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Journal of Bacteriology, April 2001, p. 2367-2371, Vol. 183, No. 7
Infectious Disease Division and Medical
Services, Massachusetts General Hospital, Harvard Medical School,
Boston, Massachusetts 02114-2696
Received 29 November 2000/Accepted 17 January 2001
NorA, a multidrug efflux pump in Staphylococcus aureus,
protects the cell from multiple drugs, including quinolones. The
flqB mutation (T Bacterial and eukaryotic cells
typically contain an array of membrane transport systems involved in
vital roles in maintenance of cellular homeostasis. Of these
transporters, multidrug resistance (MDR) efflux systems, which confer
resistance to structurally dissimilar toxic compounds, present a
clinical threat, since their acquisition or increased expression may
decrease susceptibility to a broad spectrum of chemotherapeutic agents,
including antibiotics (19).
Staphylococcus aureus is an important pathogen and has a
chromosomally encoded MDR pump, NorA. This pump protects the cell from
quinolones such as norfloxacin as well as from ethidium bromide and
cetrimide (15, 16). We have previously shown that the regulation of norA expression is complex and includes a
two-component regulatory system, ArlS-ArlR, and specific binding of an
18-kDa protein to the norA promoter (5). Many
details of the regulation of norA expression, however,
remain unclear.
The flqB mutation (T In order to understand the mechanism of the flqB mutation,
we first constructed translational and transcriptional fusions of DNA
sequences upstream of norA to the blaZ gene,
which encodes staphylococcal
0021-9193/01/$04.00+0 DOI: 10.1128/JB.183.7.2367-2371.2001
Copyright © 2001, American Society for Microbiology. All rights reserved.
A Mutation in the 5' Untranslated Region Increases
Stability of norA mRNA, Encoding a Multidrug Resistance
Transporter of Staphylococcus aureus

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ABSTRACT
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Abstract
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G) in the 5' untranslated region
upstream of norA causes norA overexpression of
4.9-fold in cis, as measured in norA::blaZ fusions. The
transcriptional initiation site of norA was unchanged in
mutant and wild-type strains, but the half-life of norA
mRNA was increased 4.8-fold in the flqB mutant compared to
the wild-type strain. Computer-generated folding of the first 68 nucleotides of the norA transcript predicts an additional
stem-loop and changes in a putative RNase III cleavage site in the
flqB mutant.
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TEXT
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Abstract
Text
References
G) located upstream of the
norA gene increases resistance to fluoroquinolones
(16). In Staphylococcus aureus MT23142
(flqB), steady-state levels of norA mRNA are
substantially greater than those in the wild-type strain ISP794
(16). It has been speculated that this mutation modifies a
perfect inverted repeat sequence that may alter the binding of a
regulatory protein (11), but a previous study in our
laboratory showed no evidence for specific protein binding to this DNA
region (5). Thus, the mechanism by which the
flqB mutation increases norA expression remains unknown.
-lactamase (Fig.
1, Table
1). The promoter containing the
flqB mutation (pBF1) produced increased
-lactamase
activity for both the translational (4.5-fold; compare pBF1 and pBF2,
Table 2) and transcriptional (4.9-fold;
compare pBF8-30 and pBF7-7, Table 2) fusions. These differences could
not be attributed to differences in plasmid copy number because the
chloramphenicol acetyltransferase activity encoded by the plasmid-borne
cat gene and measured in crude extracts of S. aureus prepared by lysis with lysostaphin (80 µg/ml for 30 min
at 37°C) (5, 17) did not differ between the two
constructs (data not shown). These findings confirmed the previous
Northern blot analysis, indicating a higher level of norA
mRNA in the flqB mutant (16) (Table 2). The
flqB mutation also appears to act entirely in
cis, since the
-lactamase activity of pBF8-30 in strains
MT23142, containing the chromosomal flqB mutation
(16), and ISP794 (wild type) did not differ (data not
shown).

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FIG. 1.
Maps of the 5' segments of the norA variants
examined in this study. Solid line, full-length or truncated
norA 5' UTR: wavy line, truncated bla 5' UTR.
Translated mRNA segments encoding the NorA protein (solid boxes) or the
-lactamase protein (hatched boxes) are also indicated. The numbers
refer to the position of the base pairs used in the cloning to contruct
the fusions (the numbering is that of Yoshida et al.
[29]). The circled base is the flqB mutation.
The
35 and
10 consensus sequences are boxed. The transcription
initiation site is indicated by an arrow. mRNA was extracted using the
RNeasy miniprep kit (Qiagen) and concentrated in a vacuum dessicator
after addition of a 10% volume of ethanol, as needed.
TABLE 1.
Bacterial strains and plasmids
TABLE 2.
