Resistance to the Macrolide Antibiotic Tylosin Is Conferred by Single Methylations at 23S Rrna Nucleotides G748 and A2058 Acting in Synergy
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Resistance to the macrolide antibiotic tylosin is conferred by single methylations at 23S rRNA nucleotides G748 and A2058 acting in synergy Mingfu Liu and Stephen Douthwaite* Department of Biochemistry and Molecular Biology, University of Southern Denmark, DK-5230 Odense M, Denmark Communicated by Harry F. Noller, University of California, Santa Cruz, CA, September 25, 2002 (received for review July 2, 2002) The macrolide antibiotic tylosin has been used extensively in modest resistance to tylosin (13–15), whereas TlrB is a methyl- veterinary medicine and exerts potent antimicrobial activity transferase that confers moderately high resistance to tylosin in against Gram-positive bacteria. Tylosin-synthesizing strains of the several Streptomyces species (16–19). Gram-positive bacterium Streptomyces fradiae protect themselves The target for methylation by S. fradiae TlrB has recently been from their own product by differential expression of four resis- identified as the base of nucleotide G748 in 23S rRNA (18). tance determinants, tlrA, tlrB, tlrC, and tlrD. The tlrB and tlrD genes After the function of TlrB was defined, numerous other bacteria encode methyltransferases that add single methyl groups at 23S have been shown to possess homologues of this protein (20, 21). rRNA nucleotides G748 and A2058, respectively. Here we show that The rRNA target of the homologues from Gram-positive bac- methylation by neither TlrB nor TlrD is sufficient on its own to give teria is identical to that of TlrB, and these enzymes have been tylosin resistance, and resistance is conferred by the G748 and collectively renamed RlmAII (Table 1). Intriguingly, however, A2058 methylations acting together in synergy. This synergistic the tylosin-resistance phenotype that is conferred by TlrB (and mechanism of resistance is specific for the macrolides tylosin and also by other RlmAII homologues) when expressed in Strepto- mycinamycin that possess sugars extending from the 5- and 14- myces could be duplicated neither in other Gram-positive bac- positions of the macrolactone ring and is not observed for macro- teria nor in a susceptible strain of the Gram-negative bacterium lides, such as carbomycin, spiramycin, and erythromycin, that have Escherichia coli. These latter strains remained sensitive to tylosin different constellations of sugars. The manner in which the G748 despite complete methylation of G748 by TlrB. Clearly some and A2058 methylations coincide with the glycosylation patterns additional factor was playing a role in the drug-resistance TlrB of tylosin and mycinamycin reflects unambiguously how these phenotype observed in Streptomyces. macrolides fit into their binding site within the bacterial 50S Here we show that interpretation of the resistance mechanism ribosomal subunit. involving TlrB has been clouded by the presence of a tlrD homologue on the chromosome of many Streptomyces species, pecies within the actinomycetes group of Gram-positive including common laboratory strains of Streptomyces lividans Sbacteria produce most of the antibiotics that are known to (Table 1). After inactivation of the tlrD homologue, tlrB no target the bacterial ribosome. To protect their own ribosomes longer confers the tylosin-resistant phenotype in S. lividans. from inhibition during antibiotic production, actinomycetes pos- Tylosin resistance is reestablished in the S. lividans tlrDϪ strain sess an arsenal of defense mechanisms (1). These defenses after transformation with plasmids that express both the TlrB include methylation of key rRNA nucleotides at the drug target and TlrD methyltransferases. Neither of these two methyltrans- site, drug modification, and active efflux of the drug from the ferases acting on its own confers any appreciable resistance to cell. Many of these resistance mechanisms have been recruited tylosin. These results have been consistently duplicated in a by pathogenic bacteria and severely compromise the efficacy of tylosin-susceptible strain of E. coli. In addition, the Gram- antibiotics in the clinical treatment of infection. positive bacterium Corynebacterium glutamicum, which pos- The actinomycete Streptomyces fradiae is the producer of the sesses its own tlrB (rlmAII) but has no intrinsic resistance to macrolide antibiotic tylosin. Tylosin has been widely used as a tylosin, becomes resistant on transformation with tlrD. The feed additive for promoting animal growth and remains in requirement for methylation at two distinct sites in the rRNA common veterinary use against bacterial dysentery and respira- represents a novel type of resistance mechanism. This synergistic tory diseases in poultry, swine, and cattle (2). Tylosin