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Antimicrobial Agents and Chemotherapy, January 2006, p. 178-184, Vol. 50, No. 1
0066-4804/06/$08.00+0 doi:10.1128/AAC.50.1.178-184.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
Department of Bacterial Pathogenesis and Infection Control, National Institute of Infectious Diseases, Tokyo,1 Department of Bacteriology and Bacterial Infection Control, Gunma University Graduate School of Medicine, Gunma Japan2
Received 7 May 2005/ Returned for modification 31 July 2005/ Accepted 28 September 2005
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was successfully transformed by electroporation with the plasmid of the parent strain, ARS68, and acquired an unusually high degree of resistance against aminoglycosides. Cloning and sequencing analyses revealed that the presence of a novel 16S rRNA methylase gene, designated rmtC, was responsible for resistance in strain ARS68 and its transformant. The G+C content of rmtC was 41.1%, and the deduced amino acid sequences of the newly identified 16S rRNA methylase, RmtC, shared a relatively low level of identity (
29%) to other plasmid-mediated 16S rRNA methylases, RmtA, RmtB, and ArmA, which have also been identified in pathogenic gram-negative bacilli. Also, RmtC shared a low level of identity (
28%) with the other 16S rRNA methylases found in aminoglycoside-producing actinomycetes. The purified histidine-tagged RmtC clearly showed methyltransferase activity against E. coli 16S rRNA in vitro. rmtC was located downstream of an ISEcp1-like element containing tnpA. Several plasmid-mediated 16S rRNA methylases have been identified in pathogenic gram-negative bacilli belonging to the family Enterobacteriaceae, and some of them are dispersing worldwide. The acceleration of aminoglycoside resistance among gram-negative bacilli by producing plasmid-mediated 16S rRNA methylases, such as RmtC, RmtB, and RmtA, may indeed become an actual clinical hazard in the near future. |
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Recently, as a new mechanism of resistance against aminoglycosides among clinically important pathogenic bacteria, plasmid-mediated 16S rRNA methylase (RmtA) was first characterized in a clinically isolated Pseudomonas aeruginosa strain, strain AR-2. This strain was isolated in 1997 in a Japanese hospital and demonstrated consistent resistance to various clinically important aminoglycosides (29). The total sequence of a large plasmid carrying genes for both CTX-M-3 and 16S rRNA methylase was then submitted to the EMBL/GenBank database (accession no. AF550415) on 18 October 2002 by M. Golebiewski et al., although they did not seem to be aware of the presence of the armA gene in the sequence deposited in the database. In 2003, the armA gene, found in a clinically isolated Klebsiella pneumoniae strain, was reported from France (7). RmtB, which was encoded on a nonconjugative plasmid of a clinically isolated Serratia marcescens strain, was also reported from Japan in 2004 (6). At present, the three types of plasmid-mediated 16S rRNA methylases described above have been found in pathogenic gram-negative rods. More recently, nosocomial outbreaks caused by 16S rRNA methylase-producing gram-negative bacteria was reported from Taiwan (28). The further global dissemination of 16S rRNA methylase genes among pathogenic bacilli will be a cause of great concern in the near future, because these genes were mediated by some bacterial site-specific recombination and translocation systems such as a transposon (6, 7, 26).
A Proteus mirabilis strain, strain ARS68, which displayed a very high level of resistance to various aminoglycosides, was isolated in 2003 from an inpatient in Japan. A preliminary PCR analysis, however, failed to detect any of the known three plasmid-mediated 16S rRNA methylase genes, rmtA, rmtB, and armA, in this strain. Therefore, it was strongly suspected that the P. mirabilis ARS68 strain would have a novel 16S rRNA methylase gene. In the present study, the molecular mechanism underlying a very high level of resistance against various aminoglycosides found in strain ARS68 was elucidated.
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TABLE 1. Bacterial strains and plasmids used in this study
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PCR amplification. The sets of PCR primers and amplification conditions used to detect the three 16S rRNA methylase genes, rmtA, rmtB, and armA, are referred to in our recent study (27).
Transfer of aminoglycoside resistance.
