Scarless and sequential gene modification in Pseudomonas using PCR product flanked by short homology regions
© Liang and Liu; licensee BioMed Central Ltd. 2010
Received: 12 April 2010
Accepted: 3 August 2010
Published: 3 August 2010
The lambda Red recombination system has been used to inactivate chromosomal genes in various bacteria and fungi. The procedure consists of electroporating a polymerase chain reaction (PCR) fragment containing antibiotic cassette flanked by homology regions to the target locus into a strain that can express the lambda Red proteins (Gam, Bet, Exo).
Here a scarless gene modification strategy based on the Red recombination system has been developed to modify Pseudomonas genome DNA via sequential deletion of multiple targets. This process was mediated by plasmid pRKaraRed encoding the Red proteins regulated by P BAD promoter, which was functional in P. aeruginosa as well as in other bacteria. First the target gene was substituted for the sacB-bla cassette flanked by short homology regions (50 bp), and then this marker gene cassette could be replaced by the PCR fragment flanking itself, generating target-deleted genome without any remnants and no change happened to the surrounding region. Twenty genes involved in the synthesis and regulation pathways of the phenazine derivate, pyocyanin, were modified, including one single-point mutation and deletion of two large operons. The recombination efficiencies ranged from 88% to 98%. Multiple-gene modification was also achieved, generating a triple-gene deletion strain PCA (PAO1, ΔphzHΔphzMΔphzS), which could produce another phenazine derivate, phenazine-1-carboxylic acid (PCA), efficiently and exclusively.
This lambda Red-based technique can be used to generate scarless and sequential gene modification mutants of P. aeruginosa efficiently, using one-step PCR product flanked by short homology regions. Single-point mutation, scarless deletion of genes can be achieved easily in less than three days. This method may give a new way to construct genetically modified P. aeruginosa strains more efficiently and advance the regulatory network study of this organism.
Obtainment of the genome sequences of more and more bacteria have provided researchers a wealth of information to restructure custom-designed microbes for therapeutic and industrial applications [1–3]. One of the most common approaches is sequence-specific deletion or insertion of the target genes or DNA fragments, and various methods have been developed based on the RecA-independent homologous recombination, such as RecET and lambda Red recombination system [4–8]. In these recombination events, selection markers, usually antibiotic markers are needed to confirm the modification procedure, which may have influence on further manipulation. To solve this problem, the Flp/FRT and Cre/loxP site-specific recombination systems have been used for the precise excision of selection markers. However, even combined with these systems, one copy of FRT or loxP site still remains on the genome after excision [9, 10].
P. aeruginosa is a gram-negative opportunistic human pathogen of growing clinical importance. The sequence analysis on the 6.3 Mb genome of P. aeruginosa PAO1 revealed 5700 predicted open reading frames (ORF) . Many genetic tools have been developed for its genome-scale and proteome-scale research, such as commercial (Affymetrix, Santa Clara, CA) P. aeruginosa GeneChips® for transcriptome analysis and the transposon mutants library for sequence-defined mutants [12–15]. Almost in all of these methods, it is necessary to use the suicide vector and the conjugation transfer to isolate the defined mutant, which is a quite tedious process. In addition, to make unmarked deletion mutants, researchers have developed several methods combining the counter-selectable markers (sacB) with the site-specific Flp or Cre recombinase [16, 17]. However, these methods can not generate the true "scarless" mutants.
Here a two-step approach was described to perform the scarless and sequential genome modification using one-step PCR product with short (50 bp) homology regions. The homologous recombination process was mediated by an RK2-derived plasmid, pRKaraRed, expressing the genes of lambda-Red system (gam, bet and exo) from the arabinose-inducible P BAD promoter. Single gene modification could be finished in three days and the efficiency is higher than 88%. Twelve scarless deletion mutants of different genes, two deletion mutants of large operons, and one single-point mutation were successfully constructed. Furthermore a strain PCA (PAO1, ΔphzHΔphzMΔphzS) with deletions in three genes was also generated, which could produce the phenazine-1-acid exclusively and efficiently. This strategy may simplify the genetic manipulation to P. aeruginosa and fasten relevant research.
Lambda Red-mediated scarless gene modification in P. aeruginosa
Initially, phzS was selected as target because the phenotype of the mutant could be differentiated from that of the wild type by its inability to produce the pseudomonas blue phenazine pigment, pyocyanin, lack of which resulting a yellowish culture.
