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Functional Characterization of Seven Γ-Glutamylpolyamine Synthetase

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Functional Characterization of Seven Γ-Glutamylpolyamine Synthetase JOURNAL OF BACTERIOLOGY, Aug. 2011, p. 3923–3930 Vol. 193, No. 15 0021-9193/11/$12.00 doi:10.1128/JB.05105-11 Copyright © 2011, American Society for Microbiology. All Rights Reserved. Functional Characterization of Seven ␥-Glutamylpolyamine Synthetase Genes and the bauRABCD Locus for Polyamine and ␤-Alanine Utilization in Pseudomonas aeruginosa PAO1ᰔ Xiangyu Yao,1† Weiqing He,1,2† and Chung-Dar Lu1,3* Department of Biology, Georgia State University, Atlanta, Georgia 303031; Institute of Medicinal Biotechnology, Chinese Academy of Medical Sciences and Peking Union Medical College, Beijing 100050, China2; and Department of Medical Laboratory Sciences and Biotechnology, China Medical University, Taichung, Taiwan 404023 Received 16 April 2011/Accepted 13 May 2011 Pseudomonas aeruginosa and many other bacteria can utilize biogenic polyamines, including diaminopropane (DAP), putrescine (Put), cadaverine (Cad), and spermidine (Spd), as carbon and/or nitrogen sources. Tran- scriptome analysis in response to exogenous Put and Spd led to the identification of a list of genes encoding putative enzymes for the catabolism of polyamines. Among them, pauA1 to pauA6, pauB1 to pauB4, pauC, and pauD1 and pauD2 (polyamine utilization) encode enzymes homologous to Escherichia coli PuuABCD of the ␥-glutamylation pathway in converting Put into GABA. A series of unmarked pauA mutants was constructed for growth phenotype analysis. The results revealed that it requires specific combinations of pauA knockouts to abolish utilization of different polyamines and support the importance of ␥-glutamylation for polyamine catabolism in P. aeruginosa. Another finding was that the list of Spd-inducible genes overlaps almost completely with that of Put-inducible ones except the pauA3B2 operon and the bauABCD operon (␤-alanine utilization). Mutation analysis led to the conclusion that pauA3B2 participate in catabolism of DAP, which is related to the aminopropyl moiety of Spd, and that bauABCD are essential for growth on ␤-alanine derived from DAP (or Spd) catabolism via the ␥-glutamylation pathway. Measurements of the pauA3-lacZ and bauA-lacZ expression indicated that these two promoters were differentially induced by Spd, DAP, and ␤-alanine but showed no apparent response to Put, Cad, and GABA. Induction of the pauA3 and bauA promoters was abolished in the bauR mutant. The recombinant BauR protein was purified to demonstrate its interactions with the pauA3 and bauA regulatory regions in vitro. In summary, the present study support that the ␥-glutamylation pathway for polyamine utilization is evolutionarily conserved in E. coli and Pseudomonas spp. and is further expanded in Pseudomonas to accommodate a more diverse metabolic capacity in this group of microorganisms. Biogenic polyamines are a group of ubiquitous polycations putrescine synthetase PuuA, followed by three more reactions found in all living organisms. They are essential for cell growth catalyzed by PuuB, PuuC, and PuuD in sequence, to convert and participate in a variety of physiological functions (2, 30, Put into ␥-aminobutyrate (GABA). These four enzymes, as 31). Depending on the specific biosynthetic pathways (12, 22, well as the Put transporter PuuP and a transcriptional regula- 26, 29), different bacteria possess a preferential set of poly- tor PuuR, are encoded in a single puu gene cluster in E. coli amines, which include the diamines diaminopropane (DAP), (17). putrescine (Put), and cadaverine (Cad); the triamines spermi- Pseudomonas species, including P. aeruginosa, grow on sev- dine (Spd) and norspermidine; and the tetramine spermine. It eral polyamine compounds as the sole source of carbon and is generally believed that polyamines form complexes with nitrogen. However, the catabolic pathways for polyamine uti- nucleic acid-containing macromolecules through charge inter- lization in Pseudomonas were not clear. Characterization of actions in vivo (8, 11, 16). In vitro, excess binding of polyamines the spu gene cluster identified four putative enzymes encoded to DNA was reported to form very condensed complexes (3), by spuIABC for Spd/Put utilization and a Spd/Put uptake sys- which might cause difficulties in DNA unwinding during rep- tem by spuDEFGH (25). The impaired growth of spuA and lication or transcription. Therefore, the intracellular concen- spuB mutants on Spd and spermine suggests major roles of the trations of polyamines need to be tightly monitored to prevent SpuA and SpuB enzymes in the catabolism of these poly- adverse effects on cell growth. amines. Although the divergent spuI and spuA promoters were When released from the cells into environments, polyamines inducible by Put and Spd, most of the spu mutants grew nor- can be recycled by many bacteria or serve as sources of carbon mally on Put. Since the SpuI and SpuB enzymes are E. coli and nitrogen. Studies conducted by Kurihara and coworkers on PuuA homologues based on sequence comparison, it is likely