functional domains
to the intermembrane space was able to prevent the aggregation of
DHFR. A number of proteins of diverse structural and functional
classes were found in the aggregate fractions of mitochondria
lacking Yme1. Amongst them were factors that are involved in the
establishment and maintenance of the mitochondrial ultrastructure,
lipid metabolism, protein translocation and respiratory growth.
Considering the diversity of the proteins affected in the absence
of Yme1 and their function in mitochondria, the pleiotropic effects
of the deletion of Yme1 can be readily explained. The findings of
the present in vivo study confirm previous hints to a
chaperone-like function of Yme1 resulting from in vitro
experiments. Yme1 thus has a dual role as protease and as chaperone
and occupies a key position in the protein quality control system
of the mitochondrial intermembrane space.