Structure of mitochondrial ribosome is revealed

The highly divergent ribosomes of human mitochondria (mitoribosomes) synthesize 13 essential proteins of oxidative phosphorylation complexes. A project to determine the structure of mitoribosome has resulted in the 3.5 Å resolution structure of the intact human mitoribosome, revealing a network of 80 proteins, 36 of which are specific to mitochondria, and mt-tRNA-Val, newly discovered rRNA.

HFSP Long-Term Fellow Alexey Amunts and colleagues
authored on Thu, 09 April 2015

The road towards revealing the structure of human mitoribosome was bedeviled by two main difficulties: their low abundance in the cell (1/1000 of cytoplasmic ribosomes) and high heterogeneity, which made them unreachable by X-ray crystallography. To overcome this, Venki Ramakrishnan and Sjors Scheres' labs have pioneered cryo-EM methodology to obtain structural data at high resolution, first using the ribosomes from yeast mitochondria obtained by Alexey Amunts [1]. After breaking the technical resolution barrier by cryo-EM, the method was applied to a human counterpart isolated from cell lines grown to the scale of tens of liters suspension [2].

Figure 1: Structure of human mitoribosome. mt-rRNAs is highlighted in blue (16S), yellow (12S) and white (mt-tRNA-Val); individual proteins are depicted in different colours.

The structure of the intact human mitoribosome represents arguably the most complex protein network unravelled, with over 200 inter-protein contacts [3]. It shows that some of the defining functional characteristics of translation that were generally accepted as universal, have substantially diverged in the human mitoribosome. Among the newly discovered unique features are adaptations to synthesizing exclusively membrane proteins, including a mitoribosomal protein that permanently tethers the mitoribosome to the membrane and an exit tunnel lined with hydrophobic amino acids. Surprisingly, a GTPase and a mitochondrial tRNA (mt-tRNA-Val) have been recruited to form intrinsic parts of the human mitoribosome, with implications for the unusual assembly and dynamics of the mitoribosome. Even the mRNA and tRNA binding sites have co-evolved to accommodate the peculiarities of translation in mitochondria.

Figure 2: mt-tRNA-Val becomes incorporated into human mitoribosome due to its location on the mtDNA, in between two rRNA genes. Hence, all three are transcribed together as a polycistronic transcript.

The structure has important implications for human health. It provides a reference for analysis of mutations that cause severe pathologies, and for future drug design, and is thus expected to trigger an avalanche of new work in the field. Furthermore, this work shows that we are moving towards a time when structural knowledge of otherwise intractable multi-component, low abundant complexes that are at the heart of many biological processes will be determined increasingly by cryo-EM thus transforming structural biology.

References

[1] Structure of the Yeast Mitochondrial Large Ribosomal Subunit. Alexey Amunts, Alan Brown, Xiao-chen Bai, Jose L. Llácer, Tanweer Hussain, Paul Emsley, Fei Long, Garib Murshudov, Sjors H. W. Scheres, V. Ramakrishnan. Science 343, 1485 (2014 DOI: 10.1126/science.1249410).

[2] Structure of the Large Ribosomal Subunit from Human Mitochondria. Alan Brown, Alexey Amunts, Xiao-chen Bai, Yoichiro Sugimoto, Patricia Edwards, Garib Murshudov, Sjors H. W. Scheres, V. Ramakrishnan. Science 346, 718 (2014 DOI: 10.1126/science.1258026).

[3] The Structure of the Human Mitochondrial Ribosome. Alexey Amunts, Alan Brown, Jaan Toots, Sjors H. W. Scheres, V. Ramakrishnan. Science 348, 95 (2015 DOI: 10.1126/science.aaa1193). 

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