Journal: Genome Biol Evol / Year: 2015 Title: Parallel Structural Evolution of Mitochondrial Ribosomes and OXPHOS Complexes. Authors: Eli O van der Sluis / Heike Bauerschmitt / Thomas Becker / Thorsten Mielke / Jens Frauenfeld / Otto Berninghausen / Walter Neupert / Johannes M Herrmann / Roland Beckmann / Abstract: The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which ...The five macromolecular complexes that jointly mediate oxidative phosphorylation (OXPHOS) in mitochondria consist of many more subunits than those of bacteria, yet, it remains unclear by which evolutionary mechanism(s) these novel subunits were recruited. Even less well understood is the structural evolution of mitochondrial ribosomes (mitoribosomes): while it was long thought that their exceptionally high protein content would physically compensate for their uniquely low amount of ribosomal RNA (rRNA), this hypothesis has been refuted by structural studies. Here, we present a cryo-electron microscopy structure of the 73S mitoribosome from Neurospora crassa, together with genomic and proteomic analyses of mitoribosome composition across the eukaryotic domain. Surprisingly, our findings reveal that both structurally and compositionally, mitoribosomes have evolved very similarly to mitochondrial OXPHOS complexes via two distinct phases: A constructive phase that mainly acted early in eukaryote evolution, resulting in the recruitment of altogether approximately 75 novel subunits, and a reductive phase that acted during metazoan evolution, resulting in gradual length-reduction of mitochondrially encoded rRNAs and OXPHOS proteins. Both phases can be well explained by the accumulation of (slightly) deleterious mutations and deletions, respectively, in mitochondrially encoded rRNAs and OXPHOS proteins. We argue that the main role of the newly recruited (nuclear encoded) ribosomal- and OXPHOS proteins is to provide structural compensation to the mutationally destabilized mitochondrially encoded components. While the newly recruited proteins probably provide a selective advantage owing to their compensatory nature, and while their presence may have opened evolutionary pathways toward novel mitochondrion-specific functions, we emphasize that the initial events that resulted in their recruitment was nonadaptive in nature. Our framework is supported by population genetic studies, and it can explain the complete structural evolution of mitochondrial ribosomes and OXPHOS complexes, as well as many observed functions of individual proteins.
History
Deposition
Apr 27, 2015
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Header (metadata) release
May 13, 2015
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Map release
May 13, 2015
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Update
Jun 3, 2015
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Current status
Jun 3, 2015
Processing site: RCSB / Status: Released
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Structure visualization
Movie
Surface view with section colored by density value
pH: 7.5 Details: 30 mM Tris-HCl, pH 7.5, 100 mM NH4Cl, 10 mM MgCl2, 4 mM 2-mercaptoethanol, 0.05% beta-D dodecyl maltoside, 0.0075% cardiolipin
Grid
Details: Quantifoil grids pre-coated with 2 nm carbon on top
Vitrification
Cryogen name: ETHANE / Chamber humidity: 95 % / Chamber temperature: 95 K / Instrument: FEI VITROBOT MARK IV / Method: Blot for 3 seconds before plunging
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Electron microscopy
Microscope
FEI POLARA 300
Date
Apr 10, 2008
Image recording
Category: FILM / Film or detector model: KODAK SO-163 FILM / Digitization - Scanner: PRIMESCAN / Number real images: 132 / Average electron dose: 20 e/Å2 / Bits/pixel: 16
Electron beam
Acceleration voltage: 300 kV / Electron source: FIELD EMISSION GUN
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