Русская версия English version   
Том 14   Выпуск 2   Год 2019
Зимин А.А.1, Никулин Н.А.1, Назипова Н.Н.2

Гомологи РНК-лигазы 2 бактериофага T4 в метагеномах океанической микробиоты

Математическая биология и биоинформатика. 2019;14(2):683-704.

doi: 10.17537/2019.14.683.

Список литературы

 

  1. Shuman S., Schwer B. RNA capping enzyme and DNA ligase: A superfamily of covalent nucleotidyl transferases. Molecular Microbiology. 1995;17:405–410. doi: 10.1111/j.1365-2958.1995.mmi_17030405.x
  2. Silber R., Malathi V.G., Hurwitz J. Purification and properties of bacteriophage T4-induced RNA ligase. Proc. Natl. Acad. Sci. U S A. 1972;69:3009–3013. doi: 10.1073/pnas.69.10.3009
  3. Wang L. K., Shuman S. Structure-function analysis of yeast tRNA ligase. RNA. 2005;11(6):966–975. doi: 10.1261/rna.2170305
  4. Ho C.K., Shuman S. Bacteriophage T4 RNA ligase 2 (gp24.1) exemplifies a family of RNA ligases found in all phylogenetic domains. Proc. Natl. Acad. Sci. U S A. 2002;99:12709–12714. doi: 10.1073/pnas.192184699
  5. Abelson J., Trotta C.R., Li H. tRNA splicing. The Journal of Biological Chemistry. 1998;273:12685–12688. doi: 10.1074/jbc.273.21.12685
  6. Englert M., Beier H. Plant tRNA ligases are multifunctional enzymes that have diverged in sequence and substrate specificity from RNA ligases of other phylogenetic origins. Nucleic Acids Research. 2005;33:388–399. doi: 10.1093/nar/gki174
  7. Blanc V., Alfonzo J.D., Aphasizhev R., Simpson L. The mitochondrial RNA ligase from Leishmania tarentolae can join RNA molecules bridged by a complementary RNA. Journal of Biological Chemistry. 1999;274:24289–24296. doi: 10.1074/jbc.274.34.24289
  8. Palazzo S.S., Panigrahi A.K., Igo R.P. Jr., Salavati R., Stuart K. Kinetoplastid RNA editing ligases: complex association, characterization, and substrate requirements. Molecular and Biochemical Parasitology. 2003;127:161–167. doi: 10.1016/S0166-6851(02)00333-X
  9. Stuart K., Brun R., Croft S., Fairlamb A., Gurtler R.E., McKerrow J., Reed S., Tarleton R. Kinetoplastids: related protozoan pathogens, different diseases. J. Clin. Invest. 2008;118:1301–1310. doi: 10.1172/JCI33945
  10. Simpson L., Da Silva A. Isolation and characterization of kinetoplast DNA from Leishmania tarentolae. J. Mol. Biol. 1971;56:443–473. doi: 10.1016/0022-2836(71)90394-9
  11. Blum B., Bakalara N., Simpson L. A model for RNA editing in kinetoplastid mitochondria: RNA molecules transcribed from maxicircle DNA provide the edited information. Cell. 1990;60:89–198. doi: 10.1016/0092-8674(90)90735-W
  12. Sturm N.R., Simpson L. Kinetoplast DNA minicircles encode guide RNAs for editing of cytochrome oxidase subunit III mRNA. Cell. 1990;61:879–884. doi: 10.1016/0092-8674(90)90198-N
  13. Rehse P.H., Tahirov T.H. Structure of a putative 2’-5’ RNA ligase from Pyrococcus horikoshii. Acta Crystallographica Section D: Biological Crystallography. 2005;61:1207–1212. doi: 10.1107/S0907444905017841
  14. Desai K.K., Bingman C.A., Phillips G.N. Jr., Raines R.T. Structures of the Noncanonical RNA Ligase RtcB Reveal the Mechanism of Histidine Guanylylation. Biochemistry. 2013;52:2518–2525. doi: 10.1021/bi4002375
  15. Desai K.K., Cheng C.L., Bingman C.A., Phillips G.N. Jr., Raines R.T. A tRNA splicing operon: archease endows RtcB with dual GTP/ATP cofactor specificity and accelerates RNA ligation. Nucleic Acids Research. 2014;42:3931–3942. doi: 10.1093/nar/gkt1375
  16. Aphasizhev R., Aphasizheva I. Mitochondrial RNA editing in trypanosomes: small RNAs in control. Biochimie. 2014;100:125–131. doi: 10.1016/j.biochi.2014.01.003
  17. Moreira S., Noutahi E., Lamoureux G., Burger G. Three-dimensional structure model and predicted ATP interaction rewiring of a deviant RNA ligase 2. BMC Struct. Biol. 2015;15. Article No. 20. doi: 10.1186/s12900-015-0046-0
