Isolation of a small DNA fragment carrying the gene for a dihydrofolate reductase from a trimethoprim resistance factor

Dual-Target Inhibitors of the Folate Pathway Inhibit Intrinsically Trimethoprim-Resistant DfrB Dihydrofolate Reductases

Trimethoprim (TMP) is widely used to treat infections in humans and in livestock, accelerating the incidence of TMP resistance. The emergent and largely untracked type II dihydrofolate reductases (DfrBs) are intrinsically TMP-resistant plasmid-borne Dfrs that are structurally and evolutionarily unrelated to chromosomal Dfrs. We report kinetic characterization of the known DfrB family members. Their kinetic constants are conserved and all are poorly inhibited by TMP, consistent with TMP resistance. We investigate their inhibition with known and novel bisubstrate inhibitors of 6-hydroxymethyl-7,8-dihydropterin pyrophosphokinase (HPPK). Importantly, all are inhibited by the HPPK inhibitors, making these molecules dual-target inhibitors of two folate pathway enzymes that are strictly microbial.

Antibiotic resistance in Escherichia coli of the normal intestinal flora of swine

Twelve hundred enterobacterial Escherichia coli isolates of porcine origin were screened phenotypically for antibiotic resistance. The bacteria were isolated from 10 herds of swine with different histories of exposure to antimicrobial agents for therapeutic purposes. The bacterial isolates were part of the normal bacterial flora of the intestines of the animals because they were isolated from healthy individuals. The strains were tested for phenotypic antibiotic resistance against sulfonamides, trimethoprim, streptomycin, ampicillin, neomycin, chloramphenicol, and tetracycline. Resistance against streptomycin was found to be most common, followed by resistance against sulfonamides and tetracycline. The highest number of resistant bacteria was found in herds where the use of antimicrobial agents was considered to be high. A selection of multiresistant bacterial isolates were further genetically characterized by hybridization with probes specific for the antibiotic resistance genes; sulI, sulII, dfrI, dfrIIb, dfrIX, and the class A, B, C, and D tetracycline resistance determinants. A PCR was developed and used for detection of the strA-strB gene pair encoding streptomycin resistance in gram-negative bacteria. The strA-strB gene pair was the most frequent resistance determinant in the isolates examined. This study indicates that nonpathogenic E. coli from swine may represent a considerable reservoir of antibiotic resistance genes that might be transferable to pathogens.

A transferable multiple drug resistance plasmid from Vibrio cholerae O1

Ten multiple antimicrobial-resistant isolates of Vibrio cholerae O1 isolated from patients in Uganda were characterized, and the transferability of resistance to bacteria of diverse origins was investigated. The isolates were toxigenic and belonged to biotype E1 Tor, serotype Ogawa, and ribotype 8, and possessed a 130-MDa plasmid of incompatibility group 6-C. This plasmid, designated pRVC1, was shown to confer resistance to trimethoprim (mediated by a dhfrI gene), sulfonamides (a suII gene), tetracycline [a tet(C) gene], chloramphenicol (a catI gene), ampicillin (a beta-lactamase gene other than blaTEM or blaSHV), and streptomycin. pRVC1 proved to be transmissible at frequencies between 1 x 10(-1) and 5 x 10(-6) transconjugants per recipient to a variety of bacterial pathogens, including those of humans, animals, and fish. Most efficient transfer was observed from V. cholerae to strains of Shigella flexneri, Escherichia coli, Vibrio parahaemolyticus, and three Aeromonas species. The present in vitro study suggests that pRVC1 may spread from V. cholerae to other bacteria pathogenic to man, animals, and fish in natural environments.

Prevalence and genetic location of non-transferable trimethoprim resistant dihydrofolate reductase genes in South African commensal faecal isolates

In a recent survey of trimethoprim resistance, 357 Gram-negative aerobic organisms were isolated from healthy volunteers from rural and urban populations in South Africa. Trimethoprim resistance did not transfer to an Escherichia coli J62-2 recipient strain by conjugation in a liquid mating in 161 (45.1%) of the isolates. These isolates which did not transfer their resistance were probed with intragenic oligonucleotide probes for the types Ia, Ib, IIIa, V, VI, VII, VIII, IX, X and XII dihydrofolate reductase genes. Contrary to all previous data, the most prevalent dihydrofolate reductase gene in this group of non-transferable isolates which hybridized, was the type VII (38%) followed by the type Ia (25%), Ib (12%), V (1.7%) and VIII (1.2%). None of the strains hybridized to the types IIIa, VI, XI, X and the XII dihydrofolate reductase probes. Southern blots of plasmid and chromosomal DNA from selective isolates revealed that the type VII dihydrofolate reductase genes were located on the chromosome and were associated with the integrase gene of Tn21. However, the type Ib and V dihydrofolate reductase genes were all found on plasmids which could not be mobilized. The type Ia dihydrofolate reductase genes were found on both non-transferable plasmids and on the chromosome. The nature of the genetic structures associated with a dihydrofolate reductase gene strongly affects the means of spread of the gene in a population.

