Disassembly of the Hibernating 100S Ribosome by an Evolutionarily Conserved GTPase

Overview

Journal Proc Natl Acad Sci U S A

Specialty Science

Date 2017 Sep 13

PMID 28894000

Citations 39

Authors

Arnab Basu

Mee-Ngan F Yap

Affiliations

Soon will be listed here.

Abstract

The bacterial hibernating 100S ribosome is a poorly understood form of the dimeric 70S particle that has been linked to pathogenesis, translational repression, starvation responses, and ribosome turnover. In the opportunistic pathogen and most other bacteria, hibernation-promoting factor (HPF) homodimerizes the 70S ribosomes to form a translationally silent 100S complex. Conversely, the 100S ribosomes dissociate into subunits and are presumably recycled for new rounds of translation. The regulation and disassembly of the 100S ribosome are largely unknown because the temporal abundance of the 100S ribosome varies considerably among different bacterial phyla. Here, we identify a universally conserved GTPase (HflX) as a bona fide dissociation factor of the 100S ribosome. The expression levels and are coregulated by general stress and stringent responses in a temperature-dependent manner. While all tested guanosine analogs stimulate the splitting activity of HflX on the 70S ribosome, only GTP can completely dissociate the 100S ribosome. Our results reveal the antagonistic relationship of HPF and HflX and uncover the key regulators of 70S and 100S ribosome homeostasis that are intimately associated with bacterial survival.

Citing Articles

HflX-mediated drug resistance through ribosome splitting and rRNA disordering in mycobacteria.

Majumdar S, Kashyap A, Koripella R, Sharma M, Hurst-Hess K, Manjari S Proc Natl Acad Sci U S A. 2025; 122(6):e2419826122.

PMID: 39913204 PMC: 11831132. DOI: 10.1073/pnas.2419826122.

RqcH supports survival in the absence of non-stop ribosome rescue factors.

Callan K, Prince C, Feaga H bioRxiv. 2024; .

PMID: 39026760 PMC: 11257542. DOI: 10.1101/2024.07.12.603306.

Staphylococcal exoribonuclease YhaM destabilizes ribosomes by targeting the mRNA of a hibernation factor.

Liponska A, Lee H, Yap M Nucleic Acids Res. 2024; 52(15):8998-9013.

PMID: 38979572 PMC: 11347170. DOI: 10.1093/nar/gkae596.

Drug resistance through ribosome splitting and rRNA disordering in mycobacteria.

Majumdar S, Kashyap A, Koripella R, Sharma M, Hurst-Hess K, Manjari S bioRxiv. 2024; .

PMID: 38915643 PMC: 11195266. DOI: 10.1101/2024.06.13.598844.

Rippling life on a dormant planet: hibernation of ribosomes, RNA polymerases, and other essential enzymes.

Helena-Bueno K, Chan L, Melnikov S Front Microbiol. 2024; 15:1386179.

PMID: 38770025 PMC: 11102965. DOI: 10.3389/fmicb.2024.1386179.

References

Polkinghorne A, Ziegler U, Gonzalez-Hernandez Y, Pospischil A, Timms P, Vaughan L . Chlamydophila pneumoniae HflX belongs to an uncharacterized family of conserved GTPases and associates with the Escherichia coli 50S large ribosomal subunit. Microbiology (Reading). 2008; 154(Pt 11):3537-3546. DOI: 10.1099/mic.0.2008/022137-0. View

Hong J, Loiselle C, Yoon D, Lee O, Becker K, Singer H . Microarray analysis in Tourette syndrome postmortem putamen. J Neurol Sci. 2004; 225(1-2):57-64. DOI: 10.1016/j.jns.2004.06.019. View

Maki Y, Yoshida H, Wada A . Two proteins, YfiA and YhbH, associated with resting ribosomes in stationary phase Escherichia coli. Genes Cells. 2001; 5(12):965-74. DOI: 10.1046/j.1365-2443.2000.00389.x. View

Davis A, Gohara D, Yap M . Sequence selectivity of macrolide-induced translational attenuation. Proc Natl Acad Sci U S A. 2014; 111(43):15379-84. PMC: 4217412. DOI: 10.1073/pnas.1410356111. View

Khusainov I, Vicens Q, Ayupov R, Usachev K, Myasnikov A, Simonetti A . Structures and dynamics of hibernating ribosomes from mediated by intermolecular interactions of HPF. EMBO J. 2017; 36(14):2073-2087. PMC: 5510003. DOI: 10.15252/embj.201696105. View