Conjugal transfer was performed by using E. coli CSH-2 (F metB, resistant to both nalidixic acid and rifampin) or E. coli HB101 (resistant to streptomycin) as a recipient by a filter-mating method. Transconjugants were selected on Luria-Bertani (LB) agar plates containing rifampin (100 µg/ml) and kanamycin (30 µg/ml) or arbekacin (10 µg/ml) when E. coli CSH-2 was used as the recipient. Two kinds of streptomycin-containing (50 µg/ml) LB agar plates supplemented with kanamycin (30 µg/ml) or arbekacin (10 µg/ml) were also prepared when E. coli HB101 was used as the recipient. The plasmid DNA of P. mirabilis ARS68 was prepared by the method of Kado and Liu (14). E. coli DH5
was transformed with the plasmids of P. mirabilis ARS68 by electroporation techniques. Transformants were selected on LB agar plates supplemented with arbekacin (4 µg/ml) or kanamycin (10 µg/ml).
Cloning and sequencing of aminoglycoside resistance determinants. Both total DNA and plasmid DNA were prepared from the bacterial strains as described previously (23) and restricted with endonucleases according to the recommendations of the supplier. The digested fragments were ligated to restriction enzyme-cleaved pBCSK+ (Stratagene, La Jolla, Calif.), and E. coli competent cells were transformed by electroporation with the mixture of recombinant plasmids. Transformants were selected on LB agar plates containing chloramphenicol (30 µg/ml) and arbekacin (4 µg/ml) or kanamycin (10 µg/ml). Both strands of the nucleotide sequences of the cloned fragment encoding the gene responsible for aminoglycoside resistance were determined with BigDye Terminator cycle sequencing ready reaction kits and an ABI 3100 DNA analyzer (Applied Biosystems, Foster City, Calif.) by using several custom sequencing primers.
PCR cloning of aminoglycoside resistance gene. The DNA fragment carrying the aminoglycoside resistance gene and its promoter region was amplified by PCR with the primers rmtC-F (5'-CGC GGA TCC AGT GTA TGA AAA ATG TCT GG-3') and rmtC-R (5'-CGG GGT ACC GGT GTG TTA GAA TTT GCC TT-3') (where the underlining indicates the restriction site of BamHI or KpnI). The resultant fragments were digested with BamHI and KpnI and ligated to pBCSK+ (Stratagene).
Expression and purification of histidine-tagged enzyme. The gene responsible for aminoglycoside resistance was amplified from plasmid pBC-E1 by using primers that introduced NdeI and XhoI sites at the ends of the amplified fragments. This fragment was ligated to the pGEM-T vector (Promega, Madison, Wis.), and one plasmid with no amplification error (pGEM-rmtC) was selected. A single nucleotide mutation which leads to the silent mutation (T to C) at position 171 was introduced to destroy the NdeI site within the fragment inserted on pGEM-rmtC by using an LA PCR in vitro mutagenesis kit (Takara Bio Inc., Ohtsu, Japan). A resultant plasmid was digested with NdeI and XhoI and ligated into the pET-29a(+) vector (Novagen, Madison, Wis.) restricted with the same enzymes. The newly constructed expression vector, pET-His-rmtC, was introduced into E. coli (DE3)pLysS (Novagen) and cultured in 1 liter of LB broth containing both kanamycin (50 µg/ml) and chloramphenicol (30 µg/ml). Isopropyl-ß-D-thiogalactopyranoside (0.5 mM) was added when the culture reached an A600 of 0.55, and the culture was incubated for an additional 3 h. The bacterial pellet harvested by centrifugation was washed with 50 mM phosphate buffer (pH 7.0) and suspended in 20 mM phosphate buffer (pH 7.4) containing 0.5 M NaCl and 10 mM imidazole. The suspension was passed through a French pressure cell (Ohtake Works Co., Ltd., Tokyo, Japan) at 120 MPa and then centrifuged at 100,000 x g for 1 h. The supernatant containing the fusion protein was loaded onto a HisTrap HP column and purified according to the manufacturer's instructions (Amersham Biosciences, K. K., Tokyo, Japan). The eluted fusion protein was dialyzed against 20 mM Tris-HCl buffer (pH 7.5), applied to an anion-exchange HiTrap Q HP column (Amersham Biosciences), and eluted with a linear gradient of NaCl. Finally, size-exclusion chromatography was performed with a Superdex 200 HR10/30 column (Amersham Biosciences). The purified protein was dialyzed against HRS buffer (10 mM HEPES-KOH, pH 7.5; 10 mM MgCl2; 50 mM NH4Cl; 3 mM 2-mercaptoethanol). The purity was checked by electrophoresis on sodium dodecyl sulfate-polyacrylamide gels. The protein concentration was estimated by use of the Coomassie Plus protein assay reagent and bovine serum albumin as a standard (Pierce Biotechnology, Rockford, Ill.). The N-terminal sequence of the purified protein was obtained by Edman degradation in a Shimadzu model PPSQ-23 automated protein sequencer.
