Abstract
Burkholderia cepacia is recognized as an important pathogen in the lung infections of patients with cystic fibrosis. An inducible beta-lactamase activity has been associated with increased resistance to beta-lactam antibiotics in clinical isolates of B. cepacia. In this study, we report the revised sequence of the penA gene, which encodes the inducible penicillinase of B. cepacia, and show that it belongs to the molecular class A beta-lactamases and exhibits a high degree of similarity to the chromosomal beta-lactamase of Klebsiella oxytoca. Analysis of the nucleotide sequence of the DNA region directly upstream of the penA coding sequence revealed an open reading frame (penR), the transcription of which was oriented opposite to that of penA and whose initiation was 130 bp away from that of penA. Two potential ribosome-binding sites and two overlapping -10 and -35 promoter sequences were identified in the intercistronic region. The predicted translation product of penR was a polypeptide of 301 amino acids with an estimated molecular size of 33.2 kDa. The deduced polypeptide of penR showed a high degree of similarity with AmpR-like transcriptional activators of class A and C beta-lactamases, with identities of 59 and 58.7% with Pseudomonas aeruginosa PAO1 AmpR and Proteus vulgaris B317 CumR, respectively. The N-terminal portion of B. cepacia PenR was predicted to include a helix-turn-helix motif, which may bind the LysR motif identified in the intercistronic region. Induction of PenA by imipenem was shown to be dependent upon the presence of PenR. Expression of the cloned B. cepacia penA and penR genes in Escherichia coli SNO302 (ampD) resulted in a high basal and hyperinducible PenA activity. These results suggest that the regulation of the PenA penicillinase of B. cepacia 249 is similar to that observed in other class A and class C beta-lactamases that are under the control of a divergently transcribed AmpR-like regulator.
Full Text
The Full Text of this article is available as a PDF (315.4 KB).
Selected References
These references are in PubMed. This may not be the complete list of references from this article.
- Ambler R. P., Coulson A. F., Frère J. M., Ghuysen J. M., Joris B., Forsman M., Levesque R. C., Tiraby G., Waley S. G. A standard numbering scheme for the class A beta-lactamases. Biochem J. 1991 May 15;276(Pt 1):269–270. doi: 10.1042/bj2760269. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Arakawa Y., Ohta M., Kido N., Mori M., Ito H., Komatsu T., Fujii Y., Kato N. Chromosomal beta-lactamase of Klebsiella oxytoca, a new class A enzyme that hydrolyzes broad-spectrum beta-lactam antibiotics. Antimicrob Agents Chemother. 1989 Jan;33(1):63–70. doi: 10.1128/aac.33.1.63. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Ballard R. W., Palleroni N. J., Doudoroff M., Stanier R. Y., Mandel M. Taxonomy of the aerobic pseudomonads: Pseudomonas cepacia, P. marginata, P. alliicola and P. caryophylli. J Gen Microbiol. 1970 Feb;60(2):199–214. doi: 10.1099/00221287-60-2-199. [DOI] [PubMed] [Google Scholar]
- Barthélémy M., Péduzzi J., Bernard H., Tancrède C., Labia R. Close amino acid sequence relationship between the new plasmid-mediated extended-spectrum beta-lactamase MEN-1 and chromosomally encoded enzymes of Klebsiella oxytoca. Biochim Biophys Acta. 1992 Jul 13;1122(1):15–22. doi: 10.1016/0167-4838(92)90121-s. [DOI] [PubMed] [Google Scholar]
