Mutations in 23S rRNA at the Peptidyl Transferase Center and Their Relationship to Linezolid Binding and Cross-Resistance

Abstract

The oxazolidinone antibiotic linezolid targets the peptidyl transferase center (PTC) on the bacterial ribosome. Thirteen single and four double 23S rRNA mutations were introduced into a Mycobacterium smegmatis strain with a single rRNA operon. Converting bacterial base identity by single mutations at positions 2032, 2453, and 2499 to human cytosolic base identity did not confer significantly reduced susceptibility to linezolid. The largest decrease in linezolid susceptibility for any of the introduced single mutations was observed with the G2576U mutation at a position that is 7.9 Å from linezolid. Smaller decreases were observed with the A2503G, U2504G, and G2505A mutations at nucleotides proximal to linezolid, showing that the degree of resistance conferred is not simply inversely proportional to the nucleotide-drug distance. The double mutations G2032A-C2499A, G2032A-U2504G, C2055A-U2504G, and C2055A-A2572U had remarkable synergistic effects on linezolid resistance relative to the effects of the corresponding single mutations. This study emphasizes that effects of rRNA mutations at the PTC are organism dependent. Moreover, the data show a nonpredictable crossresistance pattern between linezolid, chloramphenicol, clindamycin, and valnemulin. The data underscore the significance of mutations at distal nucleotides, either alone or in combination with other mutated nucleotides, in contributing to linezolid resistance.The bacterial ribosome is an important target for many clinically relevant antibiotics, including linezolid, which is effective in the treatment of infections with various multidrug-resistant Gram-positive cocci, especially methicillin-resistant Staphylococcus aureus and vancomycin-resistant enterococci (26). Several lines of evidence have established that oxazolidinones bind to the peptidyl transferase center (PTC) on the large ribosomal subunit. The evidence includes competitive binding studies with chloramphenicol and lincomycin (25), the clustering of single rRNA resistance mutations in the peptidyl transferase loop (22), in vivo cross-linking experiments (4, 23), and crystal structures of linezolid-50S subunit complexes (archaeal 50S complex [20] and bacterial 50S complex [49]). These structures show that linezolid binds to the A-site portion of the PTC (Fig. 1A) overlapping the site of the aminoacyl moiety of A-sitebound tRNA (20,49). The linezolid binding pocket is lined by eight 23S rRNA nucleotides (marked by wedges in Fig. 1B) that are highly conserved among the three domains of life (49), and the drug is not in direct contact with any ribosomal proteins. Despite this high conservation, indirect evidence suggests that linezolid affects bacterial and mitochondrial ribosomes but not cytosolic ribosomes (23,34). It has been proposed that the specificity may be determined by nucleotides a bit further away from the binding site acting through the nearby conserved nucleotides (23).The linezolid resistance mechanisms characterized thus far involve alteration at or around the PTC by modification...

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

“…6A). Similar mutations in locations somewhat distal from the actual antibiotic-binding pockets that confer resistance by allosteric rearrangements have been detected in other systems as well (54,62,63).…”

“…These structures indicate that linezolid binds to the PTC, and that linezolid blocks the A-site within the PTC. Of interest is the G2576U mutation, which is located in the second shell of the PTC and is also associated with linezolid resistance in the multidrug-resistant bacteria Enterococcus faecium, Enterococcus faecalis (53), and S. pneumoniae, as well as in Mycobacterium smegmatis, the species used in the diagnosis of Mycobacterium tuberculosis (54). G2576 is located in the second shell around the linezolid-binding pocket in the PTC, in the vicinity of the uL3 rProtein.…”

Investigation of Linezolid Resistance in Staphylococci and Enterococci

“…The linezolid binding site is surrounded by eight 23S rRNA gene nucleotides (18). Resistance to linezolid has primarily been characterized by mutations found in close proximity to the peptidyltransferase center (PTC).…”

Expression of distinct maternal and somatic 5.8S, 18S, and 28S rRNA types during zebrafish development

“…In the PTC there is just 1 nt difference: U3780C. But even a single difference in such a conserved region is worth noticing, knowing that in the prokaryote PTC-equivalent, individual nucleotides have specific roles in the translation process and some mutations result in a lethal phenotype (Beringer 2008;Polacek and Mankin 2008;Long et al 2009Long et al , 2010Yang et al 2009;Chirkova et al 2010).…”