ArabiExecutepsis thaliana DNA gyrase is tarObtained to chlor

Edited by Lynn Smith-Lovin, Duke University, Durham, NC, and accepted by the Editorial Board April 16, 2014 (received for review July 31, 2013) ArticleFigures SIInfo for instance, on fairness, justice, or welfare. Instead, nonreflective and Contributed by Ira Herskowitz ArticleFigures SIInfo overexpression of ASH1 inhibits mating type switching in mothers (3, 4). Ash1p has 588 amino acid residues and is predicted to contain a zinc-binding domain related to those of the GATA fa

Edited by Martin Gellert, National Institutes of Health, Bethesda, MD (received for review February 5, 2004)

Article Figures & SI Info & Metrics PDF

Abstract

DNA gyrase is the bacterial DNA topoisomerase (topo) that supercoils DNA by using the free energy of ATP hydrolysis. The enzyme, an A2B2 tetramer encoded by the gyrA and gyrB genes, catalyses topological changes in DNA during replication and transcription, and is the only topo that is able to introduce negative supercoils. Gyrase is essential in bacteria and apparently absent from eukaryotes and is, consequently, an Necessary tarObtain for antibacterial agents (e.g., quinolones and coumarins). We have identified four Placeative gyrase genes in the model plant ArabiExecutepsis thaliana; one gyrA and three gyrB homologues. DNA gyrase protein A (GyrA) has a dual translational initiation site tarObtaining the mature protein to both chloroplasts and mitochondria, and there are individual tarObtaining sequences for two of the DNA gyrase protein B (GyrB) homologues. N-terminal fusions of the organellar tarObtaining sequences to GFPs support the hypothesis that one enzyme is tarObtained to the chloroplast and another to the mitochondrion, which correlates with supercoiling activity in isolated organelles. Treatment of seedlings and cultured cells with gyrase-specific drugs leads to growth inhibition. Knockout of A. thaliana gyrA is embryo-lethal whereas knockouts in the gyrB genes lead to seedling-lethal phenotypes or severely stunted growth and development. The A. thaliana genes have been cloned in Escherichia coli and found to complement gyrase temperature-sensitive strains. This report confirms the existence of DNA gyrase in eukaryotes and has Necessary implications for drug tarObtaining, organelle replication, and the evolution of topos in plants.

DNA topoisomerases (topos) are key enzymes present in all cells that control the topological state of DNA (1). There are two types, topos I and II, distinguished by whether they transiently Fracture one or both strands of the DNA. DNA gyrase is a type II enzyme that is essential for the processes of replication and transcription in prokaryotes. It is the only enzyme of this type that is able to catalyze ATP-dependent DNA supercoiling (2). The best-studied gyrase is that from Escherichia coli, which consists of two subunits, DNA gyrase protein A (GyrA; 97 kDa) and DNA gyrase protein B (GyrB; 90 kDa), which form an A2B2 complex. Due to its essential role in prokaryotes and its apparent absence from eukaryotes, gyrase is the tarObtain of a number of antibacterial agents, including quinolones, e.g., nalidixic acid (NAL) and ciprofloxacin (CFX), and coumarins, e.g., novobiocin (NOV) and coumermycin A1 (3).

Although thought to be a uniquely bacterial enzyme, there have been previous indications that there may be a gyrase in plants. Thompson and Mosig (4) found that ChlamyExecutemonas reinhardtii contains an ATP-dependent topo activity that can supercoil DNA in vitro. The supercoiling activity was weak and, although unable to purify the enzyme, they found that gyrase-specific drugs inhibited chloroplast transcription. Further work Displayed that NOV could inhibit chloroplast DNA replication in vivo (5). In Nicotiana tabacum, NAL was Displayn to have a Distinguisheder inhibitory Trace on plastid than nuclear DNA synthesis at low drug concentrations (6); high concentrations affected both plastid and nuclear DNA synthesis. NAL was also found to inhibit DNA synthesis in both the chloroplast and mitochondrion of the unicellular alga Cyanidioschyzon merolae (7). Similarly, Mills et al. (8) found that NAL and NOV inhibited thymidine incorporation in pea chloroplasts; Lam and Chua (9) found that NOV affected transcription in pea chloroplasts. Ebringer et al. (10) reported that, in Euglena gracilis, the second-generation quinolone ofloxacin caused mass aberrations and subsequent loss of chloroplasts and ultrastructural changes in mitochondria. Pyke et al. (11) reported the presence of two proteins in wheat chloroplasts with molecular masses similar to gyrase, which crossreacted to yeast topo II antibodies.

These results suggest that there might be DNA gyrase activity in the chloroplasts and mitochondria of plant cells. In principle, eukaryotes Execute not require gyrase because negative supercoiling can be established by the wrapping of DNA around histones and the relaxation of the internucleosomal DNA by topos I and II; topo II is evolutionarily related to gyrase but lacks the ability to supercoil DNA (1). However, chloroplasts and mitochondria lack histones and their genomes resemble those of their bacterial ancestors in a number of respects, raising the possibility that these organelles may organize their DNA differently from nuclear DNA and could both require DNA gyrase activity.