-Lactamase activities of the different fusions of the
norA promoter in S. aureus
ISP794a
To determine if the flqB mutation resulted in a new
and stronger promoter, we next determined the transcriptional start
site of norA mRNA in ISP794(pBF8-30) (wild type)
and MT23142(pBF7-7) (flqB mutant), using the
Promega primer extension system according to the manufacturer's
instructions. For both the wild-type and flqB promoters, the
transcriptional start site was assigned to an A residue at a
position 93 nucleotides upstream of the ATG translational start
codon and 7 nucleotides downstream of the putative
10 consensus
sequence (Fig. 2).
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This promoter assignment was confirmed by construction of two
additional transcriptional fusions, one lacking the region just upstream of the promoter (plasmid pBF15-5, Fig. 1) and the other lacking the 5' untranslated region (UTR) of norA mRNA just
downstream of the transcription initiation site (plasmid pBF5-10, Fig.
1). The
-lactamase activity of strains carrying pBF15-5 and pBF5-10 was similar or decreased 2.5-fold relative to that of pBF8-30 carrying
the wild-type promoter, respectively (Table 2). The
-lactamase
activity of pBF5-10, however, was higher than that of the control
carrying the plasmid without any promoter (Table 2), suggesting that
the norA promoter was still expressed. These results are
consistent with the localization of the promoter indicated in Fig. 1
and further indicate that the flqB mutation does not generate a new transcriptional start site.
Because the flqB mutation was localized to the 5' UTR
upstream of norA, a region that has been shown in E. coli to affect mRNA stability, we measured the stability of
norA mRNA by assessing its levels in ISP794 (wild type) and
MT23142 (flqB) after addition of rifampin (200 µg/ml) to
stop new RNA synthesis. RNA levels were determined both by reverse
transcription-PCR (RT-PCR) using the SuperScript One-Step RT-PCR
(Gibco-BRL) and by Northern analysis (Fig.
3). Total RNA was extracted using the
SNAP total RNA kit (Invitrogen Inc.) and quantified
spectrophotometrically. The RT-PCR used 16S RNA as standard RNA and
norA mRNA as target RNA. Because of the low levels of
norA mRNA in ISP794, 35 cycles of amplification were needed
to produce a measurable signal in the linear range, and input RNA from
MT23142 was adjusted to allow the same conditions to be used for
reactions for both strains. Under the conditions of RT-PCR used, the
levels of product DNA were found to be linearly related to the input
RNA. The estimated half-life of norA mRNA was 7 min for
ISP794 and 34 min for MT23142. Thus, the norA mRNA half-life
was increased 4.8-fold in the flqB mutant (Fig. 3A and B),
indicating that this mutation increases mRNA stability. These differences in mRNA stability were confirmed by Northern hybridization analysis using the norA gene as a probe (Fig. 3C).
|
Computer-predicted folding of the region between the
transcriptional start site and the Shine-Dalgarno sequence of the
norA leader mRNA of strain ISP794 (wild type) showed an RNA
hairpin structure in the 5' UTR, whereas that of the flqB
mutant showed an additional hairpin (Fig.
4). The flqB mutation modified
a U-A pair, creating the new stem-loop, and was predicted to be more stable (
8.8 kcal) than the structure predicted in the wild type (
7.4 kcal). A putative RNase III cleavage site (CAUG) was present in
the 5' UTR (Fig. 4). Although cleavage sites for RNase III in S. aureus have not been defined, in Bacillus subtilis this sequence has been shown to be a target for RNase III (13,
20).
|
To estimate the effect of the flqB mutation on
norA expression in Escherichia coli, we compared
the MICs of ampicillin and the
-lactamase activities for E. coli strains carrying pBF8-30 (wild type) and pBF7-7
(flqB mutation); both measures were similar for the two
constructs and higher (16-to 14-fold) than those for the vector plasmid
alone (Table 3), indicating that the
flqB mutation did not affect the efficiency of the E. coli transcriptional machinery.
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The flqB mutation resides in the 5' UTR of the norA gene and increases norA expression in cis. Mutations in this region have been associated with increased promoter expression in the has gene of Streptococcus pyogenes (1), an increase that was postulated to be due to increased efficiency of formation of the RNA polymerase-DNA complex (23). The flqB mutation also specifically transforms the sequence TTTTT to TTGTT (Fig. 1), suggesting the possibility that the mutation interrupts reiterative transcription that is due to slippage of RNA polymerase on a homopolymeric region of nascent transcript (8). We, however, found no effect of supplemental UTP in high concentrations on the norA expression measured from the plasmid fusions (data not shown), conditions that decrease expression of other promoters (principally those involved in pyrimidine metabolism) affected by reiterative transcription (8, 26). In addition, norA expression from plasmid pBF5-10, which lacked the TTTTT sequence, was not increased, as would be predicted for a reiterative transcriptional mechanism.