- Bauernfeind A., Stemplinger I., Jungwirth R., Ernst S., Casellas J. M. Sequences of beta-lactamase genes encoding CTX-M-1 (MEN-1) and CTX-M-2 and relationship of their amino acid sequences with those of other beta-lactamases. Antimicrob Agents Chemother. 1996 Feb;40(2):509–513. doi: 10.1128/aac.40.2.509. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Bush K., Jacoby G. A., Medeiros A. A. A functional classification scheme for beta-lactamases and its correlation with molecular structure. Antimicrob Agents Chemother. 1995 Jun;39(6):1211–1233. doi: 10.1128/aac.39.6.1211. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Campbell J. I., Scahill S., Gibson T., Ambler R. P. The phototrophic bacterium Rhodopseudomonas capsulata sp108 encodes an indigenous class A beta-lactamase. Biochem J. 1989 Jun 15;260(3):803–812. doi: 10.1042/bj2600803. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Chiesa C., Labrozzi P. H., Aronoff S. C. Decreased baseline beta-lactamase production and inducibility associated with increased piperacillin susceptibility of Pseudomonas cepacia isolated from children with cystic fibrosis. Pediatr Res. 1986 Nov;20(11):1174–1177. doi: 10.1203/00006450-198611000-00026. [DOI] [PubMed] [Google Scholar]
- Datz M., Joris B., Azab E. A., Galleni M., Van Beeumen J., Frère J. M., Martin H. H. A common system controls the induction of very different genes. The class-A beta-lactamase of Proteus vulgaris and the enterobacterial class-C beta-lactamase. Eur J Biochem. 1994 Nov 15;226(1):149–157. doi: 10.1111/j.1432-1033.1994.tb20036.x. [DOI] [PubMed] [Google Scholar]
- Fonzé E., Charlier P., To'th Y., Vermeire M., Raquet X., Dubus A., Frère J. M. TEM1 beta-lactamase structure solved by molecular replacement and refined structure of the S235A mutant. Acta Crystallogr D Biol Crystallogr. 1995 Sep 1;51(Pt 5):682–694. doi: 10.1107/S0907444994014496. [DOI] [PubMed] [Google Scholar]
- Galleni M., Lindberg F., Normark S., Cole S., Honore N., Joris B., Frere J. M. Sequence and comparative analysis of three Enterobacter cloacae ampC beta-lactamase genes and their products. Biochem J. 1988 Mar 15;250(3):753–760. doi: 10.1042/bj2500753. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Goethals K., Van Montagu M., Holsters M. Conserved motifs in a divergent nod box of Azorhizobium caulinodans ORS571 reveal a common structure in promoters regulated by LysR-type proteins. Proc Natl Acad Sci U S A. 1992 Mar 1;89(5):1646–1650. doi: 10.1073/pnas.89.5.1646. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Gold R., Jin E., Levison H., Isles A., Fleming P. C. Ceftazidime alone and in combination in patients with cystic fibrosis: lack of efficacy in treatment of severe respiratory infections caused by Pseudomonas cepacia. J Antimicrob Chemother. 1983 Jul;12 (Suppl A):331–336. doi: 10.1093/jac/12.suppl_a.331. [DOI] [PubMed] [Google Scholar]
- Hanahan D. Studies on transformation of Escherichia coli with plasmids. J Mol Biol. 1983 Jun 5;166(4):557–580. doi: 10.1016/s0022-2836(83)80284-8. [DOI] [PubMed] [Google Scholar]
- Honoré N., Nicolas M. H., Cole S. T. Inducible cephalosporinase production in clinical isolates of Enterobacter cloacae is controlled by a regulatory gene that has been deleted from Escherichia coli. EMBO J. 1986 Dec 20;5(13):3709–3714. doi: 10.1002/j.1460-2075.1986.tb04704.x. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Imtiaz U., Billings E. M., Knox J. R., Mobashery S. A structure-based analysis of the inhibition of class A beta-lactamases by sulbactam. Biochemistry. 1994 May 17;33(19):5728–5738. doi: 10.1021/bi00185a009. [DOI] [PubMed] [Google Scholar]
