Везде

RAS BiologyБиохимия Biochemistry

  • ISSN (Print) 0320-9725
  • ISSN (Online) 3034-5294

RIBOSOME IN BAKER'S YEAST MITOCHONDRIA ARE HETEROGENEOUS

You can
PII
S30345294S0320972525080101-1
DOI
10.7868/S3034529425080101
Publication type
Article
Status
Published
Authors
R.A. Khannanov
  • Affiliation: Lomonosov Moscow State University
I.V. Chicherin
  • Affiliation: Lomonosov Moscow State University
M.V. Baleva
  • Affiliation: Lomonosov Moscow State University
S.A. Levitskii
  • Affiliation: Lomonosov Moscow State University
R.A. Vasilev
  • Affiliation: Lomonosov Moscow State University
U.E. Piunova
  • Affiliation: Lomonosov Moscow State University
P.A. Kamenski
  • Affiliation: Lomonosov Moscow State University
Volume/ Edition
Volume 90 / Issue number 8
Pages
1201-1218
Abstract
Ribosomes are macromolecular machines of conveyor type, which move along the mRNA from triplet to triplet and polymerize cognate amino acids. They are regarded as uniform entities with constant molecular composition bearing no regulatory capacity. However, their ability to interact with multiple proteins involved in translation suggests the existence of specialized ribosomes dedicated to biosynthesis of particular proteins. This can be easily imagined in yeast mitochondria, whose genomes encode eight polypeptides, and where protein-specific translation is already represented by translational activators – a group of proteins each regulating a single mRNA translation. Despite this, the subject remains poorly investigated. We report an exploratory approach to search for distinct populations of ribosomes in yeast mitochondria. We add affinity tags to mitochondrial ribosomal proteins, isolate ribosomes by immunoprecipitation and characterize their protein and RNA content. We show that mitochondrial ribosomes isolated from yeast strains bearing affinity tags on different ribosomal proteins recover different sets of components. The differences were rather quantitative than qualitative, because almost full sets of mitochondrial ribosomal proteins were identified in each sample, but the ratios demonstrated variance ranging from 10 to less than 0.05 molecules per ribosome. In addition, we explore the power of translational activators as a bait to recover ribosomes translating specific mRNAs in yeast mitochondria.
Keywords
митохондрии трансляция рибосомы
Date of publication
17.07.2025
Year of publication
2025
Number of purchasers
0
Views
79