Stability of mutant type II dihydrofolate reductase proteins in suppressor strains

In the course of study of a (Glu-58 to Gln-58) mutant type II dihydrofolate reductase (DHFR), it was found that the altered DHFR was poorly produced in vivo. Investigations with several common laboratory Escherichia coli strains including htpR and lon strains bearing plasmids expressing the Gln-58 DHFR indicated a correlation of rapid degradation with the presence of a sup+ phenotype. The supo strain MC1061(p3) was transformed with a series of plasmids containing the Gln-58 DHFR gene with and without an additional supF gene, and expression levels were compared. The supF+ constructs exhibited little accumulation of the Gln-58 DHFR, while reasonable levels were found in the supo cases. Experiments with extracts of plasmid-free sup+ and supo strains showed rapid degradation by certain strains compared to MC1061(p3) and this degradation was not dependent upon ATP. In another route to increasing the stability of labile DHFR derivatives, mutagenesis of a strain bearing a N-terminally shortened Gln-58 DHFR was performed. Selection and analysis of a trimethoprim-resistant stable mutant showed that this DHFR gene contained a triple repeat of leu-pro-ser in the enzymatically non-essential N-terminal portion of the protein.

Detection of novel trimethoprim resistance determinants in the United Kingdom using biotin-labelled DNA probes

Two collections of trimethoprim R plasmids, isolated from strains of Escherichia coli during 1978-83 and 1987-8 respectively, were retrospectively screened with specific biotinylated DNA probes for the presence of genes encoding particular DHFR enzymes. The results confirmed that the type I DHFR gene was the predominant plasmid-encoded gene conferring trimethoprim resistance in strains of E. coli from the Nottingham area of the UK, but indicated that genes encoding the more recently recognized types of DHFR enzymes had appeared in the bacterial gene pool and could be recognized with increased frequency in the latter plasmid collection. This was particularly true of the type IIIa and type VII enzymes which together accounted for 27% of the trimethoprim R plasmids examined in 1987-8.

Molecular characterization of trimethoprim resistance in Shigella sonnei in Sicily

During the 3-year period 1985-7, all strains of Shigella sonnei isolated in Catania, Sicily, showed a high level of resistance to trimethoprim (Tp) which was invariably associated with resistance to other antibiotics. Plasmid analysis showed 18 different electropherotypes: 35 of 37 strains harboured a plasmid of 70 Megadaltons (MDa), and 29 of 37 strains a plasmid of 130 MDa. Restriction endonuclease fingerprinting of purified 70 MDa plasmid DNA from different strains demonstrated that these plasmids were similar but not identical. In some strains with transferable Tp resistance, DNA hybridization analysis demonstrated the presence of gene coding for the production of dihydrofolate reductase (DHFR) type V. In contrast, there was no detectable hybridization with DNA probes specific for genes coding for DHFR types I, II and IV. This is the first report of the DHFR type V gene outside Sri Lanka.

A dual transcriptional activation system for the 230 kb plasmid genes coding for virulence-associated antigens of Shigella flexneri

The expression of plasmid-encoded, invasion-related antigens lpa b, c and d of Shigella flexneri was found to be positively regulated at transcriptional level by a 33kD protein produced by the previously defined, virulence-associated Region 1 on the SalI fragment B of the 230 kb invasion plasmid. The gene (designated virB) was identified and its nucleotide sequence determined. No Ipa b or c was produced in the absence of an intact virB gene although lower levels of d were produced. The previously reported regulatory activity of the virF gene some 30 kb distance away was shown to act exclusively through virB. In contrast, the activation of the virG gene necessary for intercellular spread occurred directly by virF without the requirement for virB. This study thus ascribes a critical function to a previously recognized, but functionally undefined, virulence locus on the large invasion plasmid of S. flexneri. The virF gene appears to have a central role in activation of the 230 kb plasmid-encoded virulence genes.

