Assembly of a Complex of Immature 30S Ribosomal Subunit and Era GTPase Maturation Factor from Staphylococcus aureus in vitro for Structural Studies

Cover Page

Cite item

Full Text

Open Access Open Access
Restricted Access Access granted
Restricted Access Subscription or Fee Access

Abstract

Staphylococcus aureus Era GTPase is one of the ribosome maturation factors. Era GTPase is involved in the late stages of small (30S) ribosome subunit assembly and regulates formation of the entire 70S ribosome. Study of the structure of the Era and 30S subunit complex from S. aureus will help in studying the processes of ribosome maturation and mechanisms of protein synthesis regulation in this pathogenic microorganism. This paper presents protocols for obtaining Era GTPase and immature 30S ribosome subunits from S. aureus, as well as a protocol for assembling their complex for further structural studies.

About the authors

E. A. Klochkova

Kazan Federal University

Email: konstantin.usachev@kpfu.ru
Kazan, 420008 Russia

A. D. Biktimirov

Kazan Federal University, Kazan, 420008 Russia

Kazan, 420008 Russia

A. G. Bikmullin

Kazan Federal University

Kazan, 420008 Russia

N. S. Garaeva

Kazan Federal University

Kazan, 420008 Russia

M. M. Yusupov

National Research Center “Kurchatov Institute”; Institute of Genetics, Molecular and Cellular Biology, CNRS UMR7104, INSERM U964, Universit’e de Strasbourg

Moscow, 123182 Russia; Illkirch, F‑67400 France

K. S. Usachev

Kazan Federal University

Kazan, 420008 Russia

References

  1. Rodríguez-Baño J., García L., Ramírez E., Lupión C., Muniain M.A., Velasco C., Gálvez J., del Toro M.D., Millán A.B., López-Cerero L., Pascual A. (2010) Long-term control of endemic hospital-wide methicillin-resistant Staphylococcus aureus (MRSA): the impact of targeted active surveillance for MRSA in patients and healthcare workers. Infect. Control Hosp. Epidemiol. 31(8), 786–795.
  2. Shurland S.M., Stine O.C., Venezia R.A., Johnson J.K., Zhan M., Furuno J.P., Miller R.R., Pelser C., Roghmann M.C. (2010) Prolonged colonization with the methicillin-resistant Staphylococcus aureus strain USA300 among residents of extended care facilities. Infect. Control Hosp. Epidemiol. 31(8), 838–841.
  3. Усачев К.С., Юсупов М.М., Валидов Ш.З. (2020) Гибернация — стадия функционирования рибосом. Биохимия. 85(11), 1690–1700.
  4. Shajani Z., Sykes M.T., Williamson J.R. (2011) Assembly of bacterial ribosomes. Annu. Rev. Biochem. 80, 501–526.
  5. Bennison D.J., Irving S.E., Corrigan R.M. (2019) The impact of the stringent response on TRAFAC GTPases and prokaryotic ribosome assembly. Cells. 8(11), 1313.
  6. Karbstein K. (2007) Role of GTPases in ribosome assembly. Biopolymers. 87(1), 1–11.
  7. Britton R.A. (2009) Role of GTPases in bacterial ribosome assembly. Annu. Rev. Microbiol. 63, 155–176.
  8. Gruffaz C., Smirnov A. (2023) GTPase Era at the heart of ribosome assembly. Front. Mol. Biosci. 10, 1263433.
  9. Tu C., Zhou X., Tropea J.E., Austin B.P., Waugh D.S., Court D.L., Ji X. (2009) Structure of ERA in complex with the 3’ end of 16S rRNA: implications for ribosome biogenesis. Proc. Natl. Acad. Sci. USA. 106(35), 14843–14848.
  10. Sharma M.R., Barat C., Wilson D.N., Booth T.M., Kawazoe M., Hori-Takemoto C., Shirouzu M., Yokoyama S., Fucini P., Agrawal R.K. (2005) Interaction of Era with the 30S ribosomal subunit implications for 30S subunit assembly. Mol. Cell. 18(3), 319–329.
  11. Klochkova E., Biktimirov A., Islamov D., Belousov A., Validov S., Yusupov M., Usachev K. (2020) Crystal structure of the GDP-bound GTPase Era from Staphylococcus aureus. Biochem. Biophys. Res. Commun. 735, 150852.
  12. Van Drie J.H., Tong L. (2020) Cryo-EM as a powerful tool for drug discovery. Bioorg. Med. Chem. Lett. 30(22), 127524.
  13. Stark H., Chari A. (2016) Sample preparation of biological macromolecular assemblies for the determination of high-resolution structures by cryo-electron microscopy. Microscopy (Oxf). 65(1), 23–34.
  14. Khusainov I., Vicens Q., Ayupov R., Usachev K., Myasnikov A., Simonetti A., Validov S., Kieffer B., Yusupova G., Yusupov M., Hashem Y. (2017) Structures and dynamics of hibernating ribosomes from Staphylococcus aureus mediated by intermolecular interactions of HPF. EMBO J. 36(14), 2073–2087.
  15. Bikmullin A.G., Fatkhullin B., Stetsenko A., Gabdulkhakov A., Garaeva N., Nurullina L., Klochkova E., Golubev A., Khusainov I., Trachtmann N., Blokhin D., Guskov A., Validov S., Usachev K., Yusupov M. (2023) Yet another similarity between mitochondrial and bacterial ribosomal small subunit biogenesis obtained by structural characterization of RbfA from S. aureus. Int. J. Mol. Sci. 24(3), 2118.
  16. Maksimova E., Kravchenko O., Korepanov A., Stolboushkina E. (2022) Protein assistants of small ribosomal subunit biogenesis in bacteria. Microorganisms. 10(4), 747.
  17. Gilbert R.J., Fucini P., Connell S., Fuller S.D., Nierhaus K.H., Robinson C.V., Dobson C.M., Stuart D.I. (2004) Three-dimensional structures of translating ribosomes by Cryo-EM. Mol. Cell. 14(1), 57–66.
  18. Gibson D.G., Young L., Chuang R.Y., Venter J.C., Hutchison C.A. 3rd, Smith H.O. (2009) Enzymatic assembly of DNA molecules up to several hundred kilobases. Nat. Methods. 6(5), 343–345.
  19. Клочкова Э.А., Исламов Д.Р., Биктимиров А.Д., Рогачев А.В., Валидов Ш.З., Бикмуллин А.Г., Симакин А.В., Петерс Г.С., Юсупов М.М., Усачев К.С. (2023) Выделение, очистка и кристаллизация ГТФазы Era из золотистого стафилококка. Кристаллография. 68, № 2, 276–280.
  20. Garaeva N., Fatkhullin B., Murzakhanov F., Gafurov M., Golubev A., Bikmullin A., Glazyrin M., Kieffer B., Jenner L., Klochkov V., Aganov A., Rogachev A., Ivankov O., Validov S., Yusupov M., Usachev K. (2024) Structural aspects of RimP binding on small ribosomal subunit from Staphylococcus aureus. Structure. 32(1), 74–82.
  21. Bauer M.C., Xue W.F., Linse S. (2009) Protein GB1 folding and assembly from structural elements. Int. J. Mol. Sci. 10(4), 1552–1566.
  22. Schaefer L., Uicker W.C., Wicker-Planquart C., Foucher A.E., Jault J.M., Britton R.A. (2006) Multiple GTPases participate in the assembly of the large ribosomal subunit in Bacillus subtilis. J. Bacteriol. 188(23), 8252–8258.

Supplementary files

Supplementary Files
Action
1. JATS XML

Copyright (c) 2025 Russian Academy of Sciences