Our data, however, argue, in contrast, that increased norA expression in the flqB mutant is due to increased stability of norA transcripts resulting from altered secondary structure of the 5' UTR of norA transcripts. Although, as yet, we have no direct data to confirm the computer-predicted RNA secondary structures, they are consistent with findings in studies in E. coli in which stem-loop structures of this type in the 5' UTR affect RNA stability (4, 22) and involve RNase E (2, 7, 9). In B. subtilis, which lacks RNase E, RNase III may be involved in RNA turnover (18, 28), suggesting that the predicted RNase III cleavage site upstream of norA that is affected by additional stem-loop in the flqB mutant may be relevant for mRNA stability in S. aureus, as has been shown in B. subtilis (13, 20, 22). Furthermore, the greater proximity of the second stem-loop to the 5' end of the norA transcript in the flqB mutant is consistent with such structures providing greater stability to mRNAs in E. coli (21). Interestingly, although norA expressed in E. coli could be due to recognition of the same promoter as in S. aureus (25), the flqB mutation appears to have no effect on expression in E. coli, suggesting that RNA degradation pathways relating to RNase III differ in the two species (3, 20, 28).
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ACKNOWLEDGMENTS |
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We thank Stephen Wu for preparation of some of the RNA samples and Philip Davis and Lee Kaplan of the Massachusetts Molecular Biology Core of the Center for the Study of Inflammatory Bowel Diseases (NIH P30 DK-43351) for performing the primer extension experiments.
This work was supported by U.S. Public Health Service grant AI23988 to D.C.H. from the National Institutes of Health.
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FOOTNOTES |
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* Corresponding author. Mailing address: Infectious Disease Division, Massachusetts General Hospital, 55 Fruit Street, Boston MA 02114-2696. Phone: (617) 726-3812. Fax: (617) 726-7416. E-mail: dhooper{at}partners.org.
Present address: Unité de Biochimie Microbienne, Institut
Pasteur, 75724 Paris Cedex 15, France.
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REFERENCES |
|---|
|
|
|---|
| 1. | Alberti, S., C. D. Ashbaugh, and M. R. Wessels. 1998. Structure of the has operon promoter and regulation of hyaluronic acid capsule expression in group A Streptococcus. Mol. Microbiol. 28:343-353[CrossRef][Medline]. |
| 2. | Bouvet, P., and J. G. Belasco. 1992. Control of RNase E-mediated RNA degradation by 5'-terminal base pairing in Escherichia coli. Nature 360:488-491[CrossRef][Medline]. |
| 3. |
Conrad, C.,
R. Rauhut, and G. Klug.
1998.
Different cleavage specificities of RNases III from Rhodobacter capsulatus and Escherichia coli.
Nucleic Acids Res.
26:4446-4453 |
| 4. |
Emory, S. A., and J. G. Belasco.
1990.
The ompA 5' untranslated RNA segment functions in Escherichia coli as a growth rate-regulated mRNA stabilizer whose activity is unrelated to translational efficiency.
J. Bacteriol.
172:4472-4481 |
| 5. |
Fournier, B.,
R. Aras, and D. C. Hooper.
2000.
Expression of the multidrug resistance transporter NorA from Staphylococcus aureus is modified by a two-component regulatory system.
J. Bacteriol.
182:664-671 |
| 6. | Freeman, W. M., S. J. Walker, and K. E. Vrana. 1999. Quantitative RT-PCR: pitfalls and potential. Biotechniques 26:112-125[Medline]. |
| 7. | Grunberg-Manago, M. 1999. Messager RNA stability and its role in control of gene expression in bacteria and phages. Annu. Rev. Genet. 33:193-227[CrossRef][Medline]. |
| 8. |
Han, X., and C. L. Turnbough, Jr.
1998.
Regulation of carAB expression in Escherichia coli occurs in part through UTP-sensitive reiterative transciption.
J. Bacteriol.
180:705-713 |
| 9. | Hansen, M. J., L.-H. Chen, M. L. S. Fejzo, and J. G. Belasco. 1994. The ompA 5' untranslated region impedes a major pathway for mRNA degradation in Escherichia coli. Mol. Microbiol. 12:707-716[CrossRef][Medline]. |
| 10. |
Ji, G.,
R. C. Beavis, and R. P. Novick.
1995.
Cell density control of staphylococcal virulence mediated by an octapeptide pheromone.
Proc. Natl. Acad. Sci. USA
92:12055-12059 |
| 11. |
Kaatz, G. W., and S. M. Seo.
