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Applied and Environmental Microbiology, June 2004, p. 3624-3631, Vol. 70, No. 6
0099-2240/04/$08.00+0 DOI: 10.1128/AEM.70.6.3624-3631.2004
Copyright © 2004, American Society for Microbiology. All Rights Reserved.
Max Planck Institute for Marine Microbiology, 28359 Bremen,1 Max Planck Institute for Molecular Genetics, 14195 Berlin-Dahlem, Germany2
Received 17 November 2003/ Accepted 26 February 2004
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Magnetotaxis and magnetosome formation have attracted broad interdisciplinary interest for several reasons. Magnetosome biomineralization is a well-established example of controlled mineral formation by bacteria in aquatic sediments on Earth (22, 24, 40), and magnetosome characteristics have been recently considered for use as biosignatures to identify presumptive Martian magnetofossils (21). Because of the unique characteristics of bacterial magnetite crystals, there is considerable biotechnological interest in magnetosome biomineralization (1, 35). In addition, MTB provide a simple model for studying magnetoreception, which might be useful for an understanding of this phenomenon in more complex systems such as higher animals (15). However, both magnetotaxis and magnetosome biomineralization have remained poorly understood at the molecular level, mostly because of the lack of appropriate genetic tools due to past difficulties in culturing and transforming these fastidious organisms.
Here we report a method for knockout mutagenesis by homologous recombination in Magnetospirillum gryphiswaldense, which has recently emerged as a model system to study magnetotaxis and magnetosome biomineralization (11, 32, 34). The biochemical and proteomic analysis of the magnetosome membrane in M. gryphiswaldense in combination with reverse genetics has led to the identification of a number of genes encoding magnetosome membrane proteins, which are organized in the genome in several different operons (7, 8, 10). The isolation and characterization of spontaneous nonmagnetic mutants revealed a large magnetosome island harboring most of the magnetosome membrane protein genes as well as numerous further mam genes with an implicated role in biomineralization but yet unknown function (7, 8, 31, 33). Although a conjugative system for random Tn5-based mutagenesis has been reported in M. gryphiswaldense and Magnetospirillum sp. strain AMB-1 (20, 36, 42), so far there has been no means for site-directed mutagenesis, which is particularly desirable with the increasing availability of genome sequence data from M. gryphiswaldense and other MTB (reference 7 and http://www.jgi.doe.gov/tempweb/JGI_microbial/html/index.html.) This lack has been a major impediment to elucidating the gene functions involved in magnetotaxis and biomineralization and was the impetus for the present study.
Motility is a key factor in magnetotaxis, but nearly nothing is known about its structural and molecular components. In order to establish gene disruption, we analyzed the flaA gene encoding a flagellin homologue, whose mutagenesis should yield a predictable and easily detectable phenotype. Flagellin is the principal constituent of bacterial flagellar filaments, which consist of an assembly of about 20,000 flagellin subunits (19, 28). In this study, the targeted disruption of the flagellin gene flaA was found to eliminate flagella formation and motility. The genetic technique described herein will allow future exploitation of the substantial genome data that have become available for M. gryphiswaldense.
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TABLE 1. Bacterial strains, plasmids, and primers
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Primers used for PCR are listed in Table 1. PCR amplification was performed with the Mastercycler gradient (Eppendorf, Hamburg, Germany) by using standard protocols.
RT-PCR.
The isolation of the total RNA from M. gryphiswaldense was performed by standard techniques (26). Isolated RNA was treated with DNase (MBI Fermentas) and then used in a reverse transcriptase (RT) reaction (Moloney murine leukemia virus reverse transcriptase; MBI Fermentas) with a hexanucleotide primer mix (Roche Molecular Biochemicals). For negative control reverse transcriptase was omitted from the reaction mixture. The obtained cDNA was amplified by PCR by using PCR Master Mix (Promega) and primers flaRTfo and flaRTrw, which amplify a 577-bp fragment of the flaA gene.
Biparental conjugation.