Synthesis and expression of a gene for a mini type II dihydrofolate reductase

The Type II dihydrofolate reductases (DHFR) are resistant to the folate analogs, trimethoprim and methotrexate. The monomer is very small (MW 9,000) and has no structural homology with other known DHFR types. A dhfr structural gene was synthesized which incorporates many unique restriction sites (Nco I, Nhe I, Pvu I, Hind III, Sma I, Bgl II, Xho I, and Ban I) within the coding sequence. This gene encodes a small DHFR (68 amino acids) which is 10 amino acids shorter at the amino-terminus than natural Type II DHFRs. The last 60 residues of the synthetically encoded protein are identical in sequence to R388 DHFR. The enzyme is functional and relatively stable, as evidenced by trimethoprim resistance conferred to cells expressing the synthetic gene. The gene was cloned onto a high-copy-number plasmid, pPV7SYN5, in which a trp-lac promoter drives transcription of both the dhfr gene and the primer for plasmid replication (RNA II). High levels of the small DHFR are accumulated in stationary phase cultures of MC1061(p3) containing pPV7SYN5 without the addition of IPTG.

Mapping of trimethoprim resistance genes from epidemiologically related plasmids

Trimethoprim resistance dihydrofolate reductase genes from plasmids known to be exchanging between human and animal populations were mapped. The dihydrofolate reductase gene has been highly conserved in all plasmids, but differences in the flanking regions provide evidence that the most recent exchange of plasmids between the two ecosystems has been from animals to humans.

Novel type of plasmid-borne resistance to trimethoprim

A novel trait for transferable resistance to high concentrations of trimethoprim was found to dominate among enterobacteria collected from different parts of Sri Lanka. Drug resistance was a result of the production of dihydrofolate reductase with a decreased sensitivity to antifolates. By characterization of the partially purified enzyme and by restriction enzyme digestion analysis, the newly found gene was shown to be distinct from the earlier known plasmid-borne resistance genes which express dihydrofolate reductases of types I, II, and III. Cloning of fragments containing the resistance gene and further restriction enzyme digestion analysis showed that this gene was inserted very close to a sulfonamide resistance gene. Evolution of trimethoprim resistance in Sri Lanka thus seems to have taken a different route from that taken in the industrialized world, where transposon Tn7 seems to dominate. The close combination of the new trimethoprim resistance gene with sulfonamide resistance on the plasmids studied would effect an efficient spread of these genes, since trimethoprim has most often been used in combination with a sulfonamide.

DNA sequence and product analysis of the virF locus responsible for congo red binding and cell invasion in Shigella flexneri 2a

The DNA sequence of virF, a locus associated with virulence and the ability to bind Congo red in Shigella flexneri 2a that is located on a 140-megadalton (230-kilobase) plasmid, was determined and analyzed. It was rich in A and T. The direction of transcription of virF was determined by using a chloramphenicol resistance cartridge. An open reading frame readable in this direction was found. Three proteins, 30, 27, and 21 kilodaltons, all corresponding to those predicted from the above sequence, were produced in minicells containing the virF locus. The three proteins were expressed only weakly in minicells with the 230-kilobase plasmid.

Use of bacterial DHFR-II fusion proteins to elicit specific antibodies

Plasmids containing the coding region of the type II dihydrofolate reductase (DHFR) specified by R388 have been used to alter the amino acid (aa) sequence at the C-terminus of this protein. These plasmids have a unique cloning site in the C-terminal portion of the 78-aa coding region. Insertions of DNA fragments into this site produced plasmids that code for proteins with 6- to 80-aa extensions. The vectors were constructed to terminate translation in all three phases beyond the position of insertion of foreign DNA. Random DNA fragments from the major sperm protein (MSP) gene of Caenorhabditis elegans produced by DNase I cleavage were inserted into these vectors. Cell extracts from colonies containing MSP sequences were examined by gel electrophoresis and immunoblotting. One of the hybrid DHFR-MSP proteins was isolated and antibody was prepared to it. This antibody preparation reacted with MSP in immunoblots of purified MSP and whole cell extracts of the worm. A rapid purification procedure for the DHFR is presented.

One-kilobase direct repeats of plasmid pSa

One-kilobase, direct repeats were found on either side of the chloramphenicol resistance gene of plasmid pSa. The right repeat corresponded to the region coding for sulfanilamide resistance. The repeats were not identical as judged by distances between restriction enzyme sites, hybridization, and by the ability to confer resistance to sulfanilamide.

