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Journal of Bacteriology, April 2006, p. 2774-2779, Vol. 188, No. 8
0021-9193/06/$08.00+0 doi:10.1128/JB.188.8.2774-2779.2006
Copyright © 2006, American Society for Microbiology. All Rights Reserved.
and
Mitchell Singer*
Section of Microbiology and Center for Genetics and Development, The University of California, Davis, Davis, California 95616
Received 10 November 2005/ Accepted 23 January 2006
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FIG. 1. Morphology of the M. xanthus developmental process. Shown are a pictorial representation of the major stages of development and a corresponding light micrograph of the morphology of wild-type M. xanthus DK1622 at each stage. Aggregation of the vegetative cells is apparent at 6 h and continues until 12 h when distinct, but still loose, mounds are formed. Fruiting bodies are dark, compact structures that begin to be apparent after 24 to 48 h.
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In this study, we sought to use known chemical inhibitors of DNA replication to observe their effects on the developmental process in M. xanthus. The goal of this study was not only to determine if concurrent DNA replication is essential for progression through the developmental program, but to determine the timing of this event in relation to the M. xanthus developmental program.
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Development and sporulation. Development was performed either with a submerged liquid culture buffer system (12) or on TPM agar plates (10 mM Tris [pH 7.6], 8 mM MgSO4, and 1 mM KH2PO4 containing 1.5% agar), as described below. Cells were allowed to develop in a humidity chamber at 33°C. Nalidixic acid was added when indicated at a concentration of 20 µg/ml. Quantification of heat and sonication-resistant spore production was done as previously described (11).
Isolation of spontaneous nalidixic acid-resistant mutants. Wild-type M. xanthus DK1622 was plated on CTTYE agar plates containing 40-µg/ml nalidixic acid; this higher concentration of nalidixic acid was essential for reducing the background when selecting for nalidixic acid-resistant mutants. Nalidixic acid-resistant candidates were then tested for growth in both CTTYE liquid medium and CTTYE agar containing 20 µg of nalidixic acid/ml. Purified candidates were then subjected to DNA sequencing of the gyrA locus (University of CaliforniaDavis DNA Sequencing Facility) to identify the lesion. Only those mutants that contained a lesion at the gyrA locus were used for this study. Mx8-mediated transduction was used to transfer the nalidixic acid resistance marker to a genetically clean DK1622 background as previously described (14).
Incorporation of radiolabeled nucleotide. Incorporation of 3H-labeled thymidine and 3H-labeled uridine was performed as follows. Cultures were grown in CTT (1) medium until mid-exponential phase (100 to 120 Klett units) and then split into two, with 20-µg/ml nalidixic acid added to the experimental culture. Samples were taken, pulsed for 3 min with either 2-µCi/ml of 3H-labeled thymidine ([6-3H]thymidine, 20 to 30 Ci/mmol; Amersham TRK61) or uridine ([5,6-3H]uridine, 47 Ci/mmol; Amersham TRK410), and precipitated with ice-cold 5% trichloroacetic acid. Precipitated counts were collected on a glass filter, washed three times with 3% trichloroacetic acid, and counted with a Beckman Coulter LS 6500 scintillation counter. For developmental incorporation of label, cells were allowed to develop in the submerged culture system described above for the times indicated in the text; then radiolabel was directly added to the surrounding buffer for the 3-min pulse. Cells were then harvested, and precipitated counts were quantified as described above.
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Nalidixic acid was added to wild-type M. xanthus DK1622 cells at the onset of development, using the submerged culture developmental system (12). As shown in Fig. 2, in the presence of inhibitor, development proceeded normally up to 6 h, corresponding to the early aggregation stage of development (Fig. 2A and B). Though cells began to aggregate by 6 h, similarly to what is observed in normal development, cells treated with nalidixic acid were unable to proceed past the aggregation stage and were unable to form spore-filled fruiting bodies by 48 h (Fig. 2F). Cells treated with nalidixic acid appeared to be totally incapable of forming mounds or developing into fruiting bodies, and studies done with two other inhibitors of DNA synthesis, hydroxyurea and novobiocin, showed similar results (data not shown). These observations demonstrate that inhibition of DNA synthesis severely blocks development, implying that DNA replication is essential in the normal developmental process of M. xanthus.
