Skip to main content
SpringerLink
Log in

Backbone and side chain NMR assignments for the ribosome maturation factor P (RimP) from Staphylococcus aureus

  • Article
  • Published:
Biomolecular NMR Assignments Aims and scope Submit manuscript

Abstract

The ribosomal maturation factor (RimP) is a 17.7 kDa protein and is the assembly factor of the 30S subunit. RimP is essential for efficient processing of 16S rRNA and maturation (assembly) of the 30S ribosome. It was suggested that RimP takes part in stabilization of the central pseudoknot at the early stages of the 30S subunit maturation, and this process may occur before the head domain assembly and later stages of the 30S assembly, but the mechanism of this interaction is still not fully understood. Here we report the assignment of the 1H, 13C and 15N chemical shift in the backbone and side chains of RimP from Staphylococcus aureus. Analysis of chemical shifts of the main chain using TALOS + suggests that the RimP contains eight β-strands and three α-helices with the topology α1-β1-β2-α2- β3- α3- β4- β5- β6- β7- β8. Structural studies of RimP and its complex with the ribosome by integrated structural biology approaches (NMR spectroscopy, X-ray diffraction analysis and cryoelectron microscopy) will allow further screening of highly selective inhibitors of the translation of S. aureus.

This is a preview of subscription content, log in via an institution to check access.

Access this article

Log in via an institution

Price excludes VAT (USA)
Tax calculation will be finalised during checkout.

Instant access to the full article PDF.

Institutional subscriptions

Fig.1
Fig.2

Similar content being viewed by others

Data availability

The 1H, 15N and 13C chemical shift assignments have been deposited in the BioMagResBank (http://www.bmrb.wisc.edu) under the accession number BMRB-51521.

Abbreviations

IPTG:

Isopropyl-Thio-β-d-galactoside

S. aureus :

Staphylococcus aureus

RimP:

Ribosome maturation factor P

Cryo-EM:

Cryo-electron microscopy

PIC:

Protease Inhibitor Cocktail

PMSF:

Phenylmethane sulfonyl fluoride

SEC:

Size-exclusion chromatography

TEV protease:

Tobacco etch virus protease

References

  • Berjanskii MV, Wishart DS (2005) A simple method to predict protein flexibility using secondary chemical shifts. J Am Chem Soc 127:14970–14971

    Article  Google Scholar 

  • Bogomolovas J, Simon B, Sattler M, Stier G (2009) Screening of fusion partners for high yield expression and purification of bioactive viscotoxins. Protein Expr Purif 64(1):16–23

    Article  Google Scholar 

  • Bunner AE, Nord S, Wikström PM, Williamson JR (2010) The effect of ribosome assembly cofactors on in vitro 30S subunit reconstitution. J Mol Biol 398:1–7

    Article  Google Scholar 

  • Chu T, Weng X, Law COK, Kong H-K, Lau J, Li S, Pham HQ, Wang R, Zhang L, Kao RYT et al (2019) The ribosomal maturation factor P from Mycobacterium smegmatis facilitates the ribosomal biogenesis by binding to the small ribosomal protein S12. J Biol Chem 294:372–378

    Article  Google Scholar 

  • Held WA, Ballou B, Mizushima S, Nomura M (1974) Assembly mapping of 30 S ribosomal proteins from Escherichia coli further studies. J Biol Chem 249:3103–3111

    Article  Google Scholar 

  • Khusainov I, Vicens Q, Bochler A, Grosse F, Myasnikov A, Meńetret J-F, Chicher J, Marzi S, Romby P, Yusupova G, Yusupov M, Hashem Y (2016) Structure of the 70S ribosome from human pathogen Staphylococcus aureus. Nucleic Acids Res 44:10491–10504

    Google Scholar 

  • Maksimova E, Kravchenko O, Korepanov A, Stolboushkina E (2022) Protein assistants of small ribosomal subunit biogenesis in bacteria. Microorganisms 10:747

    Article  Google Scholar 

  • Nord S, Bylund GO, Lövgren JM, Wikström PM (2009) The RimP protein is important for maturation of the 30S ribosomal subunit. J Mol Biol 386:742–753

    Article  Google Scholar 

  • Yennamalli RM, Bisht GS, Shrivastava R (2019) Ribosomal maturation factor (RimP) is essential for survival of nontuberculous mycobacteria Mycobacterium fortuitum under in vitro acidic stress conditions. 3 Biotech 9:127

    Google Scholar 

  • Sashital DG, Greeman CA, Lyumkis D, Potter CS, Carragher B, Williamson JR (2014) A combined quantitative mass spectrometry and electron microscopy analysis of ribosomal 30S subunit assembly in E. coli. Life 3:e04491

    Google Scholar 

  • Schedlbauer A, Ochoa-Lizarralde B, Iturrioz I, Çapuni R, Diercks T, de Astigarraga E, Fucini P, Connell SR (2020) Backbone and sidechain NMR assignments for the ribosome maturation factor RimP from Escherichia coli. Biomol NMR Assign 14:189–193

