Structure of a mitochondrial ribosome with minimal RNA - PubMed (original) (raw)

Structure of a mitochondrial ribosome with minimal RNA

Manjuli R Sharma et al. Proc Natl Acad Sci U S A. 2009.

Abstract

The Leishmania tarentolae mitochondrial ribosome (Lmr) is a minimal ribosomal RNA (rRNA)-containing ribosome. We have obtained a cryo-EM map of the Lmr. The map reveals several features that have not been seen in previously-determined structures of eubacterial or eukaryotic (cytoplasmic or organellar) ribosomes to our knowledge. Comparisons of the Lmr map with X-ray crystallographic and cryo-EM maps of the eubacterial ribosomes and a cryo-EM map of the mammalian mitochondrial ribosome show that (i) the overall structure of the Lmr is considerably more porous, (ii) the topology of the intersubunit space is significantly different, with fewer intersubunit bridges, but more tunnels, and (iii) several of the functionally-important rRNA regions, including the alpha-sarcin-ricin loop, have different relative positions within the structure. Furthermore, the major portions of the mRNA channel, the tRNA passage, and the nascent polypeptide exit tunnel contain Lmr-specific proteins, suggesting that the mechanisms for mRNA recruitment, tRNA interaction, and exiting of the nascent polypeptide in Lmr must differ markedly from the mechanisms deduced for ribosomes in other organisms. Our study identifies certain structural features that are characteristic solely of mitochondrial ribosomes and other features that are characteristic of both mitochondrial and chloroplast ribosomes (i.e., organellar ribosomes).

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Conflict of interest statement

The authors declare no conflict of interest.

Figures

Fig. 1.

Fig. 1.

Cryo-EM map of the Lmr (A and D) and its side-by-side comparison with the maps of an eubacterial (E. coli) 70S ribosome (18) (B and E) and a mammalian (Bos taurus) 55S mitoribosome (20) (C and F). Maps are shown from the L7/L12-stalk (A–C) and the protein L1 (D–F) sides. The SSU (yellow) and LSU (blue) are depicted. Numbers (1–9 in A and D) point to a few obvious differences in the Lmr: 1, gap caused by absence of major portion of SSU rRNA helix 44 (see Fig. 2_A_); 2 and 3, larger gaps between the head (h) of SSU and central protuberance (CP) of LSU; 4, an extended structure emerging from the CP; and 5–9, gaps caused by absence of various rRNA segments in the Lmr. Landmarks of the SSU are: b, body; mgt, mRNA gate (in C and F); pt, platform; sh, shoulder; sp, spur. Landmarks of the LSU are: L1, L1 protein (corresponding density is marked by * in D); Sb, L7/L12 stalk base; FBR, factor binding region. The scale bar is shown in D.

Fig. 2.

Fig. 2.

Structural analysis of the SSU. (A) Secondary-structure line diagram of the 9S Lm-rRNA (orange), superimposed on that of the bacterial 16S rRNA (13) (gray). RNA regions absent in the Lmr thus appear gray. RNA helices are identified by the adjacent numbers. Dashed lines correspond to unassigned segments of the 9S Lm-rRNA. (B) Stereo representation of the fitting of the conserved domains (ribbons) into the cryo-EM map of the SSU, shown from its interface side. The conserved components (orange, rRNA; green, proteins) are shown as translucent surfaces, and the Lmr-specific proteins (yellow) are shown as solid surfaces. (C) Same as B but shown from a solvent-side. Landmarks: numbers prefixed with S represent the SSU proteins; numbers prefixed with h identify the 9S rRNA helices; hd, head; bT, body tunnel; pT, platform tunnel. All other landmarks are as in Fig. 1.

Fig. 3.

Fig. 3.

Structural analysis of the LSU. (A) Secondary-structure diagram of the 12S Lm-rRNA (purple), superimposed on that of the bacterial 23S rRNA (14) (gray). Roman numerals identify the 6 domains of the rRNA, and helices are identified by numbers. Dashed lines correspond to unassigned segments of the 12S Lm-rRNA. (B) Stereo representation of the fitting of conserved domains (ribbons) into the cryo-EM map of the LSU, shown from its interface side. The conserved components (pinkish purple, rRNA; green, proteins) are shown as translucent surfaces, and the Lmr-specific proteins (blue) are shown as solid surfaces. (C) Same as B, but shown from the solvent side. Landmarks: numbers prefixed with L identify the LSU proteins; numbers prefixed with H identify the LSU rRNA helices; APSF, A- and P-site finger; CPT, CP tunnel; L9-N, N-terminal domain of L9. All other landmarks are as in Fig. 1.

Fig. 4.

Fig. 4.

Locations of intersubunit bridges. The SSU (A) and LSU (B) are shown from their interface sides. Bridges have been marked on both subunits as red ellipses and circles. Color codes for the SSU and LSU components are the same as in Figs. 2 and 3.

Fig. 5.

Fig. 5.

Stereo representation of topology of the mRNA and tRNA paths on the Lmr. (A) The tRNA path from A/T state to A site on the LSU. (B) The mRNA and tRNA paths encompassing A and P sites on the SSU. Positions of the A/T state (A/T, orange) and the A-site (A, pink) tRNAs are adopted from ref. , and the position of P-site tRNA (P, green) is adopted from ref. . The Lmr-specific protein densities (blue and yellow, respectively, in A and B) are marked by *. Landmarks: AC and CCA, anticodon and acceptor ends, respectively, of tRNAs. All other landmarks are as in previous figures.

Fig. 6.

Fig. 6.

Topology of the polypeptide-exit tunnel. (A) Cut-away view of the LSU (white surfaces correspond to the cutting plane) to reveal the tunnel. (B) The PES, as seen from the bottom of the LSU. (C) The LSU is shown from the side opposite to that in A to reveal the PAS. A model of an α-helical polypeptide chain (red) is used to delineate the tunnel (35). * in A points to location of PAS that lies behind the cutting plane. All other landmarks are as in previous figures. The orientations of the Lmr, with the area boxed in red in the thumbnail enlarged, are shown in the corresponding panels to the left.

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