  18. Williamson S.J., Rusch D.B., Yooseph S., Halpern A.L., Heidelberg K.B., Glass J.I., Andrews-Pfannkoch C., Fadrosh D., Miller C.S., Sutton G., Frazier M., Venter J.C. The Sorcerer II Global Ocean Sampling Expedition: Metagenomic Characterization of Viruses within Aquatic Microbial Samples. PLoS One. 2008;3. Article No. e1456. doi: 10.1371/journal.pone.0001456
  19. Yooseph S., Sutton G., Rusch D.B., Halpern A.L., Williamson S.J., Remington K., Eisen J.A., Heidelberg K.B., Manning G., Li W., et al. The Sorcerer II Global Ocean Sampling expedition: Expanding the universe of protein families. PLoS Biol. 2007;5. Article No. e16. doi: 10.1371/journal.pbio.0050016
  20. Jorgensen S.L., Hannisdal B., Lanzén A., Baumberger T., Flesland K., Fonseca R., Ovreås L., Steen I.H., Thorseth I.H., Pedersen R.B., Schleper C. Correlating microbial community profiles with geochemical data in highly stratified sediments from the Arctic Mid-Ocean Ridge. Proc. Natl. Acad. Sci. U S A. 2012;109. P. E2846–E2855. doi: 10.1073/pnas.1207574109
  21. Brettin T., Davis J.J., Disz T., Edwards R.A., Gerdes S., Olsen G.J., Olson R., Overbeek R., Parrello B., Pusch G.D., et al. RASTtk: a modular and extensible implementation of the RAST algorithm for building custom annotation pipelines and annotating batches of genomes. Sci. Rep. 2015;5. Article No. 8365. doi: 10.1038/srep08365
  22. King A.M.Q., Lefkowitz E.J., Mushegian A.R., Adams M.J., Dutilh B.E., Gorbalenya A.E., Harrach B., Harrison R.L., Junglen S., Knowles N.J., et al. Changes to taxonomy and the International Code of Virus Classification and Nomenclature ratified by the International Committee on Taxonomy of Viruses (2018). Arch. Virol. 2018;163:2601–2631. doi: 10.1007/s00705-018-3847-1
  23. Federhen S. The NCBI Taxonomy database. Nucleic Acids Res. 2012;4:D136–D143. doi: 10.1093/nar/gkr1178
  24. Benson D.A., Cavanaugh M., Clark K., Karsch-Mizrachi I., Lipman D.J., Ostell J., Sayers E.W. GenBank. Nucleic Acids Res. 2013;41:D36–D42. doi: 10.1093/nar/gks1195
  25. Altschul S.F., Madden T.L., Schäffer A.A., Zhang J., Zhang Z., Miller W., Lipman D.J. Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic Acids Res. 1997;25:3389–3402. doi: 10.1093/nar/25.17.3389
  26. Jones D.T., Taylor W.R., Thornton J.M. The rapid generation of mutation data matrices from protein sequences. Computer Applications in the Biosciences. 1992;8:275–282. doi: 10.1093/bioinformatics/8.3.275
  27. Felsenstein J. Confidence limits on phylogenies: An approach using the bootstrap. Evolution. 1985;39:783–791. doi: 10.1111/j.1558-5646.1985.tb00420.x
  28. Kumar S., Stecher G., Li M., Knyaz C., Tamura K.). MEGA X: Molecular Evolutionary Genetics Analysis across computing platforms. Molecular Biology and Evolution. 2018;35:1547–1549. doi: 10.1093/molbev/msy096
  29. Cavalier-Smith T. Kingdom Chromista and its eight phyla: a new synthesis emphasising periplastid protein targeting, cytoskeletal and periplastid evolution, and ancient divergences. Protoplasma. 2018;255:297–357. doi: 10.1007/s00709-017-1147-3
  30. Edgar R.C. MUSCLE: multiple sequence alignment with high accuracy and high throughput. Nucleic Acids Res. 2004;32:1792–1797. doi: 10.1093/nar/gkh340
  31. Larkin M.A., Blackshields G., Brown N.P., Chenna R., McGettigan P.A., McWilliam H., Valentin F., Wallace I.M., Wilm A., Lopez R., Thompson J.D., Gibson T.J., Higgins D.G. ClustalW and ClustalX version 2.0. Bioinformatics. 2007;23:2947–2948. doi: 10.1093/bioinformatics/btm404
Содержание Оригинальная статья
Мат. биол. и биоинф.
2019;14(2):683-704
doi: 10.17537/2019.14.683
опубликована на рус. яз.

Аннотация (рус.)
Аннотация (англ.)
Полный текст (рус., pdf)
Список литературы Перевод на англ. яз.
Мат. биол. и биоинф.
2020, 15(Suppl):t88-t108
doi: 10.17537/2020.15.t88

Полный текст (англ., pdf)

 

  Copyright ИМПБ РАН © 2005-2024