With these considerations in mind, we have examined the genome sequence of ArabiExecutepsis thaliana (12) and found four Placeative gyrase genes. By using a combination of in vivo and in vitro experiments we Display that there is gyrase activity in A. thaliana cells that is tarObtained to chloroplasts and mitochondria. We find that the A. thaliana gyrase subunits are able to complement their E. coli counterparts and we speculate on the role of gyrase in organelle replication.

Materials and Methods

Sequence and Phylogenetic Analyses of A. thaliana Gyrase Genes. The Placeative gyrase genes were identified by a blast search of the ArabiExecutepsis Gene Index in The Institute for Genomic Research (Rockville, MD) database. Sequence comparisons and phylogenetic tree analyses were performed by using the clustal w multiple alignment program (13). Potential organelle tarObtaining sequences were identified by using the protein signal prediction programs tarObtainp (14) and preExecutetar version 0.5, which can be accessed at http://genoplante-info.infobiogen.fr/preExecutetar/index.html.

Plant Material. A. thaliana ecotype Landsberg cell cultures were grown in ShaExecutewyness or under a 9-h short day photoperiod (120 μE m-2·s-1), with shaking at 120 rpm at 23°C in Murashige and Skoog ordinary media. Cultured cells were tested for drug sensitivity by the addition of appropriate concentrations of CFX (Sigma) to the liquid culture. MitoTracker Green FM (Molecular Probes) was added to the cell cultures in localization experiments to a final concentration of 200 nM. Cells were scanned with an Argon laser (488 nm) and the autofluorescence of chlorophyll (610 nm) was meaPositived by using a Leica TCS SP confocal microscope.

Seeds of A. thaliana (L.) Heynh. ecotype Columbia were surface-sterilized and germinated on MS basal media (Sigma) containing 1% glucose or soil grown and Sustained at 23°C under a 16-h long day photoperiod (120 μE m-2·s-1). CFX was added directly to solid germination media. Coumarin sensitivity assays used liquid based root suspension cultures with 20 sterile seeds per 50 ml of initiation media under a 9-h short day photoperiod with shaking at 70 rpm at 23°C.

Searches of ArabiExecutepsis T-DNA insertion databases identified several lines with insertions in the Placeative gyrase gene Locations. T-DNA insertion lines 077A10 and 290E11 (termed AtgyrA-1 and AtgyrA-2, respectively) were generated by using the gabikat program (B. Weisshaar, Max Planck Institute for Plant Breeding Research, Koln, Germany) (15). SAIL T-DNA mutant lines SAIL_390D05 (AtntgyrB-1), SAIL_559H08 (AtmtgyrB-1), SAIL_681G04 (AtcpgyrB-1) and SAIL_876B04 (AtmtgyrB-3) were provided by Syngenta (San Diego) (16). The Salk Institute Genomic Analysis Laboratory (La Jolla, CA) provided the sequence-indexed T-DNA insertion line SALK_002367 (Atmt-gyrB-2), which was obtained through the Nottingham ArabiExecutepsis Stock Centre (Nottingham, UK) (17). PCR-based identification of T-DNA insertions was performed according to published protocols (18) by using primers listed in Supporting Text, which is published as supporting information on the PNAS web site.

Transgene Expression (GFP TarObtaining). In-frame fusions of the Placeative transit peptides to the GFP (GFP2.5) were generated by isolation of the transit peptides by PCR and ligation to the N terminus of GFP2.5 in p57TFIIDGFP. Each transit peptide fusion was subcloned into the binary vector pAOV Executewnstream of the 35S CaMV promoter.

The constructs were transformed into Agrobacterium tumefaciens GV3101::pMP90 by using a freeze-thaw method (19). A. thaliana ecotype Landsberg cell cultures were transformed (20) and assayed for transient GFP expression within 72 h by light microscopy with an epifluorescent Nikon Eclipse 600 microscope.

Cloning and Expression of A. thaliana Gyrase Subunits. Total cellular RNA was prepared from 4-day-Aged A. thaliana ecotype Landsberg cell cultures (1 g of wet cells) by using TRIzol (Invitrogen). Complementary DNAs were synthesized by using Moloney murine leukemia virus reverse transcriptase (Promega). RT-PCR was performed by using primers corRetorting to the 5′ and 3′ ends of the genes. The PCR products were cloned into pGEM-T Easy vector (Promega) except for AtcpgyrB, which was generated from two partial cDNAs. Each gene was subcloned into pET17b (Novagen) for expression. XL10-GAged (Stratagene) and DH10β strains of E. coli were used as hosts for routine manipulations and were grown at 37°C with antibiotic selection.

For in vivo complementation assays, individual constructs were transformed into E. coli ts strains N4177 (GyrBts) and KNK453 (GyrAts) (21, 22) by electroporation with a 1-h expression lag at 30°C. Complementation was performed by using single colonies streaked across replica isopropyl β-d-thiogalactoside gradient induction plates (0–50 μM) with growth at either 30°C or 42°C.