Efficiencies of pRKaraRed-mediated recombination under different conditions
Positive colonies/Growing colonies (%)a
Overall efficiency (%)
Replacement with marker genesb
Deletion of marker genesc
A. L-arabinose concentration
B. Length of homology regions
C. Induction time
The influences of the L-arabinose concentration and the induction time on the recombination efficiency were also analyzed. Results indicated that when the concentration of L-arabinose went up, the recombination efficiency also increased gradually which could reach the maximum at the concentration of 0.2% and keep stable. Induction time also had influence on the recombination efficiency and efficient recombination could be achieved after the cells were induced with 0.2% L-arabinose for at least three hours (Table 1).
Gene modifications in P. aeruginosa PAO1
Efficiencies of pRKaraRed-mediated scarless modification to different targets
Positive colonies/Growing colonies (%)a
Overall efficiency (%)
Replacement using sacB-bla cassetteb
Deletion of sacB-bla cassettec
A. Deletion of genes
B. Single-point mutation
C. Deletion of operons
Sequential gene deletion and construction of strain PCA
Lambda Red recombination system first described in E. coli has been successfully applied to Yersinia, Salmonella, Shigella and Serratia[6, 7, 21–25]. The procedures involve the homologous recombination between the region of interest and a PCR product containing antibiotic cassette flanked by homology region. Although this efficient method may be applicable to other bacteria, adaptations are frequently required, such as the homology length and recombination steps .
In P. aeruginosa, construction of markerless deletion mutants is still a time-consuming and labor-intensive process. Two different plasmids were used in the traditional procedure. The first plasmid was transformed for targeting a selected region and the second plasmid was re-transformed for the unmarked deletion of the antibiotic cassette by Flp recombinase . This recombination procedure including multiple steps needs several days to accomplish one gene modification and the recombination efficiency is not very high. Furthermore, the produced "unmarked" deletion is not scarless, as normally one FRT site was left. In 2008, lambda Red system and three-step PCR products were used to replace the target gene with antibiotic cassette in P. aeruginosa PA14, which confirmed the possibility of using the lambda Red recombination system in P. aeruginosa. However, this method can not produce scarless modification as the antibiotic cassette is still left on the genome DNA, quite difficult to perform multiple genes modification in one cell. And its homology regions were quite long, meaning several rounds of PCR amplification and more manipulation steps were needed.
As previously reported, multi-copy Red plasmid pTP223 failed to promote gene replacement using the PCR-generated substrates with short homology extensions in E. coli, since the linear multimers of this plasmid generated through high dosage of lambda Gam protein drove the plasmid replication in rolling circle mode may be toxic to E. coli host or compete with the recombination substrates [27–30]. Based on these observations, we constructed plasmid pRKaraRed derived from RK2, low-copy and broad-host-range expression. As expected, plasmid pRKaraRed was able to promote efficient homologous recombination with short homology extension in E. coli, in P. aeruginosa PAO1, and also in Pseudomonas sp. M18 (data not shown). In E. coli, PCR cassettes flanked by only 35 bp homology region could induce the homologous recombination and efficient recombination happened when the PCR fragments flanked by 40 bp homology regions were used (data not shown). But in Pseudomonas PAO1 and M18, almost no transformant could be obtained using the PCR fragments with 35 bp or 40 bp homology extension, and at least 50 bp homology regions were required for efficient recombination (30~80 transformants). This is consistent with previous results that the minimum length of homology extension required for efficient recombination may be different when the lambda Red system is used in different organisms, which may have relevance to the characteristics of the organisms, such as the difference in GC content and so on [22–25]. Although the efficiency of recombination in Pseudomonas was lower than that in E. coli, plasmid pRKaraRed was still suitable for the gene modification in Pseudomonas. Differences in the expression of Red proteins, DNA uptake, sequence contexts and the species-specific restriction may result in the variations of recombination efficiency .
The scarless modification strategy based on plasmid pRKaraRed was efficient and rapid. Single-point mutation, deletion of large operons and consecutive deletion of multiple genes could be achieved easily. One plasmid and PCR cassette flanked by 50 bp homology regions were enough to induce efficient recombination, meaning only one step PCR amplification was needed. And as the marker cassettes could be used repeatedly, only the homology regions should be changed to perform the modifications of different genes, which may alleviate the workload of primer design.
Furthermore, the expression of the lambda Red proteins were driven by the tightly regulated promoter P BAD , of which the basal expression level was very low in the absence of its inducer. This will minimize the unwanted recombination and increase the efficiency of homologous recombination. On the other hand, the sucrose counter-selection procedure could also increase the selection efficiency. Therefore, the high recombination efficiency of this strategy could ease the screening step, lessen work intensity and shorten the experimental time.
