Poster abstracts

Poster number 55 submitted by Maryam Hosseini

RNA evolution in an oxidizing Environment: The mammalian mitochondrial ribosome

Poorna Roy (Department of Chemistry, Bowling Green State University), Maryam Hosseini (Department of Chemistry, Bowling Green State University), Eric Westhof (Architecture et Ractivit de lARN, Universit de Strasbourg, Institut de biologie molculaire et cellulaire du CNRS), Marie Sissler (Architecture et Ractivit de lARN, Universit de Strasbourg, Institut de biologie molculaire et cellulaire du CNRS), Neocles Leontis (Department of Chemistry, Bowling Green State University)

Abstract:
Mitochondria evolved from bacterial symbionts of early eukaryotes and have their own DNA and ribosomes. Mammalian mitochondrial (mmt) ribosomes translate just 13 polypeptides, all of which belong to the electron transport chain (ETC), located in the inner mitochondrial membrane (IMM), which is the source of reactive oxygen species (ROS). Thus mmt-ribosomes are exposed to a highly oxidizing environment and turn over every 4-5 hours, at a rate ~24 times faster than for cytosolic ribosomes (Gelfand and Attardi, 1981). Hence, we hypothesize that mitochondria are subject to strong selection for ribosomes of reduced sensitivity to oxidative damage. Comparison of mmt- and bacterial rRNA shows large-scale loss of peripheral rRNA in both mmt-ribosomal subunits and a parallel increase in the sizes and numbers of r-proteins. Analysis of recent cryo-EM structures of the mmt-SSU shows that all rRNA elements that directly contact tRNA and mRNA are nonetheless retained, but large numbers of exposed G’s in hairpin, internal and multi-helix junction “loops,” that are highly conserved in bacterial SSU (>99%), are replaced in mmt-rRNA by bases less sensitive to oxidation, A, C, or U, as revealed by structure-correlated sequence analysis of high quality rRNA sequence alignments (http://rna.bgsu.edu/r3d-2-msa, Cannone et al. 2015). We present a detailed analysis of differences between bacterial and mmt ribosomes in sequence conservation, RNA-RNA and RNA-protein interactions correlated with solvent accessible surface area, to assess this hypothesis. Our analyses show that mitochondria-specific r-proteins and expansions of bacterial r-protein homologues (1) substitute for truncated rRNA helices while preserving the mutual orientations of the remaining helices in 3D space (2) compensate missing RNA-RNA interactions, (3) reduce the solvent accessibility of exposed bases in rRNA loops, and (4) stabilize 3D motifs lacking Gs that are conserved in bacteria.

References:
Gelfand, R. and Attardi, G. (1981) “Synthesis and turnover of mitochondrial ribonucleic acid in HeLa cells: the mature ribosomal and messenger ribonucleic acid species are metabolically unstable.” Mol Cell Biol. 1981; 1(6): 497–511.

Cannone, J.J., Sweeney, B.A., Petrov, A.I., Gutell, R.R., Zirbel, C.L., and Leontis, N. (2015) “R3D-2-MSA: the RNA 3D structure-to-multiple sequence alignment server.” Nucleic Acids Res. 43(W1):W15-23. doi: 10.1093/nar/gkv543

Keywords: Evolution, ROS, Mitochondria