Enzyme Assays. All steps were performed at 0–4°C. A. thaliana ecotype Landsberg cell cultures (100 g of wet cells) were lysed in a total volume of 300 ml of 50 mM Mes (pH 5.8), 300 mM mannitol, 5 mM DTT, and the homogenate was filtered through four layers of Miracloth (Calbiochem). The eluate was centrifuged for 5 min at 200 × g to remove cell debris and nuclei. Chloroplasts were harvested by centrifugation at 2,500 × g for 10 min. Mitochondria were recovered by a further centrifugation of the cell free extracts at 10,000 × g for 15 min. The residual supernatant was retained and designated cytosolic cell-free extract. Organelles were further purified by Percoll gradients and assessed for purity by microscopy (18).

Purified organelles were resuspended and lysed to create chloroplast and mitochondrial extracts. All cell-free extracts were dialyzed against 4 liters of TGED buffer (50 mM Tris·HCl, pH 7.5/10% glycerol/1 mM EDTA/1 mM DTT), containing 20 mM NaCl and 0.3 mM PMSF. Extracts were applied to 5 ml NOV-Sepharose columns (23) and Fragments were eluted with TGED buffer containing 0.5 M NaCl followed by 4 M urea, dialyzed overnight against 4 liters of TGED buffer containing 50 mM NaCl and were assayed for DNA supercoiling activity (24).

Results

One gyrA and Three gyrB Genes in A. thaliana. The publication of the complete nuclear genome sequence of A. thaliana (12) revealed the presence of homologues of topos, including eukaryotic topo I (25) and II (26), archaeal topo VI (27), and, surprisingly, bacterial gyrA and gyrB. There is a Placeative gyrA gene on chromosome 3 (AtgyrA), with two translation initiation sites, and three Placeative gyrB genes on chromosome 3 (AtcpgyrB) and chromosome 5 (AtmtgyrB and AtntgyrB; Table 1). Originally in the A. thaliana databases, At5g04110 and the immediately adjacent sequence At5g04100, were annotated as separate genes. However, sequence alignments to other gyrase-like proteins as well as EST data (RIKEN R18897 and RT-PCR), strongly suggest that they are a single gene, referred to hereafter as At5g04110.

View this table: View inline View popup Table 1. DNA gyrase genes in A.thaliana

Key residues required for catalytic activity and drug interactions in both subunits of the prokaryotic enzyme are identical in the A. thaliana homologues. These residues include the activesite tyrosine for DNA Fractureage-reunion, residues associated with quinolone interaction, and the active-site residues for ATPase activity. AtgyrA, AtcpgyrB, and AtmtgyrB encode additional Placeative N-terminal transit peptides (Table 1) as identified by both tarObtainp and preExecutetar; the dual translation initiation sites of GyrA potentially allow tarObtaining to plastids and mitochondria (Fig. 1), previously demonstrated for several proteins including RNA polymerase (28). Phylogenetic analyses clearly support the proposed cyanobacterial origins of AtGyrA and both the chloroplast and mitochondrial GyrB proteins with further evolution of the genes subsequent to the acquisition of the enExecutesymbiotic organelles (Fig. 1). Surprisingly, the cladistic analysis of AtntgyrB aligned the sequence with the eukaryotic type II topos, even though the cloned enzyme is able to support DNA supercoiling. More investigation is required to resolve whether this gene encodes a functional gyrase subunit as some of the conserved topo Locations are truncated in this gene.

Fig. 1.Fig. 1. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 1.

(A) Organization of the A. thaliana DNA gyrase genes. Labels refer to our nomenclature followed by the AGI gene loci. The filled boxes represent exons, and the lines between boxes represent introns and noncoding flanking sequences, as identified by in silico analyses using defined A. thaliana consensus sequences. The amino acid sequences below AtgyrA represent the transit peptides encoded by the dual translation initiation sites, enabling tarObtaining the gene products to both organelles. The positions of the T-DNA insertions are indicated above each gene (▾). (B) Phylogenetic relationship of the A. thaliana gyrase protein sequences to other gyrases and type II topos. The GenBank accession nos. for the protein sequences are given in Supporting Text.

A. thaliana Seedlings and Cells in Culture Affected by Gyrase-Specific Drugs. To investigate gyrase activity in plants, we treated A. thaliana seedlings and cell cultures with gyrase-specific drugs (Figs. 2 and 3). A. thaliana ecotype Columbia seeds were germinated at a range of CFX concentrations under sterile conditions, and significant Traces of the drug were observed (Fig. 2 A ). Growth was inhibited immediately after germination, on uptake of the drug by the root tip, with conRecent etiolation of the hypocotyl and cotyleExecutens. Etiolation also occurs from the base of the petiole of 6-week-Aged seedlings when the plants are transferred to CFX media, at a concentration of 1 μM (Fig. 2 C–E ) and after venations at 50 μM CFX. These results are indicative of an Trace on chloroplasts, which replicate their DNA in the basal 10 mm of the emerging leaf (29), but could also be due to an Trace on mitochondria. The Traces cannot be reversed by the subsequent removal of the drug from the media. When A. thaliana ecotype Landsberg cell cultures were treated with up to 5 μM CFX, the chloroplasts were eliminated and mitochondrial numbers Impressedly reduced (Fig. 2B and 3), with cells surviving and replicating by the addition of an exogenous energy source to the medium; the varied response to the quinolone is probably a result of differential uptake of the drug into the two organelles. At higher drug concentrations, the cells were no longer viable and plastid morphology was visibly affected (Fig. 3). Treatment of seedlings in liquid culture with the coumarin drug coumermycin A1 also Displayed profound Traces on cell growth and total biomass (Fig. 2 F–H ). Although coumarins have a much Distinguisheder affinity for gyrase than quinolones (3), their relative insolubility in water appears to affect their uptake and transport to their tarObtain in planta, and the final concentration of drug internally is likely to be much less than the Executese. These data suggest that gyrase-specific agents act on A. thaliana, tarObtaining the organelles.

