Structural insights into unique features of the human mitochondrial ribosome recycling
Ravi K. Koripella, Manjuli R. Sharma, Paul Risteff, Pooja Keshavan, and Rajendra K. Agrawal
PNAS published ahead of print April 8, 2019
Edited by Yale E. Goldman, Pennsylvania Muscle Institute, University of Pennsylvania, Philadelphia, PA, and approved March 15, 2019 (received for review September 11, 2018)
Significance
The human mitochondrial ribosome (mitoribosome) recycling factor (RRFmt) is known to play essential roles in mitochondrial physiology, including protein synthesis, and it has been implicated in human genetic diseases. The RRFmt is among the few protein molecules that carry their N-terminal signal peptide sequence into the mitochondrial matrix that is required for RRFmt’s interaction with the mitoribosome. In this study, we present a cryo-electron microscopic structure of the human mitoribosome in complex with the RRFmt. The structure reveals hitherto unknown features of RRFmt and its interactions with the functionally important regions of the ribosomal RNA that constitute the peptidyl-transferase center and that are linked to the GTPase-associated center of the mitoribosome, shedding light on the mechanism of ribosome recycling in mitochondria.
Abstract
Mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing proteins that are essential for oxidative phosphorylation (ATP generation). Despite their common ancestry with bacteria, the composition and structure of the human mitoribosome and its translational factors are significantly different from those of their bacterial counterparts. The mammalian mitoribosome recycling factor (RRFmt) carries a mito-specific N terminus extension (NTE), which is necessary for the function of RRFmt. Here we present a 3.9-Å resolution cryo-electron microscopic (cryo-EM) structure of the human 55S mitoribosome-RRFmt complex, which reveals α-helix and loop structures for the NTE that makes multiple mito-specific interactions with functionally critical regions of the mitoribosome. These include ribosomal RNA segments that constitute the peptidyl transferase center (PTC) and those that connect PTC with the GTPase-associated center and with mitoribosomal proteins L16 and L27. Our structure reveals the presence of a tRNA in the pe/E position and a rotation of the small mitoribosomal subunit on RRFmt binding. In addition, we observe an interaction between the pe/E tRNA and a mito-specific protein, mL64. These findings help understand the unique features of mitoribosome recycling.
human mitochondrial RRFmito-specific sequence55S–RRFmt complexcryo-EM structuremito-specific interactions
Footnotes
↵1Present address: Charles River Laboratories Inc., Durham, NC 27703.
↵2To whom correspondence should be addressed. Email: Rajendra.Agrawal@health.ny.gov.
Author contributions: R.K.A. designed research; R.K.K., M.R.S., P.R., and P.K. performed research; R.K.K., M.R.S., and R.K.A. analyzed data; and R.K.K., M.R.S., and R.K.A. wrote the paper.
The authors declare no conflict of interest.
This article is a PNAS Direct Submission.
Data deposition: The cryo-EM maps and atomic coordinates have been deposited in the Electron Microscopy and PDB Data Bank (www.wwpdb.org) under accession codes EMD-0514 and PDB ID 6NU2, respectively, for the RRFmt-bound 55S mitoribosome (Complex I) and EMD-0515 and PDB ID 6NU3, respectively, for the unbound 55S mitoribosome (Complex II).
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Copyright © 2019 the Author(s). Published by PNAS.
