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Mechanisms of Resistance

Functional Characterization of a Cassette-Specific Promoter in the Class 1 Integron-Associated qnrVC1 Gene

Érica Lourenço da Fonseca, Ana Carolina Paulo Vicente
Érica Lourenço da Fonseca
Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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Ana Carolina Paulo Vicente
Laboratório de Genética Molecular de Microrganismos, Instituto Oswaldo Cruz, FIOCRUZ, Rio de Janeiro, Brazil
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DOI: 10.1128/AAC.00113-12
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ABSTRACT

Integrons are natural expression vectors due to the presence of an intrinsic promoter (Pc). Although rare, gene cassettes can harbor their own promoter. This study determined the functionality of an internal promoter in the qnrVC1 cassette whose presence was suggested by a level of transcription similar to that of the preceding cassette (aadA2) and confirmed by in silico analysis. Its functionality was determined by 5′ rapid amplification of cDNA ends (RACE) and cloning into promoter-probe vectors. PqnrVC was found in the qnrVC cassette family, stressing its role in contributing to resistance manifestation.

TEXT

The integron is a genetic element which produces an integrase capable of inserting, excising, and rearranging gene cassettes by site-specific recombination. This element is also considered a natural expression system due to the presence of a promoter (Pc) that controls the transcription of gene cassettes inserted in the array (12). Although gene cassettes are generally promoterless functional units, internal cassette-specific promoters have been identified by in silico analyses and by the resistance phenotype changes of transformed Escherichia coli (1, 2, 9, 11, 13). In general, the expression level of cassette-associated genes is influenced by their relative position in the array (cassette position effect), where genes closer to Pc are more expressed than distal ones (3), and by the presence of cassette-specific promoters.

The qnrVC1 cassette was previously found in a class 1 integron, preceded by the aadA2 cassette, from a clinical Brazilian Vibrio cholerae strain (4). Different from other gene cassettes, which have a specific attC recombination site, qnrVC1 was associated with an attC typically found in Vibrio chromosomal integrons (CIs). More precisely, its attC corresponded to a Vibrio parahaemolyticus repeat (VPR), which is one of the signatures of the V. parahaemolyticus CI. Moreover, although qnrVC1 has been found in a class 1 integron, it is more similar to the chromosomal qnr genes from Vibrionaceae than to the plasmid-borne determinants, such as qnrA1.

This work fully characterized and determined the functionality of an internal cassette promoter distributed among the qnrVC alleles that was present in several genetic elements, ensuring their expression and the emergence of the resistance phenotype.

The transcription of the aadA2-qnrVC1 array was assessed by real-time reverse transcription (RT)-PCR using Power SYBR green PCR master mix (Applied Biosystems). The transcription of gene cassettes was measured in both the wild V. cholerae strain (VC627) and in an E. coli DH5α strain transformed with the pGEM-T Easy vector (Promega) harboring the aadA2-qnrVC1 insert. The single-copy housekeeping rpoA gene from V. cholerae and the β-lactamase (bla) gene, present in the pGEM vector as a selective marker, were used for normalizing the transcription of wild-type and cloned genes, respectively (Table 1). The use of the bla gene eliminates any interference of plasmid copy number on relative quantification of cloned genes. The criteria to interpret the results are described elsewhere (5). Similar relative quantification values were obtained for the aadA2 (2.68 ± 0.04 for the wild-type strain and 2.77 ± 0.09 for recombinant strains) and qnrVC1 (2.51 ± 0.1 for the wild-type strain and 2.60 ± 0.07 for recombinant strains) genes, indicating similar transcript amounts. These results may be explained by (i) the occurrence of a read-through of the RNA polymerase along this array producing a full-length transcript (3) or (ii) the presence of an internal specific cassette promoter controlling qnrVC1 transcription.

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Table 1

Primers used in this study

Analyses in silico were performed to verify the presence of internal cassette-specific promoters of aadA2 and qnrVC1 using four promoter prediction programs: Neural Network for Promoter Prediction (NNPP) version 2.2 (Berkeley Drosophila Genome Project, http://www.fruitfly.org/index.html), BPROM (SoftBerry, http://linux1.softberry.com/berry.phtml), prokaryotic promoter analysis using SAK (6), and Prokaryotic Promoter Prediction (PPP) (http://bioinformatics.biol.rug.nl/websoftware/ppp/ppp_start.php). No reliable promoter was found for aadA2; however, a putative internal promoter for qnrVC1 was determined with high scores by all programs. This promoter (−35 TTGAGA |16 bp| −10 TAGTCT) (Fig. 1), named PqnrVC here, presented high similarity with E. coli σ70-dependent promoters (−35 TTGACA |16 to 18 bp| −10 TATAAT) once it preserved 8 (underlined above) of the 12 canonical nucleotides of the −35 and −10 hexamers (10). Most gene cassettes feature a short 5′ untranslated region (UTR); for example, this region in the aadA2 gene cassette has only 9 bp. The qnrVC1 cassette presented an unusual 5′ UTR of 216 bp, supporting the presence of expression signals such as a promoter and a translation initiation region (TIR). A Shine-Dalgarno sequence was identified seven nucleotides upstream from the qnrVC1 start codon (Fig. 1).