Feng B, Mandava C, Guo Q, Wang J, Cao W, Li N . Structural and functional insights into the mode of action of a universally conserved Obg GTPase. PLoS Biol. 2014; 12(5):e1001866. PMC: 4028186. DOI: 10.1371/journal.pbio.1001866. View

Geiger T, Kastle B, Gratani F, Goerke C, Wolz C . Two small (p)ppGpp synthases in Staphylococcus aureus mediate tolerance against cell envelope stress conditions. J Bacteriol. 2013; 196(4):894-902. PMC: 3911181. DOI: 10.1128/JB.01201-13. View

Ueta M, Yoshida H, Wada C, Baba T, Mori H, Wada A . Ribosome binding proteins YhbH and YfiA have opposite functions during 100S formation in the stationary phase of Escherichia coli. Genes Cells. 2005; 10(12):1103-12. DOI: 10.1111/j.1365-2443.2005.00903.x. View

Pattee P, Neveln D . Transformation analysis of three linkage groups in Staphylococcus aureus. J Bacteriol. 1975; 124(1):201-11. PMC: 235883. DOI: 10.1128/jb.124.1.201-211.1975. View

10.

Basu A, Yap M . Ribosome hibernation factor promotes Staphylococcal survival and differentially represses translation. Nucleic Acids Res. 2016; 44(10):4881-93. PMC: 4889938. DOI: 10.1093/nar/gkw180. View

11.

Puri P, Eckhardt T, Franken L, Fusetti F, Stuart M, Boekema E . Lactococcus lactis YfiA is necessary and sufficient for ribosome dimerization. Mol Microbiol. 2013; 91(2):394-407. DOI: 10.1111/mmi.12468. View

12.

Schneewind O, Model P, Fischetti V . Sorting of protein A to the staphylococcal cell wall. Cell. 1992; 70(2):267-81. DOI: 10.1016/0092-8674(92)90101-h. View

13.

Coatham M, Brandon H, Fischer J, Schummer T, Wieden H . The conserved GTPase HflX is a ribosome splitting factor that binds to the E-site of the bacterial ribosome. Nucleic Acids Res. 2016; 44(4):1952-61. PMC: 4770234. DOI: 10.1093/nar/gkv1524. View

14.

Iwakura N, Yokoyama T, Quaglia F, Mitsuoka K, Mio K, Shigematsu H . Chemical and structural characterization of a model Post-Termination Complex (PoTC) for the ribosome recycling reaction: Evidence for the release of the mRNA by RRF and EF-G. PLoS One. 2017; 12(5):e0177972. PMC: 5443523. DOI: 10.1371/journal.pone.0177972. View

15.

Zavialov A, Hauryliuk V, Ehrenberg M . Splitting of the posttermination ribosome into subunits by the concerted action of RRF and EF-G. Mol Cell. 2005; 18(6):675-86. DOI: 10.1016/j.molcel.2005.05.016. View

16.

Reiss S, Pane-Farre J, Fuchs S, Francois P, Liebeke M, Schrenzel J . Global analysis of the Staphylococcus aureus response to mupirocin. Antimicrob Agents Chemother. 2011; 56(2):787-804. PMC: 3264241. DOI: 10.1128/AAC.05363-11. View

17.

Yamagishi M, Matsushima H, Wada A, Sakagami M, Fujita N, Ishihama A . Regulation of the Escherichia coli rmf gene encoding the ribosome modulation factor: growth phase- and growth rate-dependent control. EMBO J. 1993; 12(2):625-30. PMC: 413246. DOI: 10.1002/j.1460-2075.1993.tb05695.x. View

18.

Zhang Y, Mandava C, Cao W, Li X, Zhang D, Li N . HflX is a ribosome-splitting factor rescuing stalled ribosomes under stress conditions. Nat Struct Mol Biol. 2015; 22(11):906-13. DOI: 10.1038/nsmb.3103. View

19.

Hirokawa G, Nijman R, Raj V, Kaji H, Igarashi K, Kaji A . The role of ribosome recycling factor in dissociation of 70S ribosomes into subunits. RNA. 2005; 11(8):1317-28. PMC: 1370814. DOI: 10.1261/rna.2520405. View

20.

Kato T, Yoshida H, Miyata T, Maki Y, Wada A, Namba K . Structure of the 100S ribosome in the hibernation stage revealed by electron cryomicroscopy. Structure. 2010; 18(6):719-24. DOI: 10.1016/j.str.2010.02.017. View