Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome

Li, Xiaojun; Sun, Quanya; Jiang, Cai; Yang, Kailu; Hung, Li‐Wei; Zhang, Junjie; Sacchettini, James C.

doi:10.1016/j.str.2015.07.014

Cited by 54 publications

(29 citation statements)

References 52 publications

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“…S5. Some of these features may provide inhibitory mechanisms similar to that of the periphery binding site of RsfS that inhibits protein synthesis by interfering with the association of the two subunits (69,70).…”

Section: Resultsmentioning

confidence: 99%

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

Eyal

Matzov

Krupkin

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

121

151

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The emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. Here we present the crystal structure of the large ribosomal subunit from Staphylococcus aureus, a versatile Gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, BC-3205. These crystal structures shed light on specific structural motifs of the S. aureus ribosome and the binding modes of the aforementioned antibiotics. Moreover, by analyzing the ribosome structure and comparing it with those of nonpathogenic bacterial models, we identified some unique internal and peripheral structural motifs that may be potential candidates for improving known antibiotics and for use in the design of selective antibiotic drugs against S. aureus.

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Section: Resultsmentioning

confidence: 99%

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

Eyal

Matzov

Krupkin

et al. 2015

Proc. Natl. Acad. Sci. U.S.A.

121

151

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show abstract

“…To identify potential differences, we subjected these ribosomes as well as ribosomes isolated from the wild-type cells to mass spectrometric analysis (Table 1). One protein that was more abundant in both of the mutant ribosomes is the ribosome silencing factor RsfS that binds the ribosome via ribosomal protein L14 (30) and interferes with subunit joining and modestly inhibits protein synthesis (31) (Table 1). However, deletion of rsfS did not rescue the inactive phenotype of Δ hpf ribosomes (Fig.…”

Section: Resultsmentioning

confidence: 99%

Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence

Feaga

Kopylov

Kim³

et al. 2019

Preprint

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18The formation of ribosome dimers during periods of quiescence is widespread among bacteria 19 and some higher eukaryotes. However, the mechanistic importance of dimerization is not well 20 understood. In bacteria ribosome dimerization is mediated by the Hibernation Promoting Factor 21 (HPF). Here, we report that HPF from the Gram-positive bacterium Bacillus subtilis preserves 22 active ribosomes by preventing the loss of essential ribosomal proteins. Ribosomes isolated from 23 strains either lacking HPF (∆hpf) or encoding a mutant allele of HPF that binds the ribosome but 24 does not mediate dimerization were substantially depleted of the small subunit proteins S2 and 25 S3. Strikingly, these proteins are located at the ribosome dimer interface. We used single particle 26 cryo-EM to further characterize ribosomes isolated from a ∆hpf mutant strain and observed that 27 many were missing S2, S3, or both. These data support a model in which the ribosome 28 dimerization activity of HPF evolved to protect labile proteins that are essential for ribosome 29 function. 31 Significance Statement 32When nutrients become scarce, many bacterial species enter an extended state of quiescence. 33 A major challenge of this state is how to attenuate protein synthesis, the most energy consuming 34 cellular process, while preserving ribosomes for the return to favorable conditions. Here, we show 35 that the ribosome-binding protein HPF which dimerizes ribosomes functions to protect essential 36 ribosomal proteins at the dimer interface. HPF is almost universally conserved in bacteria and 37 HPF deletions in diverse species exhibit decreased viability under nutrient limitation. Our data 38 provide mechanistic insight into this phenotype and establish a role for HPF in maintaining 39 translationally competent ribosomes during quiescence. 40 \body 41 42 51 Ribosomes in quiescent cells ranging from bacteria (3, 7, 8) to some mammalian cells (9, 10) 52 form dimers. However, the functional consequences of dimerization remain mysterious. In 53 bacteria, ribosome dimerization is mediated by the protein HPF. Two monomers of HPF bind two 54 70S ribosomes and interact at their C-termini to form 100S ribosome dimers (11). Most bacteria 55 encode an HPF homolog, and mutants lacking HPF exhibit pleiotropic phenotypes, including 56 decreased viability during extended stationary phase (12), increased antibiotic sensitivity (13), 57 decreased virulence (14), and a reduction in protein synthesis and growth after nutrient limitation 58 (15, 16). Ribosome dimerization may inhibit protein synthesis (17, 18) and bacteria lacking HPF 59 exhibit increased polysomes, indicative of increased protein synthesis (19). However, phenotypes 60 associated with HPF deletion may also be explained by ribosome instability as ribosomal RNA 61 has been shown to be degraded in some mutants lacking HPF (15, 20, 21). 62 Recent structures of 100S ribosome dimers from Escherichia coli, Staphylococcus aureus, 63 and B. subtilis reveal that HPF binding to the ...

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“…Considerable roles in the translation inhibition and bacterial resistance play ribosomal silencing factors (RSF) and ATP-binding cassette (ABC) proteins, respectively. Li et al solved the cryo-EM structure of the M. tuberculosis 50S subunit bound to RSF and the crystal structure of a free protein [ 59 ]. Chromatographic and crystallographic data pointed toward the presence of RSF dimer in both solution and solid state.…”

Section: Cryo-em Imaging Of Macrolide-targeted Ribosomesmentioning

confidence: 99%

Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics

Jednačak

Mikulandra

Novak

2020

IJMS

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Macrolide antibiotics are macrocyclic compounds that are clinically used and prescribed for the treatment of upper and lower respiratory tract infections. They inhibit the synthesis of bacterial proteins by reversible binding to the 23S rRNA at or near the peptidyl transferase center. However, their excellent antibacterial profile was largely compromised by the emergence of bacterial resistance. Today, fighting resistance to antibiotics is one of the greatest challenges in medicinal chemistry. Considering various physicochemical properties of macrolides, understanding their structure and interactions with macromolecular targets is crucial for the design of new antibiotics efficient against resistant pathogens. The solid-state structures of some macrolide-ribosome complexes have recently been solved, throwing new light on the macrolide binding mechanisms. On the other hand, a combination of NMR spectroscopy and molecular modeling calculations can be applied to study free and bound conformations in solution. In this article, a description of advanced physicochemical methods for elucidating the structure and interactions of macrolide antibiotics in solid state and solution will be provided, and their principal advantages and drawbacks will be discussed.

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Structure of Ribosomal Silencing Factor Bound to Mycobacterium tuberculosis Ribosome

Cited by 54 publications

References 52 publications

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

Structural insights into species-specific features of the ribosome from the pathogen Staphylococcus aureus

Ribosome dimerization prevents loss of essential ribosomal proteins during quiescence

Advanced Methods for Studying Structure and Interactions of Macrolide Antibiotics

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