Put catabolism in E. coli (17, 19) established a novel ␥-glu- that the ␥-glutamylation pathway plays a role on polyamine tamylation pathway (Fig. 1), which is initiated by ␥-glutamyl- catabolism in P. aeruginosa. Without ␥-glutamylation, spermidine dehydrogenase en- * Corresponding author. Mailing address: Department of Biology, coded by the spdH gene was reported to catalyze oxidative Georgia State University, 100 Piedmont Ave., Atlanta, GA 30303. cleavage of Spd into DAP and 4-aminobutyraldehyde, as well Phone: (404) 413-5395. Fax: (404) 413-5301. E-mail: [email protected]. † X.Y. and W.H. contributed equally to this study. as spermine, into Spd and 3-aminopropanaldehyde (5). How- ᰔ Published ahead of print on 27 May 2011. ever, synthesis of this enzyme was not inducible by exogenous 3923 3924 YAO ET AL. J. BACTERIOL. operon for ␥-glutamylpolyamine synthetase and oxidoreduc- tase and the bauABCD operon for ␤-alanine catabolism and uptake. Further analysis led to the conclusion that pauA3B2 genes participate in the catabolism of DAP, the aminopropyl moiety of Spd, and that bauABCD genes are essential for growth on ␤-alanine derived from DAP (or Spd) catabolism via the ␥-glutamylation pathway. A transcriptional regulator of the LysR family was identified in control of these two operons in response to ␤-alanine. MATERIALS AND METHODS Strains and growth conditions. Bacterial strains used in the study include E. coli DH5␣ and Top10 (Invitrogen) and P. aeruginosa PAO1. Mutants derived from PAO1 were constructed as described below or acquired from the strain stock center at University of Washington. Luria-Bertani (LB) medium was used for strain construction with the following supplements as required: ampicillin at 100 ␮g/ml for E. coli and carbenicillin at 100 ␮g/ml, streptomycin at 500 ␮g/ml, and gentamicin at 100 ␮g/ml for P. aeruginosa. Minimal medium P was used for the growth of P. aeruginosa supplemented with specific carbon (C) and nitrogen (N) sources, as indicated (9). Construction of knockout mutants. For the bauRABCD locus, the flanking regions of the intended knockout gene were amplified by PCR, and restriction enzymes sites were introduced into the primers so that the PCR products possess configurations of 5Ј-BamHI-[left arm]-EcoRI-3Ј and 5Ј-EcoRI-[right arm]- HindIII-3Ј. After restriction enzyme digestion, these two DNA fragments were ligated and cloned into the BamHI and HindIII sites of pRTP2 (24). The resulting plasmid was subjected to EcoRI digestion to insert a 1.6-kb EcoRI FIG. 1. Proposed diamine catabolic pathways of P. aeruginosa. fragment containing the gentamicin resistance (Gmr) cassette from plasmid (A) Oxidative deamination of diamines by the ␥-glutamylation path- pGM⍀1 (28). The final plasmid construct was introduced into E. coli SM10 to way. The pau genes coding enzymes for polyamine utilization in the serve as the donor in the biparental conjugation (7), with a spontaneous strep- pathway were marked. The chemical structures of three common di- tomycin-resistant mutant of PAO1 as recipient. After incubation at 37°C for 6 h, amines and the triamine spermidine are shown on the right. (B) Di- the transconjugants were spread and selected on LB plates supplemented with vergent catabolic pathways for ␤-alanine, ␥-aminobutyrate, and ␦-ami- streptomycin and gentamicin. For the construction of a series of pauA mutants, novalerate derived from diaminopropane, putrescine, and cadaverine. the protocol for gene replacement and in vivo excision by the Flp-FRT recom- Also shown are genes encoding enzymes for the proposed reactions. bination system (10) was used to generate unmarked mutants of PAO1 with deletions on multiple genes. Expected deletions in these mutants were confirmed by PCR. Construction of PbauA::lacZ and PpauA3::lacZ fusions. A DNA fragment of polyamines, and the spdH knockout mutant grew normally on 429 bp covering the bauR-bauA intergenic region was amplified by PCR from the Spd and spermine. It was concluded that P. aeruginosa PAO1 genomic DNA of PAO1 with the following two primers: 5Ј-TCTA GAG CGC does not produce sufficient amounts of SpdH to support AGG TTG AGT TCG CTG GAAC-3Ј and 5Ј-TCT AGA CTC GCG GCC CTC growth on these two polyamines. GTC GGT CAG-3Ј. The PCR products were digested with XbaI restriction enzyme and cloned into the XbaI site of pQF50 (6), and the resulting plasmid In order to understand how P. aeruginosa responds to the pBAU1 was confirmed by nucleotide sequencing. For construction of the presence of exogenous Put and Spd, DNA microarrays exper- PpauA3::lacZ fusion plasmid pPAU3, the two primers (5Ј-CGC GGA TCC GCC iments had been conducted by our group to get snapshots of GCT TTC CGG GCG TCT CT-3Ј and 5Ј-CCC AAG CTT GGG GCT CTC gene expression when the cells were exposed to these com- TTG TCG GTC TTG-3Ј) were used to amplify a DNA fragment of 467 bp and pounds in the exponential phase of growth (4, 20, 21). Analysis clone it into the BamHI and HindIII sites of pQF50. Electrophoretic mobility shift assays. DNA fragments covering the regulatory of these data has led us to report a connection of polyamine region of bauA and pauA3 (Fig.
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