Recombinant plasmids were introduced into the recipient strain M. gryphiswaldense R3/S1 by biparental conjugation with E. coli S17-1 as a donor as described previously (36). For selection of homologous recombination events, up to 1010 cells were mixed and incubated microaerobically on ACAM for 8 h. Cells were flushed from the agar surface into sterile liquid medium containing 50 µg of streptomycin to counterselect against the E. coli donor. To increase the ratio of homologous recombination events, the cells were incubated in this medium overnight before they were plated onto ACAM with rifampin (150 µg/liter) and streptomycin (50 µg/liter) and the appropriate antibiotic for plasmid selection.
Construction of flaA insertion mutations.
A 2.5-kb fragment was amplified by PCR by using primers flaAUp3 and flaALo3 and then subcloned into the pGEM-T Easy vector (Promega, Mannheim, Germany). The fragment was excised with EcoRI and ligated with the pK19mobsacB vector (the PstI restriction site of the vector was eliminated before) containing the sacB gene (27) as a counterselectable suicide marker. The gentamicin resistance cassette of the broad-host-range plasmid pBBR1MCS5 was amplified by PCR (each primer with a PstI linker) and subcloned into the pGEM-T Easy vector. The resulting plasmid, pDa102, was digested with PstI, and the purified gentamicin cassette was ligated into the PstI restriction site of the 2.5-kb fragment inside the flaA gene to yield plasmid pDa115. The construct was excised from pDa115 by EcoRI digestion and ligated into the suicide vector pK19mobGII containing the gusA gene (14) as a chromogenic marker. Correct insertion into the M. gryphiswaldense chromosome by single and double crossovers was confirmed by PCR with primers flaAFo3 and flaALo3 as well as by Southern hybridization with probe I.
Analysis of DNA and protein sequence data.
Genome sequence data from M. gryphiswaldense MSR-1 were used from the whole genome shotgun in progress (R. Reinhardt, MPI Molecular Genetics, Berlin-Dahlem, Germany), at the present stage of eightfold sequencing coverage. The basic analysis of DNA and protein sequences was done by the MacVector 7.0 software package (Oxford Molecular Ltd.). Sequence alignments were carried out by using the ClustalW algorithm (41), which is part of the same software. Protein sequences were compared to the GenBank, EMBL, and SwissProt databases. Preliminary sequence data for Magnetospirillum magnetotacticum MS-1 was obtained from the U.S. Department of Energy Joint Genome Institute at http://www.jgi.doe.gov/tempweb/JGI_microbial/html/index.html.
Electron microscopy.
Cells were adsorbed on carbon-coated copper grids and negatively stained with 2% (wt/vol) uranyl acetate. Samples were viewed and recorded with a Philips CM12 transmission electron microscope at an accelerating voltage of 120 kV.
SDS-PAGE.
Whole-cell extracts of M. gryphiswaldense were prepared by boiling the cells in sodium dodecyl sulfate (SDS) sample buffer for 10 min and then were separated by one-dimensional SDS-polyacrylamide gel electrophoresis (PAGE) (18). Approximately 20 µg of protein per lane was loaded onto a 12% polyacrylamide gel. The gels were digitized and analyzed by using ImageMaster 1D software (Amersham Pharmacia).
Motility assays.
Swarm plate assays were done by stabbing cells into semisolid 0.25% FSM agar and incubating the plate at 28°C under microaerobic conditions for 72 h. For motility assays in oxygen gradient tubes (1.5 by 15 cm), the FSM medium with 0.3% agar was inoculated with the cells and incubated for 48 h exposed to the air in the absence of an external magnetic field. In order to demonstrate magnetotaxis, a ferrite plate magnet (10 by 10 by 2.5 cm) was applied close to the tubes to generate a horizontal magnetic field, which covered the whole area of the length of the tube.
Nucleotide sequence accession numbers.
The nucleotide sequences of the M. gryphiswaldense flaA, flaB, and flaC genes have been deposited in the GenBank, EMBL, and DDJB libraries under the accession numbers CR354386, CR354387, and CR354388, respectively.
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FIG. 1. Electron micrographs of M. gryphiswaldense cells. (A) Wild type. The filament (F) appears to be connected to the cell wall by a hook-like structure (H). (B) A nonflagellated mutant strain, Da136.