    Article  Google Scholar 

  • Schedlbauer A, Iturrioz I, Ochoa-Lizarralde B, Diercks T, López-Alonso JD, Lavin JL, Kaminishi T, Çapuni R, Dhimole N, de Astigarraga E et al (2021) A conserved rRNA switch is central to decoding site maturation on the small ribosomal subunit. Sci Adv 7:eabf7547

    Article  ADS  Google Scholar 

  • Séraphin B (1995) Sm and Sm-like proteins belong to a large family: identification of proteins of the U6 as well as the U1, U2, U4 and U5 snRNPs. EMBO J 14:2089–2098

    Article  Google Scholar 

  • Shen Y, Delaglio F, Cornilescu G, Bax A (2009) TALOS plus : a hybrid method for predicting protein backbone torsion angles from NMR chemical shifts. J Biomol NMR 44:213–223

    Article  Google Scholar 

  • Traub P, Nomura M (1969) Structure and function of E. coli ribosomes. VI. Mechanism of assembly of 30S ribosomes studied in vitro. J Mol Biol 40:391–413

    Article  Google Scholar 

  • Vranken WF et al (2005) The CCPN data model for NMR spectroscopy: development of a software pipeline. Proteins 59:687–696. https://doi.org/10.1002/prot.20449

    Article  Google Scholar 

  • Yu L, Gunasekera AH, Mack J, Olejniczak ET, Chovan LE, Ruan X, Towne DL, Lerner CG, Fesik SW (2001) Solution structure and function of a conserved protein SP14.3 encoded by an essential Streptococcus pneumoniae gene. J Mol Biol 311:593–604

    Article  Google Scholar 

Download references

Acknowledgements

The work is supported by the Russian Foundation for Basic Research (RFBR): Grant 20-34-70021.

Funding

Russian Foundation for Basic Research (RFBR) Grant 20-34-70021.

Author information

Authors and Affiliations

  1. Kazan Federal University, 18 Kremlevskaya, Kazan, Russian Federation, 420008

    Natalia S. Garaeva, Aydar G. Bikmullin, Shamil Z. Validov, Marat M. Yusupov & Konstantin S. Usachev

  2. Federal Research Center, «Kazan Scientific Center of Russian Academy of Sciences», Russia, Lobachevskogo, 2/31, Kazan, Russian Federation, 420008

    Natalia S. Garaeva, Aydar G. Bikmullin, Bulat F. Fatkhullin, Shamil Z. Validov, Bruno Keiffer, Marat M. Yusupov & Konstantin S. Usachev

  3. Institut de Génétique et de Biologie Moléculaire et Cellulaire, CNRS UMR7104, INSERM U964, Université de Strasbourg, 1 rue Laurent Fries, 67400, Illkirch, France

    Bulat F. Fatkhullin, Bruno Keiffer & Marat M. Yusupov

  4. Institute of Protein Research, Russian Academy of Science, Institutskaya 4, Pushchino, Moscow Region, Russian Federation, 142290

    Bulat F. Fatkhullin

Authors
  1. Natalia S. Garaeva
    View author publications

    You can also search for this author in PubMed Google Scholar

  2. Aydar G. Bikmullin
    View author publications

    You can also search for this author in PubMed Google Scholar

  3. Bulat F. Fatkhullin
    View author publications

    You can also search for this author in PubMed Google Scholar

  4. Shamil Z. Validov
    View author publications

    You can also search for this author in PubMed Google Scholar

  5. Bruno Keiffer
    View author publications

    You can also search for this author in PubMed Google Scholar

  6. Marat M. Yusupov
    View author publications

    You can also search for this author in PubMed Google Scholar

  7. Konstantin S. Usachev
    View author publications

    You can also search for this author in PubMed Google Scholar

Contributions

KSU and MMY conceived the project: NSG and AGB cloned and purified recombinant protein under supervision of SZV, NSG and BK collected NMR data and performed data analysis. NSG, BFF and KSU wrote the manuscript with input from MMY; all authors revised the manuscript.

Corresponding author

Correspondence to Konstantin S. Usachev.

Ethics declarations

Competing interests

The authors declare no competing interests.

Conflict of interest

The authors declare that they have no conflict of interest.

Ethics approval and consent to participate

Not applicable.

Consent for publication

Not applicable.

Additional information

Publisher's Note

Springer Nature remains neutral with regard to jurisdictional claims in published maps and institutional affiliations.

Rights and permissions

Springer Nature or its licensor holds exclusive rights to this article under a publishing agreement with the author(s) or other rightsholder(s); author self-archiving of the accepted manuscript version of this article is solely governed by the terms of such publishing agreement and applicable law.

Reprints and permissions

About this article

Check for updates. Verify currency and authenticity via CrossMark

Cite this article

Garaeva, N.S., Bikmullin, A.G., Fatkhullin, B.F. et al. Backbone and side chain NMR assignments for the ribosome maturation factor P (RimP) from Staphylococcus aureus. Biomol NMR Assign 16, 373–377 (2022). https://doi.org/10.1007/s12104-022-10106-2

Download citation

  • Received:

  • Accepted:

  • Published:

  • Issue Date:

  • DOI: https://doi.org/10.1007/s12104-022-10106-2

Keywords

Search

Navigation