Russian version English version
Volume 20   Issue 1   Year 2025
References

  1. Hamashima K., Kanai A. Alternative genetic code for amino acids and transfer RNA revisited. BioMolecular Concepts. 2013;4(3):309–318. doi: 10.1515/bmc-2013-0002
  2. Pütz J., Dupuis B., Sissler M., Florentz C. Mamit-tRNA, a database of mammalian mitochondrial tRNA primary and secondary structures. RNA. 2007;13(8):1184–1190. doi: 10.1261/rna.588407
  3. Wolstenholme D.R., Macfarlane J.L., Okimoto R., Clary D.O., Wahleithner J.A. Bizarre tRNAs inferred from DNA sequences of mitochondrial genomes of nematode worms. Proceedings of the National Academy of Sciences. 1987;84(5):1324–1328. doi: 10.1073/pnas.84.5.1324
  4. Jühling F., Pütz J., Florentz C., Stadler P.F. Armless mitochondrial tRNAs in enoplea (nematoda). RNA biology. 2012;9(9):1161–1166. doi: 10.4161/rna.21630
  5. Arcari P., Brownlee G.G. The nucleotide sequence of a small (3S) seryl-tRNA (anticodon GCU) from beef heart mitochondria. Nucleic Acids Research. 1980;8(22):5207–5212. doi: 10.1093/nar/8.22.5207
  6. Masta S.E., Boore J.L. Parallel evolution of truncated transfer RNA genes in arachnid mitochondrial genomes. Molecular Biology and Evolution. 2008;25(5):949–959. doi: 10.1093/molbev/msn051
  7. Masta S.E., McCall A., Longhorn S.J. Rare genomic changes and mitochondrial sequences provide independent support for congruent relationships among the sea spiders (Arthropoda, Pycnogonida). Molecular Phylogenetics and Evolution. 2010;57(1):59–70. doi: 10.1016/j.ympev.2010.06.020
  8. Ardell D.H. Computational analysis of tRNA identity. FEBS Letters. 2010;584(2):325–333. doi: 10.1016/j.febslet.2009.11.084
  9. Salinas-Giege T., Giege R., Giege P. tRNA biology in mitochondria. International Journal of Molecular Sciences. 2015;16(3):4518–4559. doi: 10.3390/ijms16034518
  10. Senger B., Auxilien S., Englisch U., Cramer F., Fasiolo F. The modified wobble base inosine in yeast tRNAIle is a positive determinant for aminoacylation by isoleucyl-tRNA synthetase. Biochemistry. 1997;36(27):8269–8275. doi: 10.1021/bi970206l
  11. Tsunoda M., Kusakabe Y., Tanaka N., Ohno S., Nakamura M., Senda T., Moriguchi T., Asai N., Sekine M., Yokogawa T., Nishikawa K., Nakamura K.T. Structural basis for recognition of cognate tRNA by tyrosyl-tRNA synthetase from three kingdoms. Nucleic Acids Research. 2007;35(13):4289–4300. doi: 10.1093/nar/gkm417
  12. Gruic-Sovulj I., Jaric J., Dulic M., Cindric M., Weygand-Durasevic I. Shuffling of discrete tRNASer regions reveals differently utilized identity elements in yeast and methanogenic archaea. Journal of Molecular Biology. 2006;361(1):128–139. doi: 10.1016/j.jmb.2006.06.008
  13. Chen M., Kuhle B., Diedrich J., Liu Z., Moresco J.J., Yates III J.R., Pan T., Yang X.L. Cross-editing by a tRNA synthetase allows vertebrates to abundantly express mischargeable tRNA without causing mistranslation. Nucleic Acids Research. 2020;48(12):6445–6457. doi: 10.1093/nar/gkaa469
  14. Giege R., Eriani G. The tRNA identity landscape for aminoacylation and beyond. Nucleic Acids Research. 2023;51(4):1528–1570. doi: 10.1093/nar/gkad007
  15. Cantatore P., Gadaleta M.N., Roberti M., Saccone C., Wilson A.C. Duplication and remoulding of tRNA genes during the evolutionary rearrangement of mitochondrial genomes. Nature. 1987;329(6142):853–855. doi: 10.1038/329853a0
  16. Lavrov D.V., Lang B.F. Transfer RNA gene recruitment in mitochondrial DNA. Trends in Genetics. 2005;21(3):129–133. doi: 10.1016/j.tig.2005.01.004
  17. Jiang P., Li H., Song F., Cai Y., Wang J., Liu J., Cai W. Duplication and remolding of tRNA genes in the mitochondrial genome of Reduvius tenebrosus (Hemiptera: Reduviidae). International Journal of Molecular Sciences. 2016;17(6):951. doi: 10.3390/ijms17060951
