Advertisement

Heterologous Inferential Analysis (HIA) as a Method to Understand the Role of Mitochondrial rRNA Mutations in Pathogenesis

  • Joanna L. Elson
  • Paul M. Smith
  • Antón Vila-SanjurjoEmail author
Protocol
Part of the Methods in Molecular Biology book series (MIMB, volume 1264)

Abstract

Despite the identification of a large number of potentially pathogenic variants in the mitochondrially encoded rRNA (mt-rRNA) genes, we lack direct methods to firmly establish their pathogenicity. In the absence of such methods, we have devised an indirect approach named heterologous inferential analysis or HIA that can be used to make predictions on the disruptive potential of a large subset of mt-rRNA variants. First, due to the high evolutionary conservation of the rRNA fold, comparison of phylogenetically derived secondary structures of the human mt-rRNAs and those from model organisms allows the location of structurally equivalent residues. Second, visualization of the heterologous equivalent residue in high-resolution structures of the ribosome allows a preliminary structural characterization of the residue and its neighboring region. Third, an exhaustive search for biochemical and genetic information on the residue and its surrounding region is performed to understand their degree of involvement in ribosomal function. Additional rounds of visualization in biochemically relevant high-resolution structures will lead to the structural and functional characterization of the residue’s role in ribosomal function and to an assessment of the disruptive potential of mutations at this position. Notably, in the case of certain mitochondrial variants for which sufficient information regarding their genetic and pathological manifestation is available; HIA data alone can be used to predict their pathogenicity. In other cases, HIA will serve to prioritize variants for additional investigation. In the context of a scoring system specifically designed for these variants, HIA could lead to a powerful diagnostic tool.

Key words

Mitochondrial rRNA mtDNA Mitoribosome Mitochondrial deafness mtDNA mutation 

Notes

Note added in proof

Recent advances in cryo-electron microscopy have allowed the groups led by R.K. Agrawal, N. Ban, and V. Ramakrishnan to achieve medium-resolution and near-atomic-resolution structures of mammalian mitoribosomal particles. Such advances now permit the placement of sites of mutation directly on mitoribosomal structures, thus dramatically improving the predictive power of the methods described here.

