Department of Applied Microbial Technology, Sojo University, Ikeda 4-22-1, Kumamoto 860-0082, Japan1
Author for correspondence: Masayoshi Matsuoka. Tel: +81 96 326 3111. Fax: +81 96 323 1330. e-mail: matsuoka{at}bio.sojo-u.ac.jp
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ABSTRACT |
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Keywords: homologous recombination, Synechococcus, gene conversion, merodiploid, psbAI
Abbreviations: Apr, ampicillin-resistant; Cmr, chloramphenicol-resistant; Cms, chloramphenicol-sensitive; Kmr, kanamycin-resistant; Kms, kanamycin-sensitive; Smr, streptomycin-resistant; Strr, streptomycin-resistant (chromosomal); Strs, streptomycin-sensitive (chromosomal)
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INTRODUCTION |
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Some cyanobacterial strains, such as Synechococcus sp. PCC 7942 and Synechocystis sp. PCC 6803, are naturally transformable with externally added DNAs, and both integrative and replicative transformation systems are available in these strains (Chauvat et al., 1986 ; Kuhlemeier et al., 1983
; Williams, 1988
). However, due to the fact that homologous recombination mediated by recA function is essential for cell viability in cyanobacteria (Murphy et al., 1990
), recombinant plasmids containing any sequences homologous with their host chromosome are not stably maintained in cyanobacterial cells. Consequently, these homologous sequences are integrated with the aid of dominant drug resistance markers into non-essential sites of the chromosome conventionally termed platforms (Geerts et al., 1995
) or neutral sites (Bustos & Golden, 1992
). Although this method works well, one of the drawbacks is that the dominant drug resistance marker, once integrated, cannot be eliminated from the genome, and thus a subsequent genetic manipulation in the same strain is limited by the availability of other drug resistance markers.
Another difficulty in manipulating cyanobacterial genes arises from their polyploidy; i.e. the multiple copies of genomic DNA in some strains (Binder & Chisholm, 1990 ). It is therefore of great importance to have a selection scheme that allows one to obtain mutants carrying homogeneous mutant genes on every copy of genomic DNA. Such homogenote (or homoallelic) mutants are only available for genes that are not essential for growth; otherwise heterogenotes containing the mutant as well as wild-type genes are formed (e.g. Ghassemian & Straus, 1996
; Murphy et al., 1990
). In this regard, a dominant drug-sensitive marker should be easier to eliminate from the chromosome after its integration since even a single copy of the marker would reduce the ability of the polyploid host to survive in the presence of the drug.
It is well known that the rpsL gene encoding an S12 subunit protein of the 30S ribosome in Escherichia coli gives rise to strA mutations conferring the streptomycin-resistant (Strr) phenotype (Funatsu & Wittmann, 1972 ; Timms et al., 1992
). When the mutant and wild-type alleles coexist in a cell, the resulting merodiploid shows a streptomycin-sensitive (Strs) phenotype; i.e. the strA mutation is recessive (Lederberg, 1951
). The cloned rpsL gene thus behaves as a dominant Strs marker and has been utilized in a variety of genetic methods, including enforced cloning of foreign DNAs (Dean, 1981
; Hashimoto-Gotoh et al., 1993
), a detection system for specific mutations (Gondo et al., 1996
) and a gene replacement system in a recD mutant (Russell & Dahlquist, 1989
). These methods depend upon the logic that only when the rpsL gene is inactivated in an rpsL/rpsL (strA) merodiploid strain can the cells grow in the presence of streptomycin.
In this work, we have developed a methodology capable of introducing multiple gene replacements into the obligate photoautotrophic cyanobacterium Synechococcus sp. PCC 7942 based on the same strategy as the rpsL system in E. coli. For this purpose, the photosystem II psbAI gene encoding the D1 protein was chosen as a target, since the presence of three psbA genes in this strain permitted us to inactivate only the psbAI gene without affecting photoautotrophic growth (Golden et al., 1986 ). We first demonstrated that an rps12 gene encoding an S12 ribosomal protein acts as a dominant Strs marker in this cyanobacterium. We then applied the cloned rps12 gene to systematically modify the psbAI ORF without leaving any externally incorporated drug resistance markers in the final mutants. This method is thus well suited for the construction of multiple gene replacements in cyanobacteria in order to analyse complex biological processes such as photosystems I and II.