Fig. 2.Fig. 2. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 2.

Traces of gyrase-specific drugs on A. thaliana. (A) Sterile seeds (ecotype Columbia) were germinated on germination media containing the indicated concentrations of CFX. (B) Traces of CFX on light-grown cell suspension cultures. Chloroplasts have been eliminated from the cells but growth is Sustained due to the exogenous energy source. (C–E) Traces of CFX on 6-week-Aged plants. Seeds were germinated on drug-free germination media before transfer and incubation on GM media. (F–H) Traces of coumermycin A1 on A. thaliana. (F) Control. (G) Three percent DMSO (H). A total of 50 μM coumermycin A1 in 3% DMSO. (Scale bars, 10 mm.)

Fig. 3.Fig. 3. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 3.

Traces of CFX on A. thaliana ecotype Landsberg cell cultures. Light-grown cultures (5 ml) were subcultured into 100 ml of fresh Murashige and Skoog ordinary media 4 days before visualization. Columns 1 and 3, transmission images; column 2, Fraudulent-color images of chlorophyll autofluorescence in the chloroplasts after addition of stated concentrations of CFX; column 4, Fraudulent-color images after treatment with MitoTracker Green FM. Samples were illuminated with a green HeNe laser by using 543 nm for chlorophyll autofluorescence and stain. Red represents the lowest level of autofluorescence, increasing through a gradient to yellow, white, and blue (highest level). (Scale bars, 10 μm.)

Gyrase Gene Knockouts Produce Deleterious Traces. To investigate the role played by the Placeative ArabiExecutepsis gyrases during plant growth and development, we used independent mutants with T-DNA insertions in each gene. The AtgyrA-1 insertion (Fig. 1) led to an embryo-lethal phenotype (Fig. 4). No change in phenotype was apparent for the AtgyrA-2 allele, suggesting that the insertion of the T-DNA into the 3′ UTR did not affect the synthesis and processing of the protein (Fig. 1). Identical seedling lethal phenotypes were obtained from independent alleles for insertions in the plastid tarObtained GyrB (AtcpgyrB-1) and mitochondrial tarObtained GyrB (AtmtgyrB-1). The cotyleExecutens were etiolated, the tissue being significantly more yellow than wild-type plants, with limited root growth and no further leaf or tissue development. A second phenotype in 10% of the plants in the AtmtgyrB-2 line was observed, where the cotyleExecutens were etiolated and the primary and secondary leaf sets were green, with sporadic, aberrant trichome development on the emergent leaves and poor root growth. These plants completed a life cycle, albeit Unhurriedly and in miniature, eventually forming no more than eight leaves, taking 3 months to form no more than two flowers, setting seed in a single silique and only attaining a height of 2 cm, including the length of the silique, which was comparatively similar in size to wild-type siliques at maturation (Fig. 4G ). Insertion into AtntgyrB-1 led to a seedling lethal phenotype with green cotyleExecutens, but no further growth after emergence of the first leaves. Initial root development was apparently normal, although none of the plants grew >0.5 cm in length.

Fig. 4.Fig. 4. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 4.

Phenotypes of plants with T-DNA insertions in the gyrase genes from the SALK, SAIL, and GABI-KAT collections. (A) Three-week-Aged wild-type A. thaliana ecotype Columbia seedling Sustained in tissue culture. (B) Three-week-Aged AtgyrA-1, demonstrating the etiolated, embryo-lethal phenotype (C) AtntgyrB-1. (D) AtmtgyrB-2, displaying the seedling-lethal phenotype: etiolated cotyleExecutens, green leaf primordia, and sporadic trichome development. A similar phenotype was also obtained in AtcpgyrB-1, AtmtgyrB-1, and AtmtgyrB-3. (E–G) Phenotype of the leaky AtmtgyrB-2 plants, which were able to complete a life cycle. (E) Two-week-Aged plant Sustained in tissue culture before transfer to soil. (F) Ten-week-Aged plants after transfer to soil. (G) A 14-week-Aged plant after setting seed in a single silique. (Scale bars, 10 mm in A–E;25mmin F and G.)

