Structure of the 70S ribosome from human pathogen<i>Staphylococcus aureus</i>

Khusainov, Iskander; Vicens, Quentin; Bochler, Anthony; Grosse, F.; Myasnikov, Alexander G.; Ménétret, Jean‐François; Chicher, Johana; Marzi, Stefano; Romby, Pascale; Yusupov, Marat; Hashem, Yaser

doi:10.1093/nar/gkw933

Cited by 31 publications

(19 citation statements)

References 104 publications

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“…Taken together, our data suggest that C-HPF SA forms the binding platform for the adjacent 30S, which is essential for S. aureus 100S dimerization. Furthermore, the superposition of our structure and the native SA70S 19 revealed that the presence of HPF SA induces a conformational change of helices h26 and h40 (Fig. 3d ).…”

Section: Resultsmentioning

confidence: 79%

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

et al. 2017

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Formation of 100S ribosome dimer is generally associated with translation suppression in bacteria. Trans-acting factors ribosome modulation factor (RMF) and hibernating promoting factor (HPF) were shown to directly mediate this process in E. coli. Gram-positive S. aureus lacks an RMF homolog and the structural basis for its 100S formation was not known. Here we report the cryo-electron microscopy structure of the native 100S ribosome from S. aureus, revealing the molecular mechanism of its formation. The structure is distinct from previously reported analogs and relies on the HPF C-terminal extension forming the binding platform for the interactions between both of the small ribosomal subunits. The 100S dimer is formed through interactions between rRNA h26, h40, and protein uS2, involving conformational changes of the head as well as surface regions that could potentially prevent RNA polymerase from docking to the ribosome.

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Section: Resultsmentioning

confidence: 79%

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

et al. 2017

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“…Interestingly, a rod-like density, which is absent from other known prokaryotic ribosomes such as the EC 70S (Pulk and Cate, 2013 ), T . thermophilus 70S ( TT 70S) (Selmer et al, 2006 ), and Staphylococcus aureus 70S ( SA 70S) (Khusainov et al, 2016 ), locates in a pocket formed by h27, h44, and h45 close to the decoding center (DC) in the 30S subunit (Figs. 1 B, 1 D and S5E).…”

Section: Dear Editormentioning

confidence: 99%

Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers

Zhang

et al. 2017

Protein Cell

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“…An NAD captureSeq variant was also used to compare the enrichment of specific RNAs between S. aureus strains [pCG-P2, pCG-P3, and pCG-P3(Ϫ1G)]. For that, 15 fmol of NAD-RNAs of various lengths (61,104,205,302, and 400 nt) was spiked into each sample, acting as an internal standard (IS). The PCR products were purified by polyacrylamide (PA) gel electrophoresis (PAGE), and a range between 150 and 300 bp was selected (Fig.…”

Section: Methodsmentioning

confidence: 99%

The 5′ NAD Cap of RNAIII Modulates Toxin Production in Staphylococcus aureus Isolates

et al. 2020

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Nicotinamide adenosine dinucleotide (NAD) has been found to be covalently attached to the 5′ ends of specific RNAs in many different organisms, but the physiological consequences of this modification are largely unknown. Here, we report the occurrence of several NAD-RNAs in the opportunistic pathogen Staphylococcus aureus. Most prominently, RNAIII, a central quorum-sensing regulator of this bacterium’s physiology, was found to be 5′ NAD capped in a range from 10 to 35%. NAD incorporation efficiency into RNAIII was found to depend in vivo on the −1 position of the P3 promoter. An increase in RNAIII’s NAD content led to a decreased expression of alpha- and delta-toxins, resulting in reduced cytotoxicity of the modified strains. These effects seem to be caused neither by changes in RNAIII’s secondary structure nor by a different translatability upon NAD attachment, as indicated by unaltered patterns in in vitro chemical probing and toeprinting experiments. Even though we did not observe any effect of this modification on RNAIII’s secondary structure or translatability in vitro, additional unidentified factors might account for the modulation of exotoxins in vivo. Ultimately, the study constitutes a step forward in the discovery of new roles of the NAD molecule in bacteria. IMPORTANCE Numerous organisms, including bacteria, are endowed with a 5′ NAD cap in specific RNAs. While the presence of the 5′ NAD cap modulates the stability of the modified RNA species, a significant biological function and phenotype have not been assigned so far. Here, we show the presence of a 5′ NAD cap in RNAIII from S. aureus, a dual-function regulatory RNA involved in quorum-sensing processes and regulation of virulence factor expression. We also demonstrate that altering the natural NAD modification ratio of RNAIII leads to a decrease in exotoxin production, thereby modulating the bacterium’s virulence. Our work unveils a new layer of regulation of RNAIII and the agr system that might be linked to the redox state of the NAD molecule in the cell.

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Structure of the 70S ribosome from human pathogenStaphylococcus aureus

Cited by 31 publications

References 104 publications

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

The cryo-EM structure of hibernating 100S ribosome dimer from pathogenic Staphylococcus aureus

Cryo-EM structure of Mycobacterium smegmatis ribosome reveals two unidentified ribosomal proteins close to the functional centers

The 5′ NAD Cap of RNAIII Modulates Toxin Production in Staphylococcus aureus Isolates

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