  18. Rawlings T.A., Collins T.M., Bieler R. Changing identities: tRNA duplication and remolding within animal mitochondrial genomes. Proceedings of the National Academy of Sciences. 2003;100(26):15700–15705. doi: 10.1073/pnas.2535036100
  19. Saks M.E., Sampson J.R., Abelson J. Evolution of a transfer RNA gene through a point mutation in the anticodon. Science. 1998;279(5357):1665–1670. doi: 10.1126/science.279.5357.1665
  20. Seilhamer J.J., Cummings D.J. Altered genetic code in Paramecium mitochondria: possible evolutionary trends. Molecular and General Genetics MGG. 1982;187(2):236–239. doi: 10.1007/BF00331123
  21. Osawa S., Jukes T.H. Codon reassignment (codon capture) in evolution. Journal of Molecular Evolution. 1989;28:271–278. doi: 10.1007/BF02103422
  22. Schultz D.W., Yarus M. Transfer RNA mutation and the malleability of the genetic code. Journal of Molecular Biology. 1994;235(5):1377–1380. doi: 10.1006/jmbi.1994.1094
  23. Kollmar M., Mühlhausen S. How tRNAs dictate nuclear codon reassignments: Only a few can capture non-cognate codons. RNA Biology. 2017;14(3):293–299. doi: 10.1080/15476286.2017.1279785
  24. Santos M.A., Moura G., Massey S.E., Tuite M.F. Driving change: the evolution of alternative genetic codes. Trends in Genetics. 2004;20(2):95–102. doi: 10.1016/j.tig.2003.12.009
  25. Romanova E.V., Aleoshin V.V., Kamaltynov R.M., Mikhailov K.V., Logacheva M.D., Sirotinina E.A., Gornov A.Yu., Anikin A.S., Sherbakov D.Yu. Evolution of mitochondrial genomes in Baikalian amphipods. BMC Genomics. 2016;17:291–306. doi: 10.1186/s12864-016-3357-z
  26. Romanova E.V., Bukin Y.S., Mikhailov K.V., Logacheva M.D., Aleoshin V.V., Sherbakov D.Y. Hidden cases of tRNA gene duplication and remolding in mitochondrial genomes of amphipods. Molecular Phylogenetics and Evolution. 2020;144:106710. doi: 10.1016/j.ympev.2019.106710
  27. Index of animal species inhabiting lake Baikal and its catchment area. Ed. O.A. Timoshkin. Novosibirsk, 2001. Vol. I: Lake Baikal, book 1. 832 p. (In Russ.).
  28. Degli Esposti M., De Vries S., Crimi M., Ghelli A., Patarnello T., Meyer A. Mitochondrial cytochrome b: evolution and structure of the protein. Biochimica et Biophysica Acta (BBA)-Bioenergetics. 1993;1143(3):243–271. doi: 10.1016/0005-2728(93)90197-N
  29. Charif D., Lobry J.R. SeqinR 1.0-2: a contributed package to the R project for statistical computing devoted to biological sequences retrieval and analysis. In: Structural Approaches to Sequence Evolution: Molecules, Networks, Populations. Berlin, Heidelberg: Springer, 2007. P. 207–232. doi: 10.1007/978-3-540-35306-5_10
  30. Wickham H. stringr: modern, consistent string processing. The R Journal. 2010;2(2):38. doi: 10.32614/RJ-2010-012
  31. Katoh K., Standley D. M. MAFFT multiple sequence alignment software version 7: improvements in performance and usability. Molecular Biology and Evolution. 2013;30(4):772–780. doi: 10.1093/molbev/mst010
  32. Kalyaanamoorthy S., Minh B.Q., Wong T.K., Von Haeseler A., Jermiin L.S. ModelFinder: fast model selection for accurate phylogenetic estimates. Nature Methods. 2017;14(6):587–589. doi: 10.1038/nmeth.4285
  33. Nguyen L.T., Schmidt H.A., Von Haeseler A., Minh B.Q. IQ-TREE: a fast and effective stochastic algorithm for estimating maximum-likelihood phylogenies. Molecular Biology and Evolution. 2015;32(1):268–274. doi: 10.1093/molbev/msu300
  34. Hoang D. T., Chernomor O., Von Haeseler A., Minh B.Q., Vinh L.S. UFBoot2: improving the ultrafast bootstrap approximation. Molecular Biology and Evolution. 2018;35(2):518–522. doi: 10.1093/molbev/msx281
  35. Anisimova M., Gil M., Dufayard J.F., Dessimoz C., Gascuel O. Survey of branch support methods demonstrates accuracy, power, and robustness of fast likelihood-based approximation schemes. Systematic Biology. 2011;60(5):685–699. doi: 10.1093/sysbio/syr041