References

  1. 1.
    Yarham JW, McFarland R, Taylor RW, Elson JL (2012) A proposed consensus panel of organisms for determining evolutionary conservation of mt-tRNA point mutations. Mitochondrion 12:533–538PubMedCentralPubMedCrossRefGoogle Scholar
  2. 2.
    Lu J, Li Z, Zhu Y, Yang A, Li R, Zheng J, Cai Q, Peng G, Zheng W, Tang X et al (2010) Mitochondrial 12S rRNA variants in 1642 Han Chinese pediatric subjects with aminoglycoside-induced and nonsyndromic hearing loss. Mitochondrion 10:380–390PubMedCentralPubMedCrossRefGoogle Scholar
  3. 3.
    Shen Z, Zheng J, Chen B, Peng G, Zhang T, Gong S, Zhu Y, Zhang C, Li R, Yang L et al (2011) Frequency and spectrum of mitochondrial 12S rRNA variants in 440 Han Chinese hearing impaired pediatric subjects from two otology clinics. J Transl Med 9:4PubMedCentralPubMedCrossRefGoogle Scholar
  4. 4.
    Mutai H, Kouike H, Teruya E, Takahashi-Kodomari I, Kakishima H, Taiji H, Usami S, Okuyama T, Matsunaga T (2011) Systematic analysis of mitochondrial genes associated with hearing loss in the Japanese population: DHPLC reveals a new candidate mutation. BMC Med Genet 12:135PubMedCentralPubMedCrossRefGoogle Scholar
  5. 5.
    Tang J, Qi Y, Bao XH, Wu XR (1997) Mutational analysis of mitochondrial DNA of children with Rett syndrome. Pediatr Neurol 17:327–330PubMedCrossRefGoogle Scholar
  6. 6.
    Tang HY, Hutcheson E, Neill S, Drummond-Borg M, Speer M, Alford RL (2002) Genetic susceptibility to aminoglycoside ototoxicity: How many are at risk? Genet Med 4:336–345PubMedCrossRefGoogle Scholar
  7. 7.
    Trifunovic A (2006) Mitochondrial DNA and ageing. Biochim Biophys Acta 1757:611–617PubMedCrossRefGoogle Scholar
  8. 8.
    Noller HF (2005) RNA structure: reading the ribosome. Science 309:1508–1514PubMedCrossRefGoogle Scholar
  9. 9.
    Subhankar B, Dhananjaya S (2003) MITOMAP mtDNA sequence data: unpublished variant 20041220003Google Scholar
  10. 10.
    Gutell RR, Lee JC, Cannone JJ (2002) The accuracy of ribosomal RNA comparative structure models. Curr Opin Struct Biol 12:301–310PubMedCrossRefGoogle Scholar
  11. 11.
    Smith PM, Elson JL, Greaves LC, Wortmann SB, Rodenburg RJ, Lightowlers RN, Chrzanowska-Lightowlers ZM, Taylor RW, Vila-Sanjurjo A (2014) The role of the mitochondrial ribosome in human disease: searching for mutations in 12S mitochondrial rRNA with high disruptive potential. Hum Mol Genet 23:949–956PubMedCentralPubMedCrossRefGoogle Scholar
  12. 12.
    Pereira L, Freitas F, Fernandes V, Pereira JB, Costa MD, Costa S, Maximo V, Macaulay V, Rocha R, Samuels DC (2009) The diversity present in 5140 human mitochondrial genomes. Am J Hum Genet 84:628–640PubMedCentralPubMedCrossRefGoogle Scholar
  13. 13.
    Sayers E (2010) E-utilities quick start. In: Entrez programming utilities help [Internet]. National Center for Biotechnology Information (US), Bethesda (MD)Google Scholar
  14. 14.
    Andrews RM, Kubacka I, Chinnery PF, Lightowlers RN, Turnbull DM, Howell N (1999) Reanalysis and revision of the Cambridge reference sequence for human mitochondrial DNA. Nat Genet 23:147PubMedCrossRefGoogle Scholar
  15. 15.
    Katoh K, Misawa K, Kuma K, Miyata T (2002) MAFFT: a novel method for rapid multiple sequence alignment based on fast fourier transform. Nucleic Acids Res 30:3059–3066PubMedCentralPubMedCrossRefGoogle Scholar
  16. 16.
    Huang X, Miller W (1991) A time-efficient, linear-space local similarity algorithm. Adv Appl Math 12:337–357CrossRefGoogle Scholar
  17. 17.
    Cannone JJ, Subramanian S, Schnare MN, Collett JR, D’Souza LM, Du Y, Feng B, Lin N, Madabusi LV, Muller KM et al (2002) The comparative RNA web (CRW) site: an online database of comparative sequence and structure information for ribosomal, intron, and other RNAs. BMC Bioinformatics 3:2PubMedCentralPubMedCrossRefGoogle Scholar
  18. 18.