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METHODS |
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PCR and DNA manipulations.
Standard methods (Sambrook et al., 1989 ) were applied for digestion of DNA by restriction enzymes and cloning of DNA fragments into plasmids. PCR and inverse PCR were performed as described by Saiki et al. (1987)
and Triglia et al. (1988)
, respectively, with the GeneAmp PCR system 2400 (Perkin Elmer-Applied Biosystems) and the oligonucleotide primers listed in Table 2
. AmpliTaq GOLD (Perkin Elmer-Applied Biosystems) was used for most of the amplifications of DNA fragments. PCR fragments to be cloned into plasmids were amplified with Vent DNA polymerase (New England BioLabs), purified with Wizard PCR Preps (Promega) and cloned into pUC18 (SureClone Ligation Kit; Pharmacia). Nucleotide sequences were determined with a 310 Genetic Analyzer and reagents for BigDye Terminator Cycle Sequencing (Perkin Elmer-Applied Biosystems), as recommended by the supplier.
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Electroporation.
Cyanobacterial cells were grown in BG-11 medium supplemented with appropriate antibiotics to a density of 108 cells ml-1. The cells in 1·0 ml culture were collected by centrifugation in 1·5 ml sterile centrifuge tubes at 13000 g for 5 min at 4 °C, and the supernatant was discarded. The cells were suspended in 1·0 ml SH buffer (272 mM sucrose, 8 mM HEPES, pH 7·4), centrifuged, and the supernatant was removed. The cells were washed as above with 0·2 ml SH buffer, suspended in 20 µl 2xSH buffer and cooled on ice. A 20 µl aliquot of cell suspension was transferred to a cuvette of 0·1 cm path length (Bio-Rad), and necessary DNA solutions and sterile water was added to a final liquid volume of 40 µl. The cuvette was capped and cooled on ice before electroporation at 900 V, 129 , 50 µF, using an Electro Cell Manipulator (model 600M; BTX). Immediately after electroporation, 1·0 ml BG-11 medium was added into the cuvette, and the cells were suspended with a pipette, transferred into a sterile centrifuge tube and kept for 10 min on ice. The cells were then collected by centrifugation at 13000 g for 1 min at 4 °C, and the supernatant was discarded. The cells were again washed with 1·0 ml of BG-11 medium, resuspended in 1·0 ml BG-11 medium and transferred into an empty sterile glass test tube with a cotton plug. The tube was shaken on a reciprocal shaker at 100 r.p.m. in an illuminated incubator at 28 °C overnight. Finally, the cells were spread onto BG-11 agar plates and incubated at 28 °C under light for up to 2 weeks.
Curing of plasmids.
For curing of plasmids from cyanobacterial transformants, cells were cultivated photoautotrophically in BG-11 medium in the absence of the antibiotic to which the resistance had been conferred by the plasmid. When the OD730 of the culture exceeded 1·0, a portion of the culture was transferred into a tube containing fresh BG-11 medium, and the cultivation was repeated until cells had been propagated for 32 generations. The culture was then diluted and spread on BG-11 medium. The colonies formed were then replicated with nylon membrane (Hybond N+; Amersham Pharmacia) onto BG-11 medium containing appropriate antibiotics. Cured strains that no longer grew in the presence of antibiotics made up 1520% of the population after 32 generations.
Fluorescence microscopic observation.
Cellular fluorescence was observed with a fluorescence microscope (Olympus OPTICAL model BX50 microscope; BX-FLA reflected light illuminator equipped with a mercury burner). Excitation was done at 360370 nm, while 510550 nm emission was observed through an absorption filter.
Southern blot analysis.