1997.
Mechanisms of fluoroquinolone resistance in genetically related strains of Staphylococcus aureus.
Antimicrob. Agents Chemother.
41:2733-2737 |
| 12. | Kreiswirth, B. N., S. Lofdalh, M. J. Betley, M. O'Reilly, P. M. Schlievert, M. S. Bergdoll, and R. P. Novick. 1983. The toxic shock syndrome exotoxin structural gene is not detectably transmitted by a prophage. Nature (London) 305:709-712[CrossRef][Medline]. |
| 13. |
Mitra, S., and D. H. Bechhofer.
1994.
Substrate specificity of an RNase III-like activity from Bacillus subtilis.
J. Biol. Chem.
269:31450-31456 |
| 14. |
Murley, Y. M.,
J. Behari,
R. Griffin, and S. B. Calderwood.
2000.
Classical and El Tor biotypes of Vibrio cholerae differ in timing of transcription of tcpPH during growth in inducing conditions.
Infect. Immun.
68:3010-3014 |
| 15. |
Neyfakh, A. A.,
C. M. Borsch, and G. W. Kaatz.
1993.
Fluoroquinolone resistance protein NorA of Staphylococcus aureus is a multidrug efflux transporter.
Antimicrob. Agents Chemother.
37:128-129 |
| 16. |
Ng, E. Y. W.,
M. Trucksis, and D. C. Hooper.
1994.
Quinolone resistance mediated by NorA: physiologic characterization and relationship to flqB, a quinolone resistance locus on the Staphylococcus aureus chromosome.
Antimicrob. Agents Chemother.
38:1345-1355 |
| 17. | Novick, R. P. 1991. Genetic systems in staphylococci. Methods Enzymol. 204:587-636[Medline]. |
| 18. |
Oguro, A.,
H. Kakeshita,
K. Nakamura,
K. Yamane,
W. Wang, and D. H. Bechhofer.
1998.
Bacillus subtilis RNase III cleaves both 5'- and 3'-sites of the small cytoplasmic RNA precursor.
J. Biol. Chem.
273:19542-19547 |
| 19. |
Paulsen, I. T.,
M. H. Brown, and R. A. Skurray.
1996.
Proton-dependent multidrug efflux systems.
Microbiol. Rev.
60:575-608 |
| 20. |
Persson, M.,
E. Glatz, and B. Rutberg.
2000.
Different processing of an mRNA species in Bacillus subtilis and Escherichia coli.
J. Bacteriol.
182:689-695 |
| 21. | Rauhut, R., and G. Klug. 1999. mRNA degradation in bacteria. FEMS Microbiol. Rev. 23:353-370[CrossRef][Medline]. |
| 22. | Régnier, P., and M. Grunberg-Manago. 1990. RNase III cleavages in non-coding leaders of Escherichia coli transcripts control mRNA stability and genetic expression. Biochimie 72:825-834[Medline]. |
| 23. | Schickor, P., W. Metzger, W. Werel, H. Lederer, and H. Heumann. 1990. Topography of intermediates in transcription initiation in Escherichia coli. EMBO J. 9:2215-2220[Medline]. |
| 24. |
Stahl, M. L., and P. A. Pattee.
1983.
Confirmation of protoplast fusion-derived linkages in Staphylococcus aureus by transformation with protoplast DNA.
J. Bacteriol.
154:406-412 |
| 25. |
Sun, L.,
S. Sreedharan,
K. Plummer, and L. M. Fisher.
1996.
NorA plasmid resistance to fluoroquinolones: role of copy number and norA frameshift mutations.
Antimicrob. Agents Chemother.
40:1665-1669 |
| 26. |
Tu, A.-H. T., and C. L. Turnbough, Jr.
1997.
Regulation of upp expression in Escherichia coli by UTP-sensitive selection of transcriptional start sites coupled with UTP-dependent reiterative transcription.
J. Bacteriol.
179:6665-6673 |
| 27. |
Wang, P.-Z.,
S. Projan,
K. R. Leason, and R. Novick.
1987.
Translational fusion with a secretory enzyme as an indicator.
J. Bacteriol.
169:3082-3087 |
| 28. |
Wang, W., and D. H. Bechhofer.
1997.
Bacillus subtilis RNase III gene: cloning, function of the gene in Escherichia coli, and construction of Bacillus subtilis strains with altered rnc loci.
J. Bacteriol.
179:7379-7389 |
| 29. |
Yoshida, H.,
M. Bogaki,
S. Nakamura,
K. Ubukata, and M. Konno.
1990.
Nucleotide sequence and characterization of the Staphylococcus aureus norA gene, which confers resistance to quinolones.
J. Bacteriol.
172:6942-6949 |
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