Preparation of 30S ribosomal subunits.
The 30S ribosomal subunits of E. coli DH5
were prepared as described by Skeggs et al. (25). After ultracentrifugation with sucrose density gradients, fractions of the 30S ribosomal subunits were collected and concentrated by centrifugation with an Ultrafree-15 centrifugal filter device (Millipore Corporation, Bedford, Mass.). The purity of the 30S ribosomal subunit was checked by denatured agarose gel electrophoresis of the 16S rRNA derived from the material, and the 30S ribosomal subunit was stored at 80°C in aliquots until use.
Methylation assay of 30S ribosomal subunits.
The methylation assay of the 30S ribosomal subunits was carried out as described by Doi et al. (6), with some modifications, as follows. The reaction mixture contained 20 pmol 30S ribosomal subunits from E. coli DH5
, 20 pmol histidine-tagged RmtC, and 5 µCi S-adenosyl-L-[methyl-3H]methionine ([methyl-3H]SAM); and this mixture was adjusted to 200 µl with methylation buffer (50 mM HEPES-KOH, pH 7.5; 7.5 mM MgCl2; 37.5 mM NH4Cl; 3 mM 2-mercaptoethanol). In control experiments, histidine-tagged RmtC was replaced by an equal volume of heat-inactivated histidine-tagged RmtC, bovine serum albumin, and HRS buffer. Samples (35 µl) were taken at 0, 5, 15, 30, and 60 min and purified with an RNeasy Mini kit (QIAGEN K. K., Tokyo, Japan), according to the instructions provided by the manufacturer. Two micrograms of eluted 16S rRNA was spotted onto a DEAE filter mat for MicroBeta (Perkin-Elmer Life Sciences Japan Co., Ltd., Tokyo, Japan). The filter mat was then covered with MeltiLex for MicroBeta filters (Perkin-Elmer) on a hot plate. Finally, it was applied to a 1450 MicroBeta TRILUX (Perkin-Elmer), and the radioactivity of each spot was counted.
Nucleotide sequence accession number. The open reading frame of rmtC was deposited in the EMBL and GenBank databases through the DDBJ database and has been assigned accession number AB194779.
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1,024 µg/ml) to the various clinically important aminoglycosides except streptomycin and neomycin, as shown in Table 2. PCR analyses were performed preliminarily to detect three 16S rRNA methylase genes, rmtA, rmtB, and armA, which were previously found in pathogenic gram-negative bacilli; but none of them was detected in this strain. |
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TABLE 2. Results of antibiotic susceptibility testing
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was successfully transformed by electroporation with the plasmid, pARS68, prepared from P. mirabilis ARS68. The size of plasmid pARS68 was estimated to be ca. >100 kb by summation of the SacI-digested DNA fragment sizes observed by agarose gel electrophoresis (data not shown). E. coli DH5
(pARS68) demonstrated a very high degree of resistance to various aminoglycosides, as was observed in the parent strain (Table 2).
Cloning of aminoglycoside resistance determinant.