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-proteobacteria (Fig. 2). All putative Fla proteins from both M. magnetotacticum and M. gryphiswaldense display the characteristic three-domain organization of bacterial flagellins with conserved N- and C-terminal domains and a variable central domain (19, 28). Interestingly, the N- and C-terminal amino acid sequences of the FlaA proteins are very similar for the two Magnetospirillum strains, whereas the central domains are highly divergent and have different lengths. In contrast, the hypothetical FlaA protein of Rhodospirillum rubrum displays extensive sequence similarity (64% similarity; 45% identity) to M. gryphiswaldense FlaA over its whole length.
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FIG. 2. Dendrogram showing the sequence similarity of selected full-length flagellin proteins from various -proteobacteria. Abbreviations (with proteins and accession numbers): Rrub, Rhodospirillum rubrum [Fla(hyp), ZP_00013883]; Mgry, M. gryphiswaldense, Mmag, M. magnetotacticum (FlaA ZP_00056435); Ccres, Caulobacter crescentus (FliL, AAC35988; FliN, AAB95381.2; FliM, AAB95380.1; FliO, AAB95382.2; FliK, NP_420274; FliJ, P02969), Bcla, Bartonella clarridgeiae (FlaA, CAB64773); Mlot, Mesorhizobium loti (FlaA, NP_104151); Bmel, Brucella melitensis (FlaB, NP_541127); Rlup, Rhizobium lupini (FlaD, AAG14366; FlaA, AAG14364); Smel, Sinorhizobium meliloti (FlaD, AAB81422; putative FlaD*, NP_384777; FlaA, NP_384775); Atum, Agrobacterium tumefaciens [Fla(hyp), NC_003062]. Flagellin sequences determined in this study are in bold. The E. coli (Ecol) flagellin (FliC, NC_000913) was used as an outgroup marker. The multiple alignment and dendrogram were constructed by using the ClustalW program of the MacVector 7.0 software. Branch lengths are not to scale.
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The isolation of rare double recombinants can often be greatly facilitated by the use of markers, which are easily screenable or counterselectable (2, 23). To test if this is an applicable strategy for study of M. gryphiswaldense, we constructed suicide plasmids based on either the pK19mobGII vector (14) harboring the gusA gene, which encodes the enzyme ß-glucuronidase, or the pK19mobsacB vector (27), which harbors the genetically modified allele of the sacB gene of Bacillus subtilis (38) coding for the levansucrase enzyme that confers a lethal phenotype to many gram-negative bacteria in the presence of sucrose. The resulting plasmids pDa115 (sacB) (Fig. 3) and pDa116 (gusA) both contained the flaA gene with the gentamicin cassette inserted (flaA::Gm). The extent of homologous M. gryphiswaldense sequences present before and after the gentamicin marker was 1,549 and 979 bp, respectively. Conjugation with plasmid pDa116 resulted in numerous gentamicin-resistant colonies with a frequency of approximately 106 colonies per recipient cell. Every one of the 96 examined colonies resulted from a single crossover event, as detected by PCR and sensitivity to both kanamycin and gentamicin. Several clones harboring single crossovers were further propagated in liquid medium containing gentamicin, but lacking kanamycin. However, we repeatedly failed to identify double-crossover mutants by replica plating on ACAM containing either kanamycin or gentamicin for the loss of the plasmid-borne kanamycin marker. Several of the colonies eventually turned blue after prolonged incubation on 5-bromo-4-chloro-3-indoxyl-ß-D-glucuronide-containing ACAM plates. However, color development was not reproducible and was unstable during serial transfers, and no clear correlation between decolorization and a particular genotype (loss of the inserted vector) could be detected. The potential use of gusA as a screenable marker in M. gryphiswaldense thus requires further elaboration.
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FIG. 3. Scheme of construction of double crossovers. Plasmid pDa115 represents the suicide vector used to inactivate the M. gryphiswaldense flaA gene. The primers used are shown as arrows. Restriction sites and the probe used in the Southern blot analysis are indicated.