Phenazine derivates have many important biological effects [31, 32]. Although the pathway of phenazine synthesis in P. aeruginosa has been studied , the function mechanisms and regulation networks of phenazine derivates are still poorly characterized. Therefore, many knockout mutants need to be constructed, not only single gene mutant, but also the multiple-gene mutants. Based on plasmid pRKaraRed mediated method, we successfully obtained a series of scarless deletion mutants of different genes involving in the phenazine synthesis and regulation pathways, such as lasI, qscR, gacA, rsmA and etc. Using this scarless approach, mutants with modifications of multiple genes could be generated easily for further study of the cumulative effects in different combination styles. Strain PCA with the deletion in three genes was an example. It could be further used to study the regulation styles and the special functions of this compound without any disturbance of other phenazine derivates.
In a word, the plasmid pRKaraRed mediated method could perform efficient and accurate homologous recombination in Pseudomonas and in E. coli. There is only one potential shortcoming of this system, that this plasmid can not be removed easily after all the necessary modifications are accomplished. Therefore, further improvements may be done, such as using the conditional replicons (e.g. temperature-sensitive replicon) to perfect this system.
This pRKaraRed-mediated technique could be used efficiently and rapidly to generate scarless and sequential gene modification mutants in P. aeruginosa with one-step PCR product flanked by short homology regions. Single-point mutation, large operon deletion mutants and sequential deletion mutants of multiple genes could be achieved easily. This method may give a new way to generate more genetically modified P. aeruginosa strains.
Strains, plasmids, enzymes and chemicals
Bacterial strains and plasmids
Strains and Plasmids
Genotype or Description
E. coli DH5α
Sup E 44 ΔlacU169(Φ80 lacZ ΔM15) hsd R 17 recA 1 endA 1gyrA 96 thi-1 rel A 1
P. aeruginosa PAO1
Wild type prototroph
Stephen Lory's Lab
P. aeruginosa PCA
PAO1 ΔphzH ΔphzS ΔphzM
RK2-derived cloning vector, TetR
Stephen Lory's Lab, 
pBluescript II KS (+)
Universal cloning vector, AmpR
Gene replacement vector, oriT+ sacB+, AmpR
Stephen Lory's Lab, 
Vector containing araC gene and P BAD promoter, AmpR
Broad-host-range, lambda Red proteins expression vector, TetR
PCR and standard DNA procedure
PCR was performed with LA-Taq DNA polymerase or Pyrobest DNA polymerase according to the manufacyturer's protocol. DNA sequences of the oligonucleotides were listed in Additional file 1, Table S1. Oligonucleotides synthesis and DNA sequencing were performed by Invitrogen Ltd. (Shanghai, China). Plasmid DNAs were isolated using the QIA prep Mini-spin kit (Qiagen, Shanghai, China) and P. aeruginosa genomic DNA was obtained using QIA amp DNA mini kit (Qiagen, Shanghai, China). DNA fragment were purified from agarose gels utilizing the QIA quick gel extraction kit (Qiagen, Shanghai, China). Other general techniques for restriction enzyme manipulation, molecular cloning, and agarose gel electrophoresis were carried out with standard protocols.
Construction of plasmid pRKaraRed
The cassette containing araC gene and P BAD promoter was amplified from plasmid pBAD18 with primers araF and araR (Additional file 1, Table S1) . The amplified DNA fragments were digested with restriction enzymes Kpn I and Xho I, and then they were cloned into plasmid pBluescript II KS (+), generating plasmid pKS-ara. Similar method was used to amplify the three genes (exo, bet and gam) of lambda-Red recombination system from lambda phage genomes with primers RedF and RedR, and inserted it into the Xho I-Bam HI site of plasmid pKS-ara, yielding plasmid pKS-araRed. The Kpn I-Bam HI fragment containing araC gene, P BAD promoter and three Red genes was further sub-cloned into the Kpn I-Bam H I sites of RK2-derived cloning plasmid pDN18, generating the plasmid pRKaraRed able to express the lambda Red proteins (Fig. 1). DNA sequencing confirmed this construction.
Electro-transformation of P. aeruginosa
Single P. aeruginosa colony was inoculated in 3 ml LB medium and grown at 37°C overnight. 1 ml overnight culture was added to 200 ml fresh LB medium and grown at 37°C, shaking to OD600 = 0.4~0.5. The bacteria were then rendered electro-competent by four times washings of ice-cold 10% glycerol and were re-suspended in 200 μl ice-cold 10% glycerol. To generate the electro-competent cells of PAO1/pRKaraRed, L-arabinose of certain concentration should be added into the medium and cultured for several hours before the 10% glycerol washing step.