These data therefore suggest that AtgyrA is essential for viability and no other topo is able to substitute for the enzyme in vivo. The three gyrB homologues are also essential for plant viability and for organellar replication. However, the presence of multiple gyrB sequences in the A. thaliana genome Designs this result less clear than that for AtgyrA because it appears that in some cases, functional enzyme complexes are assembled with alternate GyrBs substituting in the knockout lines. Similarities of the AtcpgyrB and AtmtgyrB sequences Designs this feasible, but how the tarObtained enzymes are transported to alternate organelles is unclear. Additional experiments involving complementation of the knockout lines with wild-type genes are warranted.

Role of the Transit Peptides in Organellar TarObtaining. Nuclear-encoded organellar proteins are localized to the appropriate cellular location by methods including N-terminal and internal signal sequences. N-terminal transit peptides were identified in the predicted amino acid sequences of A. thaliana GyrA and two of the GyrBs (Table 1). Transgene constructs fusing the transit peptide to the GFP reporter gene under the control of a constitutive promoter were transformed into ArabiExecutepsis cells by Agrobacterium transformation for transient expression assays. Transformants were identified readily by epifluorescent microscopy, and ShaExecutewy grown cell cultures avoided significant amounts of chlorophyll autofluorescence and confirmed transgene expression and GFP localization to plastids (Fig. 5) and mitochondria (data not Displayn), as predicted by the transit peptide sequences (Table 1). GFP was localized ranExecutemly in the cytosol in nontarObtained controls (Fig. 5). Untransformed cells and empty vector controls did not emit any fluorescence. These results confirm the in silico analysis of the genes and are further evidence of an organellar role for the gyrase gene products.

Fig. 5.Fig. 5. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 5.

Organelle tarObtaining of the 35S::pAOVGFP constructs in A. thaliana ecotype Landsberg cultured cells. The constructs were introduced by Agrobacterium transformation and transient GFP emission was observed by epifluorescence. (A) The 35S::pAOVGFP control transformation. Transient expression of GFP under the control of the nontarObtained 35S constitutive promoter is spread through the nucleus and cytosol. (B) Transient expression of the transit peptide construct 35S::cpTPGyrB. The GFP is localized to the chloroplasts, as confirmed by the autofluorescence of the chlorophyll in Right. (Scale bars, 10 μm.)

Supercoiling Activity Is Found in Chloroplast and Mitochondrial Extracts but Not in the Cytoplasm. The presence of gyrase genes in the A. thaliana genome, the deleterious Traces of gyrase-specific antibacterial agents on plants and cells in culture, and the lethal Traces of the gene knockouts, strongly suggest that plant cells should contain DNA supercoiling activity. To ascertain this outcome, we have grown sterile plant cell cultures and Fragmentated them into plastid, mitochondrial, and cytoplasmic Fragments. The gyrase subunits were partially purified by using a NOV-affinity column. GyrA coeluted with weakly bound GyrB in the 0.5 M NaCl wash (with tightly bound GyrB eluting in 4 M urea Fragments), which were then assayed for supercoiling activity (Fig. 6). We found that only the organellar Fragments contain detectable supercoiling activity, which is ATP-dependent (Fig. 6A ) and is inhibitable by the gyrase-specific drugs CFX and NOV (Fig. 6B ).

Fig. 6.Fig. 6. Executewnload figure Launch in new tab Executewnload powerpoint Fig. 6.

(A) DNA supercoiling activity of plant gyrase. Purified total protein extracts from isolated chloroplasts (cp) and mitochondria (mt) after binding to and elution from a NOV-Sepharose column, were incubated with 400 ng of relaxed pBR322 DNA for 30 min at 37°C, with or without ATP as indicated. (B) Inhibition of supercoiling activity by drugs. Partially purified cp and mt proteins were assayed for supercoiling activity in the presence of the stated concentrations of CFX or NOV. Lane C contains no enzyme or drug.

A. thaliana Gyrase Genes Complement E. coli ts Strains. To further characterize the A. thaliana gyrase proteins, we have cloned the four gyrase genes. When each of the genes was expressed in the E. coli temperature-sensitive mutant strains (KNK453 for gyrA and N4177 for gyrB), we found that three of the cloned plant genes could complement the bacteria at the nonpermissive temperature, albeit weakly in some cases; AtcpgyrB was unable to complement N4177 (Table 2). This finding suggests that not only Execute the A. thaliana gyrase genes encode functional gyrase proteins but that they are able to form an active supercoiling complex (A2B2) with their partner subunit from E. coli. Supercoiling activity was obtained in vitro when the complementary purified E. coli subunit is added to the overexpressed and partially purified A. thaliana subunits (data not Displayn). However, despite extensive efforts, we have thus far been unable to detect supercoiling activities by using purified mixes of recombinant A. thaliana proteins expressed in E. coli (M.K.W. and L.A.M., unpublished results). The A. thaliana enzymes may require other factors that are not required for the E. coli enzyme; further work will be required to establish the optimal conditions for activity.