Five to ten micrograms of chromosomal DNA were digested with restriction enzymes, electrophoresed on agarose gel and transferred onto a nylon membrane (Hybond N+) by vacuum suction (VacuGene XL; Amersham Pharmacia). DNA probes were prepared by labelling with digoxigenin using a PCR Dig Labeling Mix (Roche Diagnostics). Hybridization of the membrane with a probe was carried out in a buffer containing 5x SSC (75 mM sodium citrate, pH 7·0, and 0·75 M NaCl) at 6265 °C overnight. The hybridized membrane was treated with anti-digoxigeninalkaline phosphatase Fab fragments (Roche Diagnostics) and luminescent substrate (Lumi-Phos 530; Wako Pure Chemical Industries) as recommended by the manufacturer, and exposed to X-ray film (XAR; Kodak).
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RESULTS |
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Within the regions sequenced, the only difference between the wild-type and the mutant rps12 genes is a single base transition from A to G at position 128 of the ORF. The point mutation occurred at the second position of the 43rd codon, resulting in a replacement of a lysine (AAA) with an arginine (AGA) codon. Accordingly, the mutant allele was designated rps12-R43. We verified that the mutation in the rps12-R43 gene is the sole change determining the Strr phenotype of the mutant by transforming Synechococcus sp. PCC 7942 R2-SPc to streptomycin resistance with a PCR-generated 375 bp DNA fragment of the rps12-R43 ORF. An Strr transformant was obtained and was found by sequencing of its rps12 gene to have the same point mutation as the rps12-R43 allele. This strain was named GRPS1, and it was used as the standard rps12-R43 mutant. Using an rps12 probe, a single band was detected in genomic Southern hybridization with several restriction digests, indicating a single-copy rps12 gene (data not shown).
Merodiploid analysis for the recessiveness of rps12-R43 allele
We tested the dominance/recessiveness of the rps12-R43 allele by constructing merodiploid strains in which a wild-type rps12 gene was inserted into a non-essential psbAI locus in the rps12-R43 background. For this purpose, pEXE1, carrying the psbAI 5' and 3' flanking sequences with a precise deletion of the D1 protein coding sequence, was used to clone the wild-type rps12 gene with its own promoter or the rps12 ORF fragment followed by the kan gene, generating the gene disruption plasmids pEXR11, pEXR12 and pEXR21 (Table 1). These plasmids were linearized by BamHI digestion prior to transformation of strain GRPS1 to facilitate two-point homologous recombination (see Fig. 2a
) rather than a single-point insertion of the whole plasmid into the psbAI locus.
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At first, we employed plasmids unable to replicate in cyanobacteria as template DNAs to replace the psbAI gene with foreign sequences. One of the template plasmids, pEXGFP, was used to precisely replace the psbAI ORF with the gfp ORF encoding a green fluorescent protein (GFPuv), whereas pEXE1 bearing the psbAIORF gene was employed to introduce a precise deletion of the psbAI ORF. Two Strs merodiploid strains, GRPS11 and GRPS21 (Tables 1
and 3
), were selected and electroporated with pEXGFP or pEXE1. The results of four independent experiments showed that the frequencies of Strr Kms recombinants were low, reaching a maximum of only 3/96 using 1 µg intact plasmid (Table 4
, last column). No Strr Kms recombinant was detected among 96 Strr colonies using 2 µg linearized plasmid.
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Functional expression of the gfp ORF integrated at the psbAI locus
To investigate whether or not the gene replacement at the psbAI locus led to expression of the gfp ORF under the control of the constitutive psbAI promoter, we analysed GFPuv protein in cyanobacterial cells under a fluorescence microscope. GFPuv absorbs ultraviolet light at 360400 nm, and emits green fluorescence with a maximum at 509 nm (Crameri et al., 1996 ). Since cyanobacterial chlorophylls also absorb ultraviolet light, and emit red fluorescence with a maximum at 668 nm, only emission in the range 510550 nm was visualized through an absorption filter. Moreover, the intracellularly emitted light might have been quenched by various absorbing pigment molecules. Nonetheless, the above cyanobacterial recombinants with a psbAI::gfpORF genotype, as well as a control strain GLC1 (Table 1
) with a psbAI::gfpORF-nak genotype did emit the dim fluorescence which was absent in the parental GRPS1 strain (data not shown). We also detected the expression of green fluorescent protein by Western blotting of cell-free extracts from the recombinant cyanobacterial strains (data not shown). These data clearly demonstrated that the gfp ORF inserted at the psbAI locus is intact and functional after gene replacement.