- Jacob F., Joris B., Lepage S., Dusart J., Frère J. M. Role of the conserved amino acids of the 'SDN' loop (Ser130, Asp131 and Asn132) in a class A beta-lactamase studied by site-directed mutagenesis. Biochem J. 1990 Oct 15;271(2):399–406. doi: 10.1042/bj2710399. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Jelsch C., Mourey L., Masson J. M., Samama J. P. Crystal structure of Escherichia coli TEM1 beta-lactamase at 1.8 A resolution. Proteins. 1993 Aug;16(4):364–383. doi: 10.1002/prot.340160406. [DOI] [PubMed] [Google Scholar]
- Jones M. E., Bennett P. M. Inducible expression of the chromosomal cdiA from Citrobacter diversus NF85, encoding an ambler class A beta-lactamase, is under similar genetic control to the chromosomal ampC, encoding an ambler class C enzyme, from Citrobacter freundii OS60. Microb Drug Resist. 1995 Winter;1(4):285–291. doi: 10.1089/mdr.1995.1.285. [DOI] [PubMed] [Google Scholar]
- Joris B., Galleni M., Frère J. M., Labia R. Analysis of the penA gene of Pseudomonas cepacia 249. Antimicrob Agents Chemother. 1994 Feb;38(2):407–408. doi: 10.1128/aac.38.2.407. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Joris B., Ghuysen J. M., Dive G., Renard A., Dideberg O., Charlier P., Frère J. M., Kelly J. A., Boyington J. C., Moews P. C. The active-site-serine penicillin-recognizing enzymes as members of the Streptomyces R61 DD-peptidase family. Biochem J. 1988 Mar 1;250(2):313–324. doi: 10.1042/bj2500313. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Joris B., Ledent P., Dideberg O., Fonzé E., Lamotte-Brasseur J., Kelly J. A., Ghuysen J. M., Frère J. M. Comparison of the sequences of class A beta-lactamases and of the secondary structure elements of penicillin-recognizing proteins. Antimicrob Agents Chemother. 1991 Nov;35(11):2294–2301. doi: 10.1128/aac.35.11.2294. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Kahn M., Kolter R., Thomas C., Figurski D., Meyer R., Remaut E., Helinski D. R. Plasmid cloning vehicles derived from plasmids ColE1, F, R6K, and RK2. Methods Enzymol. 1979;68:268–280. doi: 10.1016/0076-6879(79)68019-9. [DOI] [PubMed] [Google Scholar]
- Lamotte-Brasseur J., Knox J., Kelly J. A., Charlier P., Fonzé E., Dideberg O., Frére J. M. The structures and catalytic mechanisms of active-site serine beta-lactamases. Biotechnol Genet Eng Rev. 1994;12:189–230. doi: 10.1080/02648725.1994.10647912. [DOI] [PubMed] [Google Scholar]
- Lenzini V. M., Magdalena J., Fraipont C., Joris B., Matagne A., Dusart J. Induction of a Streptomyces cacaoi beta-lactamase gene cloned in S. lividans. Mol Gen Genet. 1992 Oct;235(1):41–48. doi: 10.1007/BF00286179. [DOI] [PubMed] [Google Scholar]
- Lindberg F., Normark S. Sequence of the Citrobacter freundii OS60 chromosomal ampC beta-lactamase gene. Eur J Biochem. 1986 May 2;156(3):441–445. doi: 10.1111/j.1432-1033.1986.tb09601.x. [DOI] [PubMed] [Google Scholar]