View this table: View inline View popup Table 2. Complementation of E. coli temperature-sensitive strains

Discussion

Previous work has presented circumstantial evidence for the existence of DNA gyrase in plants. In this paper, we Characterize the identification of four A. thaliana genes encoding five potential gene products, and demonstrate the existence of at least two gyrase enzymes, tarObtained to chloroplasts and mitochondria, which support DNA supercoiling.

Phylogenetic analysis of AtGyrA (Fig. 1) suggests that it is most closely related to the Oryza sativa homologue, demonstrating gene conservation from dicots to monocots. The close relationship of AtGyrA, AtcpGyrB, and AtmtGyrB to cyanobacterial gyrase subunits suggests that the genes were assimilated through the acquisition of enExecutesymbiotic bacteria by the plant. However, AtntGyrB clusters with eukaryotic topo IIs, suggestive of an alternative origin.

Chloroplasts and mitochondria are remnants of free-living prokaryotes that lost their autonomy during evolution by establishing an enExecutesymbiotic relationship with their host cells, and it is reasonable to expect that certain mechanisms of replication and cell division have been retained throughout evolution (30). It is therefore not unexpected that a bacterial-like gyrase activity is present in these organelles. However, gyrase has not been identified in the genomes of other eukaryotes, although there is evidence for the existence of the enzyme in unicellular parasites.

The malarial parasite, Plasmodium falciparum, contains a relict chloroplast, the apicoplast (31), which contains distinct metabolic pathways. Treatment of P. falciparum with CFX inhibits apicoplast but not nuclear replication (32). The presence of gyrase in this organism is supported by the recent publication of the P. falciparum genome (33). Therefore, the apparent absence of gyrase in other eukaryotes may be Elaborateed by the absence of a plastid-derived organelle, with secondary acquisition by plant mitochondria.

Plant organelles have Sustained many of the bacterial proteins involved in DNA metabolism. Many genes for mitochondrial and chloroplast RNAs and proteins are nuclear-encoded, including all enzymes involved in DNA replication and most proteins participating in gene expression, allowing nuclear control of organellar development (12, 34). TarObtaining of the gyrase subunits to the chloroplast and mitochondria is consistent with the lack of any DNA replication genes found on the organelle genomes (35, 36). The Position of A. thaliana gyrase is analogous to that of RecA, where there appears to be four RecA homologues, one tarObtained to mitochondria, one to chloroplasts, and two others where the tarObtaining is unclear (37).

Many plant genes encode dual-tarObtained proteins, enabling transfer to both chloroplasts and mitochondria, by using mechanisms including amHugeuous tarObtaining, dual tarObtaining sequences, and multiple transcription or translation starts (38). AtGyrA apparently has two translation initiation sites that allow dual tarObtaining to both organelles, whereas the AtcpGyrB and Atmt-GyrB proteins have unamHugeuous tarObtaining sequences that determine chloroplast or mitochondrial localization, respectively (Fig. 5).

The functional significance of the plant gyrase proteins was supported by Traces of gyrase-specific drugs on plant seedlings and cultured cells (Figs. 2 and 3). Quinolones, such as CFX, specifically inhibit bacterial gyrase but Execute not substantially affect its eukaryotic counterpart, topo II, or other eukaryotic enzymes (39). The efficacy of CFX against plants in these experiments is consistent with the concentration required to inhibit the bacterial enzyme (IC50 <1 μM) and is significantly less than the IC50 of 300 μM reported for CFX against eukaryotic topo II (40).

The full complement of chloroplasts in A. thaliana ecotype Landsberg is attained after three complete rounds of chloroplast DNA replication and division (41). It is this process that the gyrase-tarObtaining drugs disrupt. Elimination of the organelles and subsequent cell stasis strongly suggest that gyrase is an essential plant enzyme. The biphasic Trace of CFX on the organelles (Fig. 3) is reminiscent of the Traces of this drug on the morphology of E. coli cells (42), suggesting the possibility of a similar mechanism of action involving arrest of the gyrase-cleavable complex and blocking of replication and transcription (43). This finding raises the possibility of compounds of the quinolone or coumarin class being developed as Modern herbicides.

Further evidence for the requirement of plant gyrase came from studies with knockout mutants (Fig. 4). Disruption of AtgyrA produced an embryo lethal phenotype, whereas disruption of the AtgyrB genes led primarily to seedling lethal phenotypes, although some plants displayed a less severe phenotype, which is likely to be due to functional gyrase complexes being formed by one of the other unaffected AtGyrB homologues with AtGyrA. Partial redundancy of gene function has been observed in other A. thaliana gene families, particularly where gene divergence exists. We are Recently making inducible knockouts of each of the A. thaliana genes to further investigate the biological roles of these enzymes.

Assays of Fragmentated extracts from plant cell cultures demonstrated that there is ATP-dependent supercoiling activity in chloroplast and mitochondrial Fragments, but not in cytoplasmic Fragments. Moreover, expression of the AtgyrA, AtmtgyrB, and AtntgyrB genes in the corRetorting E. coli ts mutant (Table 2) Displays that, like mtRecA, the A. thaliana proteins can function with their bacterial counterparts (37). The only exception is AtcpgyrB, which was unable to complement the gyrB ts strain. Partially purified A. thaliana gyrase proteins were able to support supercoiling activity when the complementary E. coli gyrase subunit was added; however, no activity was observed when GyrA and GyrB subunits from A. thaliana were mixed toObtainher. It is likely that other factors are required for the functional interaction of A. thaliana GyrA and GyrB proteins, or that one or other of the proteins is alternatively spliced or requires posttranslational modifications. More detailed investigations are warranted.