DNA sequence of a plasmid-encoded dihydrofolate reductase

The sequence of the methotrexate-resistant dihydrofolate reductase (DHFR) gene borne by the plasmid R-388 was determined. The gene was subcloned and mapped by an in vitro mutagenesis method involving insertion of synthetic oligonucleotide decamers encoding the BamHI recognition site. Sites of insertion that destroyed the methotrexate resistance fell in two regions separated by 300 bp within a 1.2 kb fragment. One of these regions encodes a 78 amino acid polypeptide homologous to another drug-resistant DHFR. The second region essential for DHFR expression appears to be the promoter of the DHFR gene.

Characterization of a R plasmid-associated, trimethoprim-resistant dihydrofolate reductase and determination of the nucleotide sequence of the reductase gene

The trimethoprim-resistant dihydrofolate reductase associated with the R plasmid R388 was isolated from strains that over-produce the enzyme. It was purified to apparent homogeneity by affinity chromatography and two consecutive gel filtration steps under native and denaturing conditions. The purified enzyme is composed of four identical subunits with molecular weights of 8300. A 1100 bp long DNA segment which confers resistance to trimethoprim was sequenced. The structural gene was identified on the plasmid DNA by comparing the amino acid composition of the deduced proteins with that of the purified enzyme. The gene is 234 bp long and codes for 78 amino acids. No homology can be found between the deduced amino acid sequence of the R388 dihydrofolate reductase and those of other prokaryotic or eukaryotic dihydrofolate reductases. However, it differs in only 17 positions from the enzyme associated with the trimethoprim-resistance plasmid R67.

Isolation and characterization of DNA fragments containing the dihydrofolate-reductase gene of coliphage T4

DNA of a mutant of the bacteriophage T4, which contains cytosine instead of glucosylated hydroxymethylcytosine, was shown to direct the synthesis of enzymatically active dihydrofolate reductase in a coupled in vitro transcription-translation system. The DNA-directed synthesis of the enzyme was used to localize the dihydrofolate-reductase gene frd on a 2300 bp long restriction-nuclease-generated DNA fragment. Fine structure mapping showed that the gene is encoded on a segment of less than 1850 bp but more than 700 bp length. The enzyme, which is synthesized in vitro from the DNA fragment, has a molecular weight of 18 500 to 19 500. A restriction map was constructed which extends about 10 kb to both sides of the reductase gene and which covers the T4 genome between the genes 55 and 63. The two genes which flank the frd gene, genes 32 and td (thymidylate synthetase), were mapped in detail. A correlation between the physical and genetic maps was established.

Cloning of the Escherichia coli K-12 dihydrofolate reductase gene following mu-mediated transposition

The dihydrofolate reductase structural gene, folA, has been closed into the multicopy vector pBR322 following the gene's enrichment by bacteriophage Mu-mediated transposition. Strains carrying the resultant plasmid, pJFM8, produce 25 to 30 times more dihydrofolate reductase than control strains. Consequently they are resistant to trimethoprim, an inhibitor of this enzyme. This elevation in enzyme production is due to an increase in the number of folA gene copies per cell. The higher yield of dihydrofolate reductase obtained will be extremely useful for purifying and characterising this trimethoprim-sensitive chromosomally derived enzyme. The plasmid will also be invaluable for studying the structure, function and regulation of dihydrofolate reductase.

Protein expression in Escherichia coli minicells containing recombinant plasmids specifying trimethoprim-resistant dihydrofolate reductases

Deoxyribonucleic acid fragments containing the structural genes for several trimethoprim-resistant dihydrofolate reductases from naturally occurring plasmids were inserted into small cloning vehicles. The genetic expression of these hybrid plasmids was studied in purified Escherichia coli minicells. The type I dihydrofolate reductase, encoded by plasmid R483 and residing within transposon 7 (Tn7), had a subunit molecular weight of 18,000. The type II dihydrofolate reductase, specified by plasmid R67, had a subunit molecular weight of 9,000. These two enzymes were antigenically distinct in that anti-type II dihydrofolate reductase (R67) antibody did not cross-react with the type I (R483) protein. The trimethoprim-resistant reductase specified by plasmid R388 had a subunit molecular weight of about 10,500 and was immunologically related to the type II (R67) enzyme. A 9,000 subunit of the dihydrofolate encoded by the transposition element Tn402 was also antigenically related to the R67 reductase.