- Lindberg F., Westman L., Normark S. Regulatory components in Citrobacter freundii ampC beta-lactamase induction. Proc Natl Acad Sci U S A. 1985 Jul;82(14):4620–4624. doi: 10.1073/pnas.82.14.4620. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lindquist S., Lindberg F., Normark S. Binding of the Citrobacter freundii AmpR regulator to a single DNA site provides both autoregulation and activation of the inducible ampC beta-lactamase gene. J Bacteriol. 1989 Jul;171(7):3746–3753. doi: 10.1128/jb.171.7.3746-3753.1989. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Livrelli V., Peduzzi J., Joly B. Sequence and molecular characterization of the ROB-1 beta-lactamase gene from Pasteurella haemolytica. Antimicrob Agents Chemother. 1991 Feb;35(2):242–251. doi: 10.1128/aac.35.2.242. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lodge J. M., Minchin S. D., Piddock L. J., Busby S. J. Cloning, sequencing and analysis of the structural gene and regulatory region of the Pseudomonas aeruginosa chromosomal ampC beta-lactamase. Biochem J. 1990 Dec 15;272(3):627–631. doi: 10.1042/bj2720627. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Lodge J., Busby S., Piddock L. Investigation of the Pseudomonas aeruginosa ampR gene and its role at the chromosomal ampC beta-lactamase promoter. FEMS Microbiol Lett. 1993 Aug 1;111(2-3):315–320. doi: 10.1111/j.1574-6968.1993.tb06404.x. [DOI] [PubMed] [Google Scholar]
- Naas T., Livermore D. M., Nordmann P. Characterization of an LysR family protein, SmeR from Serratia marcescens S6, its effect on expression of the carbapenem-hydrolyzing beta-lactamase Sme-1, and comparison of this regulator with other beta-lactamase regulators. Antimicrob Agents Chemother. 1995 Mar;39(3):629–637. doi: 10.1128/AAC.39.3.629. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Naas T., Nordmann P. Analysis of a carbapenem-hydrolyzing class A beta-lactamase from Enterobacter cloacae and of its LysR-type regulatory protein. Proc Natl Acad Sci U S A. 1994 Aug 2;91(16):7693–7697. doi: 10.1073/pnas.91.16.7693. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Nielsen H., Engelbrecht J., Brunak S., von Heijne G. Identification of prokaryotic and eukaryotic signal peptides and prediction of their cleavage sites. Protein Eng. 1997 Jan;10(1):1–6. doi: 10.1093/protein/10.1.1. [DOI] [PubMed] [Google Scholar]
- Normark S., Burman L. G. Resistance of Escherichia coli to penicillins: fine-structure mapping and dominance of chromosomal beta-lactamase mutations. J Bacteriol. 1977 Oct;132(1):1–7. doi: 10.1128/jb.132.1.1-7.1977. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Normark S. beta-Lactamase induction in gram-negative bacteria is intimately linked to peptidoglycan recycling. Microb Drug Resist. 1995 Summer;1(2):111–114. doi: 10.1089/mdr.1995.1.111. [DOI] [PubMed] [Google Scholar]
- Perilli M., Franceschini N., Segatore B., Amicosante G., Oratore A., Duez C., Joris B., Frère J. M. Cloning and nucleotide sequencing of the gene encoding the beta-lactamase from Citrobacter diversus. FEMS Microbiol Lett. 1991 Sep 15;67(1):79–84. doi: 10.1016/0378-1097(91)90448-j. [DOI] [PubMed] [Google Scholar]
- Prince A., Wood M. S., Cacalano G. S., Chin N. X. Isolation and characterization of a penicillinase from Pseudomonas cepacia 249. Antimicrob Agents Chemother. 1988 Jun;32(6):838–843. doi: 10.1128/aac.32.6.838. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Proenca R., Niu W. W., Cacalano G., Prince A. The Pseudomonas cepacia 249 chromosomal penicillinase is a member of the AmpC family of chromosomal beta-lactamases. Antimicrob Agents Chemother. 1993 Apr;37(4):667–674. doi: 10.1128/aac.37.4.667. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Péduzzi J., Reynaud A., Baron P., Barthélémy M., Labia R. Chromosomally encoded cephalosporin-hydrolyzing beta-lactamase of Proteus vulgaris RO104 belongs to Ambler's class A. Biochim Biophys Acta. 1994 Jul 20;1207(1):31–39. doi: 10.1016/0167-4838(94)90048-5. [DOI] [PubMed] [Google Scholar]