exerts its mechanism by which the single methyl groups at G748 and antimicrobial action by binding in the peptide exit tunnel of the A2058 confer resistance could provide S. fradiae with an effec- bacterial 50S ribosomal subunit, where it inhibits protein syn- tive means of fine-tuning its response to varying intracellular thesis by interfering with peptide bond formation as well as by tylosin concentrations during its life cycle. blocking the passage of the nascent peptide chain through the tunnel. S. fradiae has four resistance gene products (TlrA, TlrB, Materials and Methods TlrC, and TrlD) to protect itself against these inhibitory effects Bacterial Strains and Plasmids. The bacterial strains and plasmids (3, 4). TlrA and TlrD are members of the Erm family of used in this study are listed in Table 4, which is published as methyltransferases (and for the sake of consistency in the supporting information on the PNAS web site, www.pnas.org. nomenclature, they have recently been renamed, Table 1). TlrD Briefly, the E. coli strain DH10B was used for cloning proce- attaches a single methyl group to the N6 position of nucleotide dures; the drug-permeable strains E. coli AS19(rlmAIϪ), S. A2058 in 23S rRNA (5), whereas TlrA dimethylates the same lividans 1326 (WT), and S. lividans(lrmϪmgtϪ) were used for the position (6). Monomethylation at A2058 confers high resistance determination of the minimal inhibitory concentrations (MICs) to lincosamides, but low resistance to macrolides and strepto- of macrolide and lincosamide antibiotics and are described gramin B antibiotics, whereas dimethylation gives high resistance below. For plasmid maintenance, ampicillin was used at 100 to each of the three drug types and confers what is commonly termed the MLSB (macrolide, lincosamide, and streptogramin B antibiotics) phenotype (7, 8). Erm dimethyltransferases have Abbreviations: MLSB, macrolide, lincosamide, and streptogramin B antibiotics; MIC, mini- become one of the most prevalent forms of MLSB resistance in mal inhibitory concentration. pathogenic bacteria (9–12). TlrC is an efflux pump that confers *To whom correspondence should be addressed. E-mail: [email protected]. 14658–14663 ͉ PNAS ͉ November 12, 2002 ͉ vol. 99 ͉ no. 23 www.pnas.org͞cgi͞doi͞10.1073͞pnas.232580599 Downloaded by guest on October 1, 2021 Table 1. Nomenclature of the rRNA methyltransferases referred to in the text Original gene name (original host) Target nucleotide in 23S rRNA Reference New gene name Reference rrmA (E. coli) G745 56 rlmAI 21 tlrB (S. fradiae) G748 18 rlmAII 21 myrA (M. griseorubida) G748 18, 53 rlmAII 21 tlrD (S. fradiae) A2058 monomethylation 5 ermN 57 myrB (M. griseorubida) A2058 monomethylation 53; M.L., unpublished work ermW 57 lrm (S. lividans) A2058 monomethylation 25 ermO 57 tlrA (S. fradiae) A2058 dimethylation 6 ermS 57 ermE (Saccharopolyspora erythaea) A2058 dimethylation 58 ermE (unchanged) To aid readability the original Streptomyces tlr gene names are retained in the text, whereas the new nomenclature is used for any recently discovered homologues in other organisms. g͞ml, kanamycin at 25 g͞ml, tetracycline at 12.5 g͞ml, yltransferase gene or a Gram-positive rlmAII G748 methyltrans- apramycin at 100 g͞ml, and thiostrepton at 10–50 g͞ml. For ferase gene (see Table 4). The second plasmid was under control MIC determinations, the macrolide and lincosamide antibiotics of the p15A replicon and contained either the S. fradiae tlrD listed in Tables 2 and 3 were serially diluted in 2-fold steps. A2058 monomethyltransferase gene or the S. erythraea ermE A2058 dimethyltransferase gene. All of the methyltransferase Inactivation of lrm and mgt Genes in S. lividans. The gene pair lrm genes in the E. coli vectors were under the control of the lac and mgt (approximately 2.2 kb) was amplified by PCR using the promoter. MICs were measured by using an agar dilution primers 5Ј-ATAGAATTCTCCTGTCACGGAAGACAAG- method (29). Approximately 104 E. coli cells were applied to the GACCG and 5Ј-ATCAAGCTTGTCTGACCGGCACGCCG- surface of LB agar plates (30), which contained ampicillin, TCG. The PCR product was cloned into pUC19 at the EcoRI tetracycline, 1 mM isopropyl -D-thiogalactoside, and serial and HindIII sites, after restricting at the sequences underlined. dilutions of the macrolide and lincosamide drugs (Table 3). The lrm and mgt genes were then cut with SexA1 to remove a Growth was evaluated after Ϸ20 h of incubation at 37°C. All fragment composed of 180 bp from the 3Ј end of lrm and 360 bp MIC values were measured a minimum of three times and were from the 5Ј end of mgt, and an apramycin-resistance gene highly reproducible. cassette (22) was inserted into the gap to create plasmid pSD113. A 3.4-kb fragment from the E. coli–Streptomyces shuttle vector Quantification of Base Methylation. The levels of methylation at pGM160, containing the pSG5