A cloning experiment was performed to confirm the genetic aminoglycoside resistance determinant of P. mirabilis ARS68 and its transformant, E. coli DH5
(pARS68). As a result, one recombinant plasmid (pBC-E1) with a 7.7-kb EcoRI insert derived from pARS68 was obtained by selection with arbekacin and chloramphenicol, and the insert was then sequenced. A part of the cloned fragment sequenced is shown in Fig. 1A. The first 0.5 kb of the insert contained the 3' end of the tnpA gene with a terminal inverted repeat (IR). This region containing the IR had a high degree of similarity at the nucleotide level with the ISEcpI element, which was often identified upstream of several genes encoding CTX-M-type ß-lactamases and CMY-type cephalosporinases (2, 4, 10, 20, 21). One open reading frame, which encoded 281 amino acids, was located downstream of tnpA. A BLAST analysis of the deduced amino acid sequence revealed that the gene product exhibited low-level identities to the 16S rRNA methylases, RmtA, RmtB, and ArmA (28%, 29%, and 28%, respectively), found in pathogenic gram-negative bacilli. The predicted enzyme was designated RmtC, and a comparison of the deduced amino acid sequences of RmtA, RmtB, and ArmA is shown in Fig. 2. RmtC also has a low degree of similarity (
28%) to other 16S rRNA methylases found in aminoglycoside-producing Streptomyces and Micromonospora species. The amino acid similarities among 16S rRNA methylases are summarized in Table 3. The putative promoter region of rmtC appeared to be located within the ISEcpI-like element, just upstream of the IR generally found among several CTX-M-type and CMY-type ß-lactamase genes (Fig. 1B) (4, 10, 20, 22). One Sau3AI fragment carrying the aminoglycoside phosphotransferase gene, aph(3'), was also cloned from P. mirabilis strain ARS68 when kanamycin was used as a selection marker.
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FIG. 1. (A) Schematic presentation of the 7.7-kb EcoRI fragment on pBC-E1 and the 1.2-kb PCR fragment on pBC-KB1. (B) Part of the nucleotide sequences encoding the 3' end of an ISEcp1-like element and the start region of rmtC. The predicted 35 and 10 promoter sequences and the +1 position of the putative transcriptional start of rmtC are boxed. These positions were cited elsewhere (4). Arrows indicate the transcription orientation. The deduced amino acid sequences are designated in single-letter code. The right inverted repeat (IR) of an ISEcp1-like element is underlined.
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FIG. 2. Alignment of the deduced amino acid sequence of RmtC with those of RmtA, RmtB, and ArmA. Asterisks indicate the conserved residues among the above four 16S rRNA methylases.
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TABLE 3. Amino acid identities among various 16S rRNA methylases
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(pARS68), E. coli DH5
(pBC-E1), and E. coli DH5
(pBC-KB1) are shown in Table 2. E. coli DH5
(pARS68) demonstrated resistance to all the various aminoglycosides except streptomycin and neomycin. RmtC-producing strains E. coli DH5
(pBC-E1) and E. coli(pBC-KB1) showed high levels of resistance to 4,6-disubstituted deoxystreptamine antimicrobials belonging to the kanamycin and gentamicin groups but were susceptible to the 4,5-disubstituted deoxystreptamine antimicrobial neomycin and another aminoglycoside, streptomycin. E. coli DH5
(pBC-Sa1), which carried the aminoglycoside phosphotransferase gene, aph(3'), showed resistance to both neomycin (MIC, 1,024 µg/ml) and kanamycin (MIC, >1,024 µg/ml). The resistance to neomycin found in strain ARS68 seemed to be attributable to the presence of aph(3').
Identification of RmtC as a 16S rRNA methyltransferase.
Histidine-tagged RmtC-producing E. coli BL21(DE3)pLysS showed resistance to arbekacin, while E. coli BL21(DE3)pLysS and E. coli BL21(DE3)pLysS, which carried the pET29a(+) vector, were susceptible to arbekacin. This finding indicated that the production of histidine-tagged RmtC was responsible for the aminoglycoside resistance in E. coli BL21(DE3)pLysS. The N-terminal sequence of the purified protein was determined to be MKTND. The result of the methylation assay is shown in Fig. 3. Purified histidine-tagged RmtC readily methylated 30S ribosomal subunits prepared from E. coli DH5
in the presence of the methyl group donor [methyl-3H]SAM as a cosubstrate in a time-dependent manner. On the other hand, incubation with heat-inactivated histidine-tagged RmtC did not increase the counts of radioactivity. When an equal volume of bovine serum albumin or HRS buffer was used in place of purified histidine-tagged RmtC, no increase in the radioactivity counts was observed (data not shown).