Electroporation was carried out using 50 μl of bacterial suspension (about 1×109 cells) and no more than 10 μl of DNA (at least 200 ng/μl) in a 0.2 cm ice-cold electroportation cuvette, transformed on a Bio-Rad GenePulser II at 200Ω, 25 μF and 2.5 kV. Uninduced cells and induced cells without plasmid or without DNA fragments were set as negative controls for each transformation. The electroporated cells were diluted in 1 ml LB and incubated at 37°C for three hours. The transformants were then selected on the antibiotic-imbued plates.
Scarless gene modification in P. aeruginosa
Scarless gene modification strategy was described in Fig. 2. First the sacB-bla cassettes were amplified from plasmid pEX18Ap with the primers F1 and R1 . The numbers of primers corresponded to the steps of PCR amplification. The electro-transformation of the sacB-bla cassette into the PAO1/pRKaraRed competent cells was performed as described above. Transformants were screened on LB plates supplemented with 500 μg/ml carbenicillin and 50 μg/ml tetracyclin. The colonies with CarbRTetR phenotypes confirmed by PCR detection and DNA sequencing were regarded as positive clones. Next, the sacB-bla removal cassettes were amplified from the genomic DNA of the first-step strain with the primers F2 and R2. Then this fragment was electro-transformed into the competent cells of the first-step to perform the second recombination. Electro-transformed cells were spread on LB plates supplemented with 10% sucrose and 50 μg/ml tetracycline. The transformants were further selected parallel on the LB plates with 10% sucrose and 50 μg/ml tetracycline, and the LB plates with 500 μg/ml carbenicillin and 50 μg/ml tetracycline. The colonies with SucRCarbS phenotypes confirmed by PCR detection and DNA sequencing were regarded as positive recombinants.
Twelve genes, two large operons and one nucleotide site were selected as target and their primers for PCR amplification were listed in Additional file 1, Table S1.
System efficiency analysis
The influences of L-arabinose concentration, induction time and the length of homology region on the efficiency of homologous recombination were analyzed. phzS gene was selected as target. First, the PAO1/pRKaraRed cultures were induced with L-arabinose of different concentrations (ranging from 0.05% to 1.0%) for three hours. Then the PAO1/pRKaraRed cultures were induced with L-arabinose of suitable concentration for different time (from 1 h to 12 h). Finally, the PCR products with homology regions of different lengths (50 bp, 60 bp, 100 bp) were used to perform homologous recombination. Control experiments and screen procedures were set same as described above. The efficiencies of recombination were calculated by dividing the number of positive colonies with the number of growing colonies.
Construction of three-gene deleted strain PCA and HPLC analysis of phenazine derivatives
Sequential gene modifications of multiple target genes were achieved by several rounds of recombination steps. The recombination efficiency was also detected using phenotype screen, PCR detection and DNA sequencing. The strain with three-gene deletions (PAO1, ΔphzHΔphzMΔphzS) was named as PCA.
HPLC analysis of phenazine derivatives were performed as previously described . PAO1 and PCA strains were cultured in PB medium at 28°C for 72 h and then centrifugation was performed to remove the cells. The recovered medium was acidified to pH 4.0 with HCl and filtered through 0.22 μm membrane. The filtrates were extracted with chloroform. The organic phase was dried with nitrogen and dissolved in acetonitrile. 10 μl samples were loaded onto a Unimicro Kromasil C18 column (5 μm; 4.6 by 250 mm, ScienHome Co., USA) for reverse-phase HPLC analysis in a Waters HPLC Integrity system consisting of a Waters 510 separation module and a 490E programmable multi-wavelength detector. The column was washed at a flow rate 500 μl/min with 8% acetonitrile in 25 mM ammonium acetate for 2 min and a linear gradient acetonitrile from 8% to 80% in 25 mM ammonium acetate for 25 min. The HPLC was monitored simultaneously at 257 nm. The peak fractions were collected separately and identified by mass spectrometry with HP1100 HPLC-MSD (API-ES/APCI) (Hewlett-Packard Co., USA).
We are grateful to Dr. Stephen Lory (Harvard Medical School) for providing bacterial strains and plasmids to initiate this work.
This work was supported by grant from the National Natural Science Foundation of China [grant number 30900010, 30870512]; grant from the Science Foundation for the Excellent Youth Scholars of Ministry of Education of China [grant number No. 20090073120066]; the Major State Basic Research Development Program of China (973 Program) [grant number 2009CB118906, 2007CB914504].
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