References

  1. 1. Sharma, M. R., Koc, E. C., Datta, P. P., Booth, T. M., Spremulli, L. L., and Agrawal, R. K. (2003) Structure of the mammalian mitochondrial ribosome reveals an expanded functional role for its component proteins, Cell, 115, 97-108, https://doi.org/10.1016/s0092-8674 (03)00762-1.
  2. 2. Levitskii, S. A., Baleva, M. V., Chicherin, I. V., Krasheninnikov, I. A., and Kamenski, P. A. (2020) Protein biosynthesis in mitochondria: past simple, present perfect, future indefinite, Biochemistry (Moscow), 85, 257-263, https://doi.org/10.1134/S0006297920030013.
  3. 3. Greber, B. J., and Ban, N. (2016) Structure and function of the mitochondrial ribosome, Annu. Rev. Biochem., 85, 103-132, https://doi.org/10.1146/annurev-biochem-060815-014343.
  4. 4. Amunts, A., Brown, A., Bai, X. C., Llácer, J. L., Hussain, T., Emsley, P., Long, F., Murshudov, G., Scheres, S. H. W., and Ramakrishnan, V. (2014) Structure of the yeast mitochondrial large ribosomal subunit, Science, 343, 1485-1489, https://doi.org/10.1126/science.1249410.
  5. 5. Itoh, Y., Andréli, J., Choi, A., Richter, U., Maiti, P., Best, R. B., Barrientos, A., Battersby, B. J., and Amunts, A. (2021) Mechanism of membrane-tethered mitochondrial protein synthesis, Science, 371, 846-849, https://doi.org/10.1126/science.abe0763.
  6. 6. Kummer, E., Leibundgut, M., Rackham, O., Lee, R. G., Boehringer, D., Filipovska, A., and Ban, N. (2018) Unique features of mammalian mitochondrial translation initiation revealed by cryo-EM, Nature, 560, 263-267, https://doi.org/10.1038/s41586-018-0373-y.
  7. 7. Desai, N., Yang, H., Chandrasekaran, V., Kazi, R., Minczuk, M., and Ramakrishnan, V. (2020) Elongational stalling activates mitoribosome-associated quality control, Science, 370, 1105-1110, https://doi.org/10.1126/science.abe7782.
  8. 8. Kummer, E., Schubert, K. N., Schoenhut, T., Scaiola, A., and Ban, N. (2021) Structural basis of translation termination, rescue, and recycling in mammalian mitochondria, Mol. Cell, 81, 2566-2582.e6, https://doi.org/10.1016/j.molecl.2021.03.042.
  9. 9. Rebelo-Guiomar, P., Pellegrino, S., Dent, K. C., Sas-Chen, A., Miller-Fleming, L., Garone, C., Van Haute, L., Rogan, J. F., Dinan, A., Firth, A. E., Andrews, B., Whitworth, A. J., Schwartz, S., Warren, A. J., and Minczuk, M. (2022) A late-stage assembly checkpoint of the human mitochondrial ribosome large subunit, Nat. Commun., 13, 929, https://doi.org/10.1038/s41467-022-28503-5.
  10. 10. Itoh, Y., Khawaja, A., Laptev, I., Cipullo, M., Atanasov, I., Sergiev, P., Rorbach, J., and Amunts, A. (2022) Mechanism of mitoribosomal small subunit biogenesis and preinitiation, Nature, 606, 603-608, https://doi.org/10.1038/s41586-022-04795-x.
  11. 11. Ferretti, M. B., and Karbstein, K. (2019) Does functional specialization of ribosomes really exist? RNA, 25, 521-538, https://doi.org/10.1261/rna.069823.118.
  12. 12. Palade, G. E. (1955) A small particulate component of the cytoplasm, J. Biophys. Biochem. Cytol., 1, 59-68, https://doi.org/10.1083/jcb.1.1.59.
  13. 13. Crick, F. H. (1958) On protein synthesis, Symp. Soc. Exp. Biol., 12, 138-163.
  14. 14. Brenner, S., Jacob, F., and Meselson, M. (1961) An unstable intermediate carrying information from genes to ribosomes for protein synthesis, Nature, 190, 576-581, https://doi.org/10.1038/190576a0.
  15. 15. Genuth, N. R., and Barna, M. (2018) The discovery of ribosome heterogeneity and its implications for gene regulation and organismal life, Mol. Cell, 71, 364-374, https://doi.org/10.1016/j.molecl.2018.07.018.
  16. 16. Tomal, A., Kwasniak-Owczarek, M., and Janska, H. (2019) An update on mitochondrial ribosome biology: the plant mitochondrion in the spotlight, Cells, 8, 1562, https://doi.org/10.3390/cells8121562.