  36. Rambaut A. FigTree-v1.4.4. 2014. http://tree.bio.ed.ac.uk/software/figtree/ (accessed 13 February 2025).
  37. Rice P., Longden I., Bleasby A. EMBOSS: the European molecular biology open software suite. Trends in Genetics. 2000;16(6):276–277. doi: 10.1016/S0168-9525(00)02024-2
  38. Waterhouse A., Bertoni M., Bienert S., Studer G., Tauriello G., Gumienny R., Heer F.T., De Beer T.A.P., Rempfer C., Bordoli L., Lepore R., Schwede T. SWISS-MODEL: homology modelling of protein structures and complexes. Nucleic Acids Research. 2018;46(W1):W296–W303. doi: 10.1093/nar/gky427
  39. DeLano W.L. Pymol: An open-source molecular graphics tool. CCP4 Newsl. Protein Crystallogr. 2002;40(1):82–92.
  40. Seddigh S., Darabi M. Functional, structural, and phylogenetic analysis of mitochondrial cytochrome b (cytb) in insects. Mitochondrial DNA Part A. 2018;29(2):236–249. doi: 10.1080/24701394.2016.1275596
  41. Ghosh R., Upadhyay A.D., Roy A.K., Tiwari A. Structural and functional analysis of cytochrome b protein of Indian major carps Labeo rohita. Journal of Entomology and Zoology Studies. 2020;8(2):540–550.
  42. Barrell B.G., Bankier A.T., Drouin J. A different genetic code in human mitochondria. Nature. 1979;282(5735):189–194. doi: 10.1038/282189a0
  43. Perseke M., Hetmank J., Bernt M., Stadler P.F., Schlegel M., Bernhard D. The enigmatic mitochondrial genome of Rhabdopleura compacta (Pterobranchia) reveals insights into selection of an efficient tRNA system and supports monophyly of Ambulacraria. BMC Evolutionary Biology. 2011;11:1–12. doi: 10.1186/1471-2148-11-134
  44. Ling J., Daoud R., Lajoie M.J., Church G.M., Söll D., Lang B.F. Natural reassignment of CUU and CUA sense codons to alanine in Ashbya mitochondria. Nucleic Acids Research. 2014;42(1):499–508. doi: 10.1093/nar/gkt842
  45. Tomita K., Ueda T., Watanabe K. The presence of pseudouridine in the anticodon alters the genetic code: a possible mechanism for assignment of the AAA lysine codon as asparagine in echinoderm mitochondria. Nucleic Acids Research. 1999;27(7):1683–1689. doi: 10.1093/nar/27.7.1683
  46. Blazquez J., Oliver A., Gomez-Gomez J.M. Mutation and evolution of antibiotic resistance: antibiotics as promoters of antibiotic resistance? Current Drug Targets. 2002;3(4):345–349. doi: 10.2174/1389450023347579
  47. Santos M.A., Cheesman C., Costa V., Moradas‐Ferreira P., Tuite M.F. Selective advantages created by codon ambiguity allowed for the evolution of an alternative genetic code in Candida spp. Molecular Microbiology. 1999;31(3):937–947. doi: 10.1046/j.1365-2958.1999.01233.x
  48. Mats V.D., Shcherbakov D.Y., Efimova I.M. Late Cretaceous-Cenozoic History of the Lake Baikal Depression and Formation of Its Unique Biodiversity. Stratigraphy and Geological Correlation. 2011;19(4):404-423. doi: 10.1134/S0869593811040058
Table of Contents Original Article
Yudinceva A.V., Romanova E.V., Sherbakov D.Y., Bukin Y.S. The Effect of Codon Reassignment on the Properties and Structure of the Mitochondrial Proteins of the Baikal Amphipods. Ìàthematical biology and bioinformatics. 2025;20(1):54-70. doi: 10.17537/2025.20.54
(published in Russian)

Abstract (rus.)
Abstract (eng.)
Full text (rus., pdf)
References
Supplementary data

 

  Copyright IMPB RAS © 2005-2026