    Schuwirth BS, Borovinskaya MA, Hau CW, Zhang W, Vila-Sanjurjo A, Holton JM, Cate JH (2005) Structures of the bacterial ribosome at 3.5 A resolution. Science 310:827–834PubMedCrossRefGoogle Scholar
  19. 19.
    Pulk A, Cate JH (2013) Control of ribosomal subunit rotation by elongation factor G. Science 340:1235970PubMedCentralPubMedCrossRefGoogle Scholar
  20. 20.
    Kleywegt GJ, Alwyn JT (1997) Model building and refinement practice. Meth Enzymol 277:208–230PubMedCrossRefGoogle Scholar
  21. 21.
    Pettersen EF, Goddard TD, Huang CC, Couch GS, Greenblatt DM, Meng EC, Ferrin TE (2004) UCSF chimera – a visualization system for exploratory research and analysis. J Comput Chem 25:1605–1612PubMedCrossRefGoogle Scholar
  22. 22.
    Jeffrey G (1997) An introduction to hydrogen bonding. Oxford University Press, OxfordGoogle Scholar
  23. 23.
    Triman KL (2007) Mutational analysis of the ribosome. Adv Genet 58:89–119PubMedCrossRefGoogle Scholar
  24. 24.
    Berk V, Zhang W, Pai RD, Doudna Cate JH (2006) Structural basis for mRNA and tRNA positioning on the ribosome. Proc Natl Acad Sci U S A 103:15830–15834PubMedCentralPubMedCrossRefGoogle Scholar
  25. 25.
    Selmer M, Dunham CM, Murphy FV 4th, Weixlbaumer A, Petry S, Kelley AC, Weir JR, Ramakrishnan V (2006) Structure of the 70S ribosome complexed with mRNA and tRNA. Science 313:1935–1942PubMedCrossRefGoogle Scholar
  26. 26.
    Gabdulkhakov A, Nikonov S, Garber M (2013) Revisiting the haloarcula marismortui 50S ribosomal subunit model. Acta Crystallogr D Biol Crystallogr 69:997–1004PubMedCrossRefGoogle Scholar
  27. 27.
    Rabl J, Leibundgut M, Ataide SF, Haag A, Ban N (2011) Crystal structure of the eukaryotic 40S ribosomal subunit in complex with initiation factor 1. Science 331:730–736PubMedCrossRefGoogle Scholar
  28. 28.
    Ben-Shem A, Garreau de Loubresse N, Melnikov S, Jenner L, Yusupova G, Yusupov M (2011) The structure of the eukaryotic ribosome at 3.0 A resolution. Science 334:1524–1529PubMedCrossRefGoogle Scholar
  29. 29.
    Laurberg M, Asahara H, Korostelev A, Zhu J, Trakhanov S, Noller HF (2008) Structural basis for translation termination on the 70S ribosome. Nature 454:852–857PubMedCrossRefGoogle Scholar
  30. 30.
    Korostelev A, Asahara H, Lancaster L, Laurberg M, Hirschi A, Zhu J, Trakhanov S, Scott WG, Noller HF (2008) Crystal structure of a translation termination complex formed with release factor RF2. Proc Natl Acad Sci U S A 105:19684–19689PubMedCentralPubMedCrossRefGoogle Scholar
  31. 31.
    Zhou J, Lancaster L, Donohue JP, Noller HF (2013) Crystal structures of EF-G-ribosome complexes trapped in intermediate states of translocation. Science 340:1236086PubMedCentralPubMedCrossRefGoogle Scholar
  32. 32.
    Gao YG, Selmer M, Dunham CM, Weixlbaumer A, Kelley AC, Ramakrishnan V (2009) The structure of the ribosome with elongation factor G trapped in the posttranslocational state. Science 326:694–699PubMedCentralPubMedCrossRefGoogle Scholar
  33. 33.
    Voorhees RM, Schmeing TM, Kelley AC, Ramakrishnan V (2010) The mechanism for activation of GTP hydrolysis on the ribosome. Science 330:835–838PubMedCentralPubMedCrossRefGoogle Scholar
  34. 34.
    Voorhees RM, Weixlbaumer A, Loakes D, Kelley AC, Ramakrishnan V (2009) Insights into substrate stabilization from snapshots of the peptidyl transferase center of the intact 70S ribosome. Nat Struct Mol Biol 16:528–533PubMedCentralPubMedCrossRefGoogle Scholar

Copyright information

© Springer Science+Business Media New York 2015

Authors and Affiliations

  • Joanna L. Elson
    • 1
  • Paul M. Smith
    • 2
  • Antón Vila-Sanjurjo
    • 3
    Email author
  1. 1.Institute of Genetic MedicineNewcastle UniversityNewcastle upon TyneUK
  2. 2.Institute of Medical Sciences, Ninewells Hospital and Medical SchoolDundee UniversityDundeeUK
  3. 3.Dept. Bioloxía Celular e Molecular, Facultade de CienciasUniversidade da Coruña (UDC)A CoruñaSpain

Personalised recommendations