  17. 17. Shi, Z., Fujii, K., Kovary, K. M., Genuth, N. R., Röst, H. L., Teruel, M. N., and Barna, M. (2017) Heterogeneous ribosomes preferentially translate distinct subpools of mRNAs genome-wide, Mol. Cell, 67, 71-83.e7, https://doi.org/10.1016/j.molecl.2017.05.021.
  18. 18. Gao, Y., and Wang, H. (2024) Ribosome heterogeneity in development and disease, Front. Cell Dev. Biol., 12, 1414269, https://doi.org/10.3389/fcell.2024.1414269.
  19. 19. Genuth, N. R., Shi, Z., Kunimoto, K., Hung, V., Xu, A. F., Kerr, C. H., Tiu, G. C., Oses-Prieto, J. A., Salomon-Shulman, R. E. A., Axelrod, J. D., Burlingame, A. L., Loh, K. M., and Barna, M. (2022) A stem cell roadmap of ribosome heterogeneity reveals a function for RPL10A in mesoderm production, Nat. Commun., 13, 5491, https://doi.org/10.1038/s41467-022-33263-3.
  20. 20. Milenkovic, I., Santos Vieira, H. G., Lucas, M. C., Ruiz-Orera, J., Patone, G., Kesteven, S., Wu, J., Fenely, M., Espadas, G., Sabidó, E., Hühner, N., van Heesch, S., Volkers, M., and Novoa, E. M. (2023) Dynamic interplay between RPL3- and RPL3L-containing ribosomes modulates mitochondrial activity in the mammalian heart, Nucleic Acids Res., 51, 5301-5324, https://doi.org/10.1093/nar/gkad121.
  21. 21. Simsek, D., Tiu, G. C., Flynn, R. A., Byeon, G. W., Leppek, K., Xu, A. F., Chang, H. Y., Barna, M. (2017) The mammalian ribo-interactome reveals ribosome functional diversity and heterogeneity, Cell, 169, 1051-1065.e18, https://doi.org/10.1016/j.cell.2017.05.022.
  22. 22. David, F., Roussel, E., Froment, C., Draia-Nicolau, T., Pujol, F., Butler-Schlitz, O., Henras, A. K., Lacazette, E., Morfoisse, F., Tatin, F., Diaz, J. J., Catez, F., Garmy-Susini, B., and Prats, A.-C. (2024) Mitochondrial ribosomal protein MRPS15 is a component of cytosolic ribosomes and regulates translation in stressed cardiomyocytes, Int. J. Mol. Sci., 25, 3250, https://doi.org/10.3390/ijms25063250.
  23. 23. Zhang, X., Gao, X., Coots, R. A., Conn, C. S., Liu, B., and Qian, S.-B. (2015) Translational control of the cytosolic stress response by mitochondrial ribosomal protein L18, Nat. Struct. Mol. Biol., 22, 404-410, https://doi.org/10.1038/nsmb.3010.
  24. 24. Zeng, R., Smith, E., and Barrientos, A. (2018) Yeast mitoribosome large subunit assembly proceeds by hierarchical incorporation of protein clusters and modules on the inner membrane, Cell Metab., 27, 645-656.e7, https://doi.org/10.1016/j.cmet.2018.01.012.
  25. 25. Del'Olio, S., and Barrientos, A. (2023) Systematic analysis of assembly intermediates in yeast to decipher the mitoribosome assembly pathway, Methods Mol. Biol., 2661, 163-191, https://doi.org/10.1007/978-1-0716-3171-3_11.
  26. 26. Mays, J.-N., Camacho-Villasana, Y., Garcia-Villegas, R., Perez-Martinez, X., Barrientos, A., and Fontanesi, F. (2019) The mitoribosome-specific protein mS38 is preferentially required for synthesis of cytochrome c oxidase subunits, Nucleic Acids Res., 47, 5746-5760, https://doi.org/10.1093/nar/gkz266.
  27. 27. Segev, N., and Gerst, J. E. (2018) Specialized ribosomes and specific ribosomal protein paralogs control translation of mitochondrial proteins, J. Cell Biol., 217, 117-126, https://doi.org/10.1083/jcb.201706059.
  28. 28. Desai, N., Brown, A., Amunts, A., and Ramakrishnan, V. (2017) The structure of the yeast mitochondrial ribosome, Science, 355, 528-531, https://doi.org/10.1126/science.aall2415.
  29. 29. Antonicka, H., and Shoubridge, E. A. (2015) Mitochondrial RNA granules are centers for posttranscriptional RNA processing and ribosome biogenesis, Cell Rep., 10, 920-932, https://doi.org/10.1016/j.celrep.2015.01.030.
  30. 30. Herrmann, J. M., Woellhaf, M. W., and Bonnefoy, N. (2013) Control of protein synthesis in yeast mitochondria: the concept of translational activators, Biochim. Biophys. Acta, 1833, 286-294, https://doi.org/10.1016/j.bbamcr.2012.03.007.