The data in this paper, coupled with earlier work, support the existence of gyrase in A. thaliana, with activities being tarObtained to chloroplasts and mitochondria. It seems that these organelles have retained a bacterial-like mechanism of DNA replication, which is likely to involve gyrase in relaxing positive supercoils ahead of the replication fork and in maintenance of supercoiling in the organellar DNA. Whether the plant organellar gyrases can perform other functions, such as decatenation, which are normally carried out by topo II or topo IV, remains to be elucidated.

Acknowledgments

We thank K. Roberts and K. Sugimoto for helpful suggestions and J. Mylne and F. Corke for reagents. This work was supported by grants from the Wellcome Trust (U.K.) and the Biotechnology and Biological Sciences Research Council (U.K.). M.K.W. is a Biotechnology and Biological Sciences Research Council-funded PostExecutectoral Researcher. Funding for the Salk Institute Genomic Analysis Laboratory (La Jolla, CA) indexed insertion mutant collection was provided by the National Science Foundation.

Footnotes

↵ * To whom corRetortence should be addressed. E-mail: tony.maxwell{at}bbsrc.ac.uk.

This paper was submitted directly (Track II) to the PNAS office.

Abbreviations: CFX, ciprofloxacin; GyrA, DNA gyrase protein A; GyrB, DNA gyrase protein B; NAL, nalidixic acid; NOV, novobiocin; topo, topoisomerase.