Transformation of rps12 merodiploids with replicating template plasmids
The frequency at which gene replacement products are established from rps12 merodiploids depends upon the availability of template DNA within the cyanobacterial cells. When a template plasmid replicates after incorporation into a cell to supply multiple copies of templates, then the probability of homologous recombination between the plasmid DNA and the chromosomal DNA should be elevated as compared with a non-replicating template plasmid which is diluted out during cell propagation. To test the above hypothesis, a pUC303-derived plasmid, pUC3032 (Table 1), carrying the psbAI
ORF gene and cyanobacterial replication machinery was constructed. pUC3032 is devoid of the plasmid-borne Smr gene but carries the Cmr gene and repAB genes necessary for autonomous replication in PCC 7942 or its cognate strains lacking endogenous pUH24 (van der Plas et al., 1992
). This plasmid was used to introduce a deletion of the psbAI gene ORF by gene replacement in the rps12 merodiploid strains.
As shown in the last row of Table 4, transformation of strains GRPS11 and GRPS21 using pUC3032 resulted in three and sixteen recombinants exhibiting the Cmr Strr Kms phenotype from GRPS11 and GRPS21, respectively, among 100 Strr clones tested. These recombinants were homogenotes as judged from their inability to grow on BG-11 medium containing kanamycin. The apparent frequencies of Kms recombinants among Strr clones (3 and 16%) using a replicating plasmid were improved in comparison with those (less than 3%) using non-replicating plasmids.
Three clones of each Cmr Strr Kms recombinant from GRPS11 and GRPS21 were cured for their pUC3032 (see Methods), and one chloramphenicol-sensitive (Cms) strain was recovered from each clone. When these Cms Strr Kms recombinant strains were analysed by PCR using the same primers as in Fig. 3, DNA fragments of an expected size (0·6 kb) were amplified (data not shown). Southern hybridization of ScaI-digested chromosomal DNA from the above six cured strains using a probe specific for the psbAI 5' and 3' non-coding sequences detected the same 2·6 kb bands corresponding to a 1·08 kb deletion of the psbAI gene ORF, as compared with a 3·7 kb band in GRPS1 and 4·4/4·2 kb bands in strains GRPS11 and GRPS21, depending on the insertions (rps12-nak or rps12ORF-kan) which they carry at the psbAI locus (Fig. 5
). This result provides direct evidence that the psbAI
ORF gene is transferred from a replicating plasmid to the chromosomal psbAI locus with a concomitant loss of rps12 and kan genes at the same locus.
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DISCUSSION |
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The dominant nature of the wild-type rps12 gene over the rps12-R43 allele was demonstrated unambiguously by the Strs phenotype of merodiploid strains bearing the rps12-R43 allele and the rps12 gene inserted at the psbAI locus. The difference in the ability of promoters to express the ectopic rps12 gene, i.e. the natural rps12 promoter or the psbAI promoter, did not influence the apparent Strs phenotype of the merodiploids, although the psbAI promoter seemed stronger than the rps12 promoter. However, rps12 gene and rps12 ORF sequences have different tendencies to suffer gene conversion. Thus, the spontaneous segregation rate of Strr progeny was about seven times higher in the GRPS11 merodiploid carrying the rps12 gene than in the GRPS21 merodiploid carrying the rps12 ORF (see Table 4, fifth column). Although its basis is not known exactly, this difference in gene conversion frequencies might arise from a site-specific recombination at a highly iterated palindromic sequence (HIP1), 5'-GCGATCGC-3', which has been found in many cyanobacteria (Robinson et al., 1995
, 1997
; Akiyama et al., 1998
) and is present once in the promoter region of the 579 bp rps12 gene but absent from the 375 bp rps12 ORF. We therefore postulate that rps12 merodiploids would be a good experimental system to study mechanistic details of intrachromosomal gene conversion in cyanobacteria.