  31. 31. Mulero, J. J., and Fox, T. D. (1993) PET111 acts in the 5'-leader of the Saccharomyces cerevisiae mitochondrial COX2 mRNA to promote its translation, Genetics, 133, 509-516, https://doi.org/10.1093/genetics/133.3.509.
  32. 32. Malina, C., Larsson, C., and Nielsen, J. (2018) Yeast mitochondria: an overview of mitochondrial biology and the potential of mitochondrial systems biology, FEMS Yeast Res., 18, https://doi.org/10.1093/femsyr/foy040.
  33. 33. Kuzmenko, A., Derbikova, K., Salvatori, R., Tankov, S., Atkinson, G. C., Tenson, T., Ott, M., Kamenski, P., and Hauryliuk, V. (2016) Aim-less translation: loss of Saccharomyces cerevisiae mitochondrial translation initiation factor mIF3/Aim23 leads to unbalanced protein synthesis, Sci. Rep., 6, 18749, https://doi.org/10.1038/srep18749.
  34. 34. Knop, M., Siegers, K., Pereira, G., Zachariae, W., Winsor, B., Nasmyth, K., and Schiebel, E. (1999) Epitope tagging of yeast genes using a PCR-based strategy: more tags and improved practical routines, Yeast, 15, 963-972, https://doi.org/10.1002/ (SICI)1097-0061(199907)15:10B3.0.CO;2-W.
  35. 35. Gietz, R. D., and Schiestl, R. H. (2007) High-efficiency yeast transformation using the LiAc/SS carrier DNA/PEG method, Nat. Protoc., 2, 31-34, https://doi.org/10.1038/nprot.2007.13.
  36. 36. Baleva, M. V., Chicherin, I., Piunova, U., Zgoda, V., Patrushev, M. V., Levitskii, S., and Kamenski, P. (2022) Pentatriopeptide protein PTCD2 regulates COIII translation in mitochondria of the HeLa cell line, Int. J. Mol. Sci., 23, 14241, https://doi.org/10.3390/ijms232214241.
  37. 37. Cox, J., and Mann, M. (2008) MaxQuant enables high peptide identification rates, individualized p.p.b-range mass accuracies and proteome-wide protein quantification, Nat. Biotechnol., 26, 1367-1372, https://doi.org/10.1038/nbt.1511.
  38. 38. Cox, J., Neuhauser, N., Michalski, A., Scheltema, R. A., Olsen, J. V., and Mann, M. (2011) Andromeda: a peptide search engine integrated into the MaxQuant environment, J. Proteome Res., 10, 1794-1805, https://doi.org/10.1021/pr101065j.
  39. 39. Klein, M., Swinnen, S., Thevelein, J. M., and Nevoigt, E. (2017) Glycerol metabolism and transport in yeast and fungi: established knowledge and ambiguities, Environ. Microbiol., 19, 878-893, https://doi.org/10.1111/1462-2920.13617.
  40. 40. Rath, S., Sharma, R., Gupta, R., Ast, T., Chan, C., Durham, T. J., Goodman, R. P., Grabarek, Z., Haas, M. E., Hung, W. H. W., Joshi, P. R., Jourdain, A. A., Kim, S. H., Kotrys, A. V., Lam, S. S., McCoy, J. G., Meisel, J. D., Miranda, M., Panda, A., Patgiri, A., Rogers, R., Sadre, S., Shah, H., Skinner, O. S., To, T. L., Walker, M. A., Wang, H., Ward, P. S., Wengrod, J., Yuan, C. C., Calvo, S. E., and Mootha, V. K. (2021) MitoCarta3.0: an updated mitochondrial proteome now with sub-organelle localization and pathway annotations, Nucleic Acids Res., 49, D1541-D1547, https://doi.org/10.1093/nar/gkaa1011.
  41. 41. Ghaemmaghami, S., Huh, W. K., Bower, K., Howson, R. W., Belle, A., Dephoure, N., O'Shea, E. K., and Weissman, J. S. (2003) Global analysis of protein expression in yeast, Nature, 425, 737-741, https://doi.org/10.1038/nature02046.
  42. 42. Lavidovskaja, E., Hanitsch, E., Linden, A., Pašen, M., Challa, V., Horokhovskyi, Y., Roetschke, H. P., Nadler, F., Welp, L., Steube, E., Heinrichs, M., Mai, M. M., Urlaub, H., Liepe, J., and Richter-Dennerlein, R. (2024) A roadmap for ribosome assembly in human mitochondria, Nat. Struct. Mol. Biol., 31, 1898-1908, https://doi.org/10.1038/s41594-024-01356-w.
QR
Translate

Indexing

Scopus

Scopus

Scopus

Crossref

Scopus

Higher Attestation Commission

At the Ministry of Education and Science of the Russian Federation

Scopus

Scientific Electronic Library