- Rasmussen B. A., Bush K., Keeney D., Yang Y., Hare R., O'Gara C., Medeiros A. A. Characterization of IMI-1 beta-lactamase, a class A carbapenem-hydrolyzing enzyme from Enterobacter cloacae. Antimicrob Agents Chemother. 1996 Sep;40(9):2080–2086. doi: 10.1128/aac.40.9.2080. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Reynaud A., Péduzzi J., Barthélémy M., Labia R. Cefotaxime-hydrolysing activity of the beta-lactamase of Klebsiella oxytoca D488 could be related to a threonine residue at position 140. FEMS Microbiol Lett. 1991 Jun 15;65(2):185–192. doi: 10.1016/0378-1097(91)90301-p. [DOI] [PubMed] [Google Scholar]
- Sanger F., Nicklen S., Coulson A. R. DNA sequencing with chain-terminating inhibitors. Proc Natl Acad Sci U S A. 1977 Dec;74(12):5463–5467. doi: 10.1073/pnas.74.12.5463. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Schell M. A. Molecular biology of the LysR family of transcriptional regulators. Annu Rev Microbiol. 1993;47:597–626. doi: 10.1146/annurev.mi.47.100193.003121. [DOI] [PubMed] [Google Scholar]
- Schultz S. C., Dalbadie-McFarland G., Neitzel J. J., Richards J. H. Stability of wild-type and mutant RTEM-1 beta-lactamases: effect of the disulfide bond. Proteins. 1987;2(4):290–297. doi: 10.1002/prot.340020405. [DOI] [PubMed] [Google Scholar]
- Seoane A., Francia M. V., García Lobo J. M. Nucleotide sequence of the ampC-ampR region from the chromosome of Yersinia enterocolitica. Antimicrob Agents Chemother. 1992 May;36(5):1049–1052. doi: 10.1128/aac.36.5.1049. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Seoane A., García Lobo J. M. Nucleotide sequence of a new class A beta-lactamase gene from the chromosome of Yersinia enterocolitica: implications for the evolution of class A beta-lactamases. Mol Gen Genet. 1991 Aug;228(1-2):215–220. doi: 10.1007/BF00282468. [DOI] [PubMed] [Google Scholar]
- Spratt B. G., Hedge P. J., te Heesen S., Edelman A., Broome-Smith J. K. Kanamycin-resistant vectors that are analogues of plasmids pUC8, pUC9, pEMBL8 and pEMBL9. Gene. 1986;41(2-3):337–342. doi: 10.1016/0378-1119(86)90117-4. [DOI] [PubMed] [Google Scholar]
- Stragier P., Patte J. C. Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. III. Nucleotide sequence and regulation of the lysR gene. J Mol Biol. 1983 Aug 5;168(2):333–350. doi: 10.1016/s0022-2836(83)80022-9. [DOI] [PubMed] [Google Scholar]
- Stragier P., Richaud F., Borne F., Patte J. C. Regulation of diaminopimelate decarboxylase synthesis in Escherichia coli. I. Identification of a lysR gene encoding an activator of the lysA gene. J Mol Biol. 1983 Aug 5;168(2):307–320. doi: 10.1016/s0022-2836(83)80020-5. [DOI] [PubMed] [Google Scholar]
- Urabe H., Ogawara H. Nucleotide sequence and transcriptional analysis of activator-regulator proteins for beta-lactamase in Streptomyces cacaoi. J Bacteriol. 1992 May;174(9):2834–2842. doi: 10.1128/jb.174.9.2834-2842.1992. [DOI] [PMC free article] [PubMed] [Google Scholar]
- Vieira J., Messing J. Production of single-stranded plasmid DNA. Methods Enzymol. 1987;153:3–11. doi: 10.1016/0076-6879(87)53044-0. [DOI] [PubMed] [Google Scholar]
- Zafaralla G., Manavathu E. K., Lerner S. A., Mobashery S. Elucidation of the role of arginine-244 in the turnover processes of class A beta-lactamases. Biochemistry. 1992 Apr 21;31(15):3847–3852. doi: 10.1021/bi00130a016. [DOI] [PubMed] [Google Scholar]