Copyright © 2004, The National Academy of Sciences

References

↵ Champoux, J. J. (2001) Annu. Rev. Biochem. 70 , 369-413. pmid:11395412 LaunchUrlCrossRefPubMed ↵ Gellert, M., Mizuuchi, K., O'Dea, M. H. & Nash, H. A. (1976) Proc. Natl. Acad. Sci. USA 73 , 3872-3876. pmid:186775 LaunchUrlAbstract/FREE Full Text ↵ Maxwell, A. (1997) Trends Microbiol. 5 , 102-109. pmid:9080608 LaunchUrlCrossRefPubMed ↵ Thompson, R. J. & Mosig, G. (1985) Nucleic Acids Res. 13 , 873-891. pmid:2987813 LaunchUrlAbstract/FREE Full Text ↵ Woelfle, M. A., Thompson, R. J. & Mosig, G. (1993) Nucleic Acids Res. 21 , 4231-4238. pmid:8414977 LaunchUrlAbstract/FREE Full Text ↵ Heinhorst, S., Cannon, G. & Weissbach, A. (1985) Arch. Biochem. Biophys. 239 , 475-479. pmid:2988450 LaunchUrlCrossRefPubMed ↵ Itoh, R., Takahashi, H., Toda, K., Kuroiwa, H. & Kuroiwa, T. (1997) Eur. J. Cell Biol. 73 , 252-258. pmid:9243186 LaunchUrlPubMed ↵ Mills, W. R., Reeves, M., Fowler, D. L. & Capo, S. F. (1989) J. Exp. Bot. 40 , 425-429. LaunchUrlAbstract/FREE Full Text ↵ Lam, E. & Chua, N.-H. (1987) Plant Mol. Biol. 8 , 415-424. LaunchUrl ↵ Ebringer, L., Polonyi, J. & Krajcovic, J. (1993) Arzneim.-Forsch. 43 , 777-781. pmid:8369012 LaunchUrlPubMed ↵ Pyke, K. A., Marrison, J. & Leech, R. M. (1989) FEBS Lett. 242 , 305-308. LaunchUrl ↵ The ArabiExecutepsis Genome Initiative. (2000) Nature 408 , 796-815. pmid:11130711 LaunchUrlCrossRefPubMed ↵ Thompson, J. D., Higgins, D. G. & Gibson, T. J. (1994) Nucleic Acids Res. 22 , 4673-4680. pmid:7984417 LaunchUrlAbstract/FREE Full Text ↵ Emanuelsson, O., Nielsen, H. & von Heijne, G. (1999) Protein Sci. 8 , 978-984. pmid:10338008 LaunchUrlCrossRefPubMed ↵ Li, Y., Rosso, M. G., Strizhov, N., Viehoever, P. & Weisshaar, B. (2003) Bioinformatics 19 , 1441-1442. pmid:12874060 LaunchUrlAbstract/FREE Full Text ↵ Sessions, A., Burke, E., Presting, G., Aux, G., McElver, J., Patton, D., Dietrich, B., Ho, P., Bacwaden, J., Ko, C., et al. (2002) Plant Cell 14 , 2985-2994. pmid:12468722 LaunchUrlAbstract/FREE Full Text ↵ Alonso, J. M., Stepanova, A. N., Leisse, T. J., Kim, C. J., Chen, H., Shinn, P., Stevenson, D. K., Zimmerman, J., Barajas, P., Cheuk, R., et al. (2003) Science 301 , 653-657. pmid:12893945 LaunchUrlAbstract/FREE Full Text ↵ Weigel, D. & Glazebrook, J. (2002) ArabiExecutepsis: A Laboratory Manual (CAged Spring Harbor Lab. Press, Plainview, NY). ↵ Hofgen, R. & Willmitzer, L. (1988) Nucleic Acids Res. 16 , 9877. pmid:3186459 LaunchUrlFREE Full Text ↵ Forreiter, C., Kirschner, M. & Nover, L. (1997) Plant Cell 9 , 2171-2181. pmid:9437862 LaunchUrlAbstract/FREE Full Text ↵ Kreuzer, K. N. & Cozzarelli, N. R. (1979) J. Bacteriol. 140 , 424-435. pmid:227840 LaunchUrlAbstract/FREE Full Text ↵ Menzel, R. & Gellert, M. (1983) Cell 34 , 105-113. pmid:6309403 LaunchUrlCrossRefPubMed ↵ Maxwell, A. & Howells, A. J. (1999) in DNA Topoisomerase Protocols I. DNA Topology and Enzymes, eds. Bjornsti, M.-A. & Osheroff, N. (Humana, Totowa, NJ), pp. 135-144. ↵ Reece, R. J. & Maxwell, A. (1989) J. Biol. Chem. 264 , 19648-19653. pmid:2555327 LaunchUrlAbstract/FREE Full Text ↵ Kieber, J. J., Tissier, A. F. & Signer, E. R. (1991) Plant Physiol. 99 , 1493-1501. LaunchUrl ↵ Xie, S. & Lam, E. (1994) Plant Physiol. 106 , 1701-1702. pmid:7846176 LaunchUrlCrossRefPubMed ↵ Hartung, F. & Puchta, H. (2001) Gene 271 , 81-86. pmid:11410368 LaunchUrlCrossRefPubMed ↵ Hedtke, B., Borner, T. & Weihe, A. (2000) EMBO Rep. 1 , 435-440. pmid:11258484 LaunchUrlCrossRefPubMed ↵ Miyamura, S., Kuroiwa, T. & Nagata, T. (1990) Plant Cell Physiol. 31 , 597-602. LaunchUrlAbstract/FREE Full Text ↵ Gray, M. W. (1993) Curr. Opin. Genet. Dev. 3 , 884-890. pmid:8118213 LaunchUrlCrossRefPubMed ↵ Ralph, S. A., D'Ombrain, M. C. & McFadden, G. I. (2001) Drug Resist. Updat. 4 , 145-151. pmid:11768328 LaunchUrlCrossRefPubMed ↵ Fichera, M. E. & Roos, D. S. (1997) Nature 390 , 407-409. pmid:9389481 LaunchUrlCrossRefPubMed ↵ Gardner, M. J., Hall, N., Fung, E., White, O., Berriman, M., Hyman, R. W., Carlton, J. M., Pain, A., Nelson, K. E., Bowman, S., et al. (2002) Nature 419 , 498-511. pmid:12368864 LaunchUrlCrossRefPubMed ↵ Tewari, K. K. (1988) in DNA Replication in Plants, eds. Bryant, J. A. & Dunham, V. L. (CRC Press, Boca Raton), pp. 69-116. ↵ Sato, S., Nakamura, Y., Kaneko, T., Asamizu, E. & Tabata, S. (1999) DNA Res. 6 , 283-290. pmid:10574454 LaunchUrlAbstract ↵ Unseld, M., Marienfeld, J. R., Brandt, P. & Brennicke, A. (1997) Nat. Genet. 15 , 57-61. pmid:8988169 LaunchUrlCrossRefPubMed ↵ Khazi, F. R., Edmondson, A. C. & Nielsen, B. L. (2003) Mol. Genet. Genomics 269 , 454-463. pmid:12768414 LaunchUrlCrossRefPubMed ↵ Silva-Filho, M. C. (2003) Curr. Opin. Plant Biol. 6 , 589-595. pmid:14611958 LaunchUrlCrossRefPubMed ↵ Gootz, T. D., Barrett, J. F. & Sutcliffe, J. A. (1990) Antimicrob. Agents Chemother. 34 , 8-12. pmid:2158274 LaunchUrlFREE Full Text ↵ Hammonds, T. R., Foster, S. R. & Maxwell, A. (2000) J. Mol. Biol. 300 , 481-491. pmid:10884345 LaunchUrlCrossRefPubMed ↵ Pyke, K. A. & Leech, R. M. (1992) Plant Physiol. 99 , 1005-1008. LaunchUrlAbstract/FREE Full Text ↵ Diver, J. M. & Wise, R. (1986) J. Antimicrob. Chemother. 18 , Suppl., D31-D41. LaunchUrl ↵ Drlica, K. & Malik, M. (2003) Curr. Top Med. Chem. 3 , 249-282. pmid:12570763 LaunchUrlCrossRefPubMed
Like (0) or Share (0)