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By using plasmid pDa115, numerous gentamicin-resistant colonies were obtained in conjugation experiments on ACAM plates containing 5% sucrose. As revealed by PCR and Southern blot analysis, all colonies resulted from homologous recombination with the M. gryphiswaldense flaA locus. Three classes of mutants could be distinguished based on their different genotypes. Two classes of single-crossover mutants resulted from a single-crossover event with either the left arm (5'-insertion) or the right arm (3'-insertion). The ratio of the number of left- to the number of right-arm insertion mutants was approximately 1:20. As these mutants were still found to contain the inserted plasmid pDa115, we concluded that the gained insensitivity to sucrose was due to the loss of the sacB function by spontaneous mutation, which has repeatedly been observed before (3, 6, 13). Both 5' and 3' single-crossover insertion mutants displayed motility, which was virtually indistinguishable from the wild-type strain. This finding indicates that the insertion of the plasmid, which results in cells that are merodiploid for flaA, has no polar effects on the expression of downstream genes that might putatively affect motility and flagellar assembly.
Approximately 1% of the mutants, however, were found to represent a third class of mutants, which was due to reciprocal crossover events (Fig. 3) as revealed by replica plating and Southern blot analysis (Fig. 4). One clone, dubbed strain Da136, was selected for further analysis.
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FIG. 4. Confirmation of flaA disruption by Southern blot analysis of genomic DNA from the wild type (lanes 1 and 3) and strain Da136 (lanes 2 and 4). DNA was digested with SalI (lanes 1 and 2) and KpnI (lane 3 and 4). Lane M, molecular weight markers. The blot was hybridized with probe I (shown in Fig. 3), which overlaps the KpnI restriction site. Digesting with SalI revealed a larger band for Da136 because of the insertion of the gentamicin cassette. As expected, digesting with KpnI yielded two signals for the wild type and strain Da136. The smaller hybridizing fragments of the wild-type and Da136 DNA have identical sizes, while the positions of the larger bands differ by the size of the inserted gentamicin cassette.
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FIG. 5. Motility assays in semisolid agar. (A) Growth in the absence of a magnetic field. At the top (i), wild-type (wt) M. gryphiswaldense grew as sharp microaerophilic bands (arrow) in oxygen gradients, while growth of the nonmotile mutant strain Da136 was fuzzy. At the bottom (ii), bacteria were stabbed into motility agar in a petri dish. The wild type formed a large chemotactic swarming halo (H) with a diameter of approximately 4 cm after 48 h, while no spreading of mutant strain Da136 was visible. (B) Magnetotactic patterns of wild-type M. gryphiswaldense in the presence of a horizontal magnetic field. On the left side of the panel, at the wall facing the magnetic South pole, cells accumulated as a line (L) leading into a nose-like tip (N) close to the agar surface. On the right side of the panel, at the opposite side (distal to the South pole of the magnet), a cell pellet (P) was visible close to the bottom of the same tube. In addition, a spherical pattern resembling a bubble (B) was formed in the center of the tube.
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FIG. 6. (A) Analysis of the expression of the flaA gene in M. gryphiswaldense wild type and mutant strain Da136 by RT-PCR using various DNA templates. Lane 1, genomic DNA used as a template (positive control); lane 2, cDNA of the wild type; lane 3, cDNA of strain Da136; lane 4, wild-type RNA, reverse transcriptase omitted (negative control); lane 5, Da136 RNA, reverse transcriptase omitted (negative control). DNA was amplified by using primers flaRTfo and flaRTrw. (B) Analysis of the flagellin synthesis by SDS-12% PAGE. Whole-cell extracts of the wild type (lane 1) and the mutant Da136 (lane 2) were stained with Coomassie brilliant blue. A putative flagellin polypeptide was present in the wild-type strain (arrow) but absent from the mutant strain. M, molecular weight markers.
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We thank Katja Junge and Susanne Ullrich for help and Katja Schmidt for excellent technical assistance. We are grateful to Harald Engelhardt and Günter Pfeifer (MPI f. Biochemistry, Martinsried, Germany) for help and access to the electron microscope. We thank Richard Reinhardt (MPI f. Molecular Genetics, Berlin-Dahlem, Germany) for access to genomic sequencing data. Douglas Bartlett (La Jolla, Calif.), Matthias Keller, Alfred Pühler (Bielefeld, Germany), and Gerrit Voordouw (Calgary, Canada) are acknowledged for their kind gifts of plasmids and bacterial strains. Preliminary sequence data for M. magnetotacticum MS-1 was obtained from the U.S. Department of Energy Joint Genome Institute at http://www.jgi.doe.gov/tempweb/JGI_microbial/html/index.html.
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