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FIG. 3. Methylation of 16S rRNA. The 16S rRNA from E. coli DH5 was incubated with purified histidine-tagged RmtC (His-RmtC) by using [methyl-3H]SAM as a cofactor. The value of each point was calculated with three datum points. Error bars indicate standard deviations.
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Interestingly, all the plasmid-mediated 16S rRNA methylase genes found so far were associated with some genes implicated in gene recombination systems. For example, the rmtA gene was flanked by a 262-bp sequence called the 
element that was initially found in Tn5041 and that was predicted to be a relic of mobile genetic elements (26). The rmtB gene was located just downstream of the 3' end of the insertion sequence of Tn3 (6). As for the two genes described above, the mode of actual translocation of the fragments containing the 16S rRNA methylase genes has not been elucidated in detail. On the other hand, it was reported that the armA gene was mediated by a composite transposon Tn1548 and was successfully transposed in vitro (8). Although the rmtC gene was also associated with a tnpA gene encoding a probable transposase, the actual mode of translocation of the regions carrying the rmtC gene is unclear. However, it is speculated that the presence of an ISEcpI-like element located upstream of rmtC would be responsible for the actual translocation process, because several CTX-M-type ß-lactamase genes located downstream of tnpA within the ISEcpI element were able to be transposed in vitro (4, 21). Characterization of the genetic environment mediating the rmtC gene and the mode of translocation will be undertaken in another study.
As was observed in the phylogenic tree (Fig. 4), a cluster of plasmid-mediated 16S rRNA methylases is antithetical to that of the 16S rRNA methylases from actinomycetes. Although no progenitor of plasmid-mediated 16S rRNA methylases, including RmtA, RmtB, RmtC, and ArmA, has been found to date, these genes might have been derived from unknown environmental aminoglycoside-producing bacteria.
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FIG. 4. Dendrogram of 16S rRNA methylases. Sequences are from P. mirabilis (RmtC; GenBank accession number AB194779), P. aeruginosa (RmtA; GenBank accession number AB083212) (29), S. marcescens (RmtB; GenBank accession number AB103506) (6), K. pneumoniae (ArmA; GenBank accession number AY220558) (7), Micromonospora zionensis (Sgm; GenBank accession number A45282) (16), Micromonospora rosea (Grm; GenBank accession number M55521) (15), Micromonospora inyoensis (Srm1; GenBank accession number AY661430), Micromonospora echinospora (GrmA; GenBank accession number AY524043), Streptomyces sp. (Kan; GenBank accession number AJ414669), Streptomyces tenebrarius (NebM; GenBank accession number AJ550991), S. tenebrarius (KgmB; GenBank accession number S60108) (13), Streptoalloteichus hindustanus (NbrB; GenBank accession number AF038408), Streptoalloteichus kanamyceticus (Kmr; GenBank accession number AJ582817) (5), Micromonospora olivasterospora (FmrO; GenBank accession number D13171) (19), M. echinospora (GrmO; GenBank accession number AY524043), and Chlorobium tepidum TLS (putative methytransferase; GenBank accession number AAM72273). The "0.1" scale represents a genetic unit reflecting 10% of the amino acid substitutions calculated with the ClustalW program (http://www.ddbj.nig.ac.jp/search/Welcome-e.html) provided by the DDBJ (http://www.ddbj.nig.ac.jp/Welcome-e.html).
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This study was supported by the Ministry of Health, Labor and Welfare, Japan (grants H15-Shinkou-9 and H15-Shinkou-10). The research activity of J. Wachino was supported by a Scholarship for Young Scientists, provided by the Japan Society for the Promotion of Science.
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