PDZD8 is a functional metazoan orthologue of the ERMES subunit Mmm1, in budding yeast

Identification: Pernice, Wolfgang


PDZD8 is a functional metazoan orthologue of the ERMES subunit Mmm1, in budding yeast
Wolfgang M. Pernice5#, Yusuke Hirabayashi1-4#, Donald S. Petrey6-7, Liza A. Pon5 and Franck Polleux1-3 *
1Department of Neuroscience, Columbia University Medical Center, 2Mortimer B. Zuckerman Mind Brain Behavior Institute, 3Kavli Institute for Brain Science, 4JST, PRESTO, 5Department of Pathology and Cell Biology, Columbia University, 6Center for Computational Biology and Bioinformatics, 7Department of Systems Biology, Columbia University, New York, NY 10032, USA
#equal contribution, *Corresponding author
ER-mitochondrial contact sites (ERMCs) have emerged as central metabolic and signaling hubs. Next to roles in Ca2+ transfer, and the regulation of mitochondrial fission and genome replication, one primary ERMC-function is lipid-exchange between the two organelles. Our recent results (Hirabayashi et al., 2017) revealed that the largely uncharacterized protein, PDZD8, functions as a bona fide ER-mitochondrial tethering protein in mammalian cells and is required for Ca2+ transport between ER and mitochondria.  In budding yeast, the ER-mitochondrial encounter structure (ERMES) forms the primary ER-mitochondrial tethering complex and is required for a majority of ERMC-associated functions. Three of four ERMES-subunits contain the synaptotagmin-like mitochondrial-lipid binding protein (SMP) domain that is implicated in direct lipid-transfer. We employed structural homology modeling to query the mammalian proteome for SMP-proteins as potential ERMES orthologues. We find that, like Mmm1, mammalian PDZD8 contains an N-terminal transmembrane (TM) followed by a predicted SMP-domain. PDZD8 also localizes to the ER and is present at ERCMs in mammalian cells and when expressed in yeast. Despite these predictions we find that PDZD8 and Mmm1 SMP-domains are not functionally equivalent. However, we find that structural divergence between mammalian and yeast SMP-domains remains limited to two small 'hyper-variable' loops within the SMP β-sheet, and we demonstrate, that accounting for these, SMP-domains between PDZD8 and ERMES' Mdm12 and Mmm1 are functionally complimentary. Finally, we show this allows for functional complementation of Mmm1 by expression of the N-terminal half of PDZD8 (containing TM and SMP-domains). These results (1) demonstrate functional equivalence of SMP-domains and (2) suggest that PDZD8 may be a functional orthologue of ERMES' Mmm1 in metazoans.


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