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FIG. 2. Fruiting body morphology with addition of DNA synthesis inhibitors at the onset of development. Nalidixic acid was added to the surrounding buffer medium of developing M. xanthus wild-type DK1622 cells at the onset of development (0 h). Shown are light micrographs taken at 6, 12, and 48 h and corresponding to aggregation (A and B), mound formation (C and D), and fruiting body (E and F) stages of development, respectively.
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As demonstrated in Fig. 3, when M. xanthus cells are developing in submerged culture, the developmental process becomes independent of DNA replication by 12 h. This corresponds morphologically to the transition between the aggregation phase and early mound formation (Fig. 1). This was apparent when observing two snapshots of development, at 12 h and at 48 h. At 12 h into development, both samples with nalidixic acid added previously at 0 h (Fig. 3E) and at 6 h (Fig. 3F) appeared almost identical to the sample where nalidixic acid had just been added at 12 h (Fig. 3G) and similar to the no-addition case (Fig. 3H). In all cases at 12 h into development, cells were arranged into streams leading toward aggregation centers. However, at later times, such as 48 h into development, the samples with nalidixic acid added at either 0 h (Fig. 3I) or 6 h (Fig. 3J) had not formed the dense, darkened fruiting body structures that are normally associated with development at this time (Fig. 2E). Darkened fruiting bodies were clearly seen in the samples with inhibitor added at 12 h (Fig. 3K) or 18 h (Fig. 3L), and these fruiting bodies appeared visually to be identical those formed in the absence of nalidixic acid (Fig. 2E).
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FIG. 3. Fruiting body morphology with addition of nalidixic acid at specific times after the initiation of development. Shown are light micrographs of developmental morphology of wild-type DK1622 taken at 6, 12, and 48 h into development with 20-µg/ml nalidixic acid added to the surrounding buffer medium at specific times (0, 6, 12, and 18 h). Viable spore production is shown in a table below. The total numbers of viable spores produced at the end of development were determined for each specific time of addition, were compared to untreated samples, and are shown as a percentage.
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Mutants in gyrA are resistant to the developmental block imposed by nalidixic acid. If nalidixic acid specifically inhibits DNA replication and this inhibition directly leads to the developmental block, then we would predict that a mutant that is specifically resistant to the DNA replication block would be able to develop normally. Six spontaneously occurring nalidixic acid-resistant mutants were isolated from wild-type DK1622 cells and then sequenced for mutations in a known target of nalidixic acid, gyrA, which encodes the A subunit of DNA gyrase. Sequencing of the predicted M. xanthus gyrA locus revealed two candidates with mutations in gyrA, both at a position corresponding to a previously characterized nalidixic acid-resistant mutant from E. coli (16). In both of these mutants, an aspartic acid residue was changed to valine at amino acid position 118 (corresponding to amino acid position 87 in E. coli) (Fig. 4). Mx8-mediated transduction was used to move the gyrA mutation back into DK1622 by selecting for nalidixic acid resistance. The gyrA loci of 10 nalidixic acid-resistant transductants were then sequenced; 9 of 10 transductants were found to contain the appropriate nucleotide change as in the original mutant, while the 10th candidate failed to provide a readable DNA sequence. This nalidixic acid-resistant mutant was designated MS1701.
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FIG. 4. Protein sequence alignment comparing the M. xanthus MS1701 nalidixic acid-resistant GyrA with E. coli GyrA. Shown is the GyrA protein sequence in the M. xanthus nalidixic acid-resistant mutant with its aspartic acid-to-valine substitution at amino acid position 118 indicated by a black box. This alignment was produced with the BioEdit Sequence Alignment Editor (7).
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FIG. 5. Effect of nalidixic acid on DNA and RNA synthesis. Shown are the radiolabel incorporations of 3H-labeled thymidine (A) and 3H-labeled uridine (B) for both the wild type and the nalidixic acid-resistant mutant MS1701 in the presence of 20-µg/ml nalidixic acid. Inhibitor was added in mid-exponential phase. The x axis represents