Fig 1
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Fig 1

Schematic representation of the transcription/translation motifs found in the class 1 integron harboring the qnrVC1 gene cassette. The recombination core site representing the beginning of the qnrVC1 cassette is highlighted in bold and thickly underlined. The PqnrVC and the first base (+1) of its corresponding TSS (underlined base) are shown. The Shine-Dalgarno (SD) sequence and the start codon of qnrVC1 are indicated in italics and in boldface, respectively.

Interestingly, PqnrVC had been found in qnrVC2, qnrVC3, and qnrVC4 (4, 7, 14). The 5′ UTRs of these alleles are very similar in sequence and length to that of qnrVC1. Moreover, not only qnrVC alleles, but all BLAST hits obtained in January 2012, showed conservation of PqnrVC. These results demonstrate that PqnrVC is a general property of these qnr determinants.

The functionality of PqnrVC was experimentally assessed by cloning into promoterless vector-probe plasmids (pLQ and pGlow) to test its ability in driving expression of a resistance gene (cat) and a reporter gene (gfp). The strong Pc version from the class 1 integron was also cloned as a positive control. These promoters were amplified with modified primers (Table 1) and were cloned into the polylinker region of the pLQ896 and pLQ897 vectors (2), kindly provided by Paul H. Roy. Recombinants transformed with both pLQ896-Pc and pLQ896-PqnrVC were able to grow in 25 mg/liter of chloramphenicol and presented MIC values of ≥256 mg/liter, while E. coli DH5α, used as a control strain, had a MIC of 8 mg/liter.

The PqnrVC and Pc were amplified with primers modified as recommended (Table 1) and cloned into the pGlow-TOPO TA expression kit (Invitrogen). After fixation, ampicillin-resistant fluorescent clones harboring the constructions pGlow-PqnrVC and pGlow-Pc were visualized in an Axio Imager M1 fluorescence microscope (Carl Zeiss) with a 60× objective lens by using a fluorescein isothiocyanate (FITC) filter (excitation/emission peaks of 489 nm/509 nm). Only background fluorescence was observed in the negative-control recombinant (E. coli transformed with recircularized pGlow vector) (Fig. 2). This in vitro analysis is one more demonstration of PqnrVC functionality.

Fig 2
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Fig 2

In vitro PqnrVC promoter activity in the qnrVC1 gene cassette. Panel A shows an image of E. coli::pGlow-TOPO TA, corresponding to the recircularized vector used as a negative control for background fluorescence. Panels B and C show the green fluorescent protein (GFP)-fluorescent E. coli::pGlow-Pc and E. coli::pGlow-PqnrVC, respectively, resulting from transformation of E. coli TOP10 cells with the pGlow-TOPO TA containing the promoter regions fused into the ATG codon of gfp.

In order to determine whether qnrVC1 transcription begins under the control of its putative internal promoter, its transcription start site (TSS) was assessed by the 5′ rapid amplification of cDNA ends (RACE) strategy as previously described (5). Sequence analysis revealed a TSS with the +1 position located 14 bp upstream from the initiation codon of qnrVC1. PqnrVC was placed 14 bp upstream from this TSS (Fig. 1), an interval which is considered an acceptable distance between a promoter and its start site (8).

The lack of a promoter region is a remarkable characteristic of gene cassettes, and the identification of structures harboring such motifs is, so far, rare. The possibility of internal cassette promoters is, in fact, an extra element in the evolution of the antimicrobial resistance phenotype, minimizing the position effect, since the cassette-specific promoter guarantees the transcription of even genes that are distal relative to Pc.

ACKNOWLEDGMENTS

We thank the Cellular Ultrastructure Laboratory (IOC/FIOCRUZ)/Equipamento solidário Project (FAPERJ) for fluorescence microscopy technical assistance.

This work was supported by FAPERJ, CNPq, and an Oswaldo Cruz Institute grant.

FOOTNOTES

    • Received 16 January 2012.
    • Returned for modification 12 February 2012.
    • Accepted 26 February 2012.
    • Accepted manuscript posted online 5 March 2012.
  • Copyright © 2012, American Society for Microbiology. All Rights Reserved.

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Functional Characterization of a Cassette-Specific Promoter in the Class 1 Integron-Associated qnrVC1 Gene
Érica Lourenço da Fonseca, Ana Carolina Paulo Vicente
Antimicrobial Agents and Chemotherapy May 2012, 56 (6) 3392-3394; DOI: 10.1128/AAC.00113-12

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Functional Characterization of a Cassette-Specific Promoter in the Class 1 Integron-Associated qnrVC1 Gene
Érica Lourenço da Fonseca, Ana Carolina Paulo Vicente
Antimicrobial Agents and Chemotherapy May 2012, 56 (6) 3392-3394; DOI: 10.1128/AAC.00113-12
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