The present study established a novel technique utilizing a dominant Strs rps12 gene to replace any non-essential chromosomal sequences in cyanobacteria with desired insertions, substitutions or deletions, yet generating the final mutants free from foreign drug resistance markers. Essentially, this method consists of an elimination of the chromosomally integrated rps12 gene via homologous recombination with externally added template DNA. A similar strategy was employed previously to select plasmid-to-chromosome gene replacement in E. coli recD rpsL (str) mutants (Russell & Dahlquist, 1989 ). In E. coli, however, a strong exonucleolytic activity conferred by the recBCD gene product makes linear DNA fragments impractical for use as template DNA, and, therefore, it is still mandatory to use a recBCD-deficient mutant for efficient gene replacement (Murphy, 1998
). Although cyanobacteria do not seem to degrade linear DNA so extensively, linearized template DNAs were much less effective than circular DNAs for gene replacement. Taking it for granted that recA-mediated homologous recombination requires sufficient length of sequences flanking the sequence to be integrated, we employed template plasmids carrying the psbAI 5' and 3' non-coding sequences extending to more than 500 bp. Whether or not a specific sequence such as HIP1 is required for high frequency of recombination is not known, although both psbAI 5' and 3' flanking sequences used here contain at least one HIP1 site (unpublished results).
Compared with the haploid genome of E. coli, the polyploid nature of the cyanobacterial genome poses an additional difficulty in isolating homogenote recombinants. Available data indicate that the mean copy number of chromosomes per cell in Synechococcus spp. PCC 6301 and PCC 7942 is four to six, depending on growth rate and temperature (Binder & Chisholm, 1990 ). Accordingly, several rounds of successive replacements at psbAI loci in a polyploid genome should be necessary to establish homogenote recombinants. Considering the transient maintenance of non-replicating plasmids after incorporation into the cell, it is somewhat surprising that gene replacement was achieved at a frequency up to 3% of the Strr progeny using a circular form of a non-replicating plasmid. This frequency corresponds to about 3x10-6 per cell, a value not impractical to screen for recombinants among 108 cells.
When the template plasmids replicate, gene replacement was induced via three steps: first, transformation with the Cmr plasmid; second, induction of recombination to give Strr Kms progeny; and finally, curing of the plasmid. This procedure has an advantage in the availability of multiple copies of template plasmids in all transformant cells, resulting in an increased frequency of gene replacement of up to 16% among survivors. Although the curing of the plasmid is an added labour, most of the shuttle vector plasmids currently available in cyanobacteria are unstable and therefore could be removed relatively easily.
The ease with which gene replacements were screened is an urgent requirement for routine work with mutant constructions. So far, a conditional lethal sacB gene encoding levansucrase can cause death of host cells of Gram-negative bacteria on sucrose-containing media (Gay et al., 1985 ), and has been utilized as a tool for construction of gene replacement mutants in a plant pathogen, Erwinia chrysanthemi (Ried & Collmer, 1987
), and a filamentous cyanobacterium, Anabaena sp. PCC 7120 (Cai & Wolk, 1990
). The sacB gene, however, suffers inactivation through spontaneous mutations, leading to false recombinants. In the rps12-mediated gene replacement, segregation of false Strr recombinants from the rps12/rps12-R43 merodiploids by gene conversion is unavoidable when using the 100% homologous rps12 gene in the recA+ background. However, we expect to suppress the gene conversion frequency in merodiploids by using an rps12 gene homologue such as the E. coli rpsL gene or by using a mutant strain deficient in an as yet unidentified gene conversion system. There is a tenable experimental basis for the heterologous expression of S12 proteins in different hosts (Liu et al., 1989
). We are at present exploring the feasibility of employing heterologous rps12 genes to obtain cyanobacterial merodiploids with a stable Strs phenotype.
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ACKNOWLEDGEMENTS |
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Received 13 November 2000;
revised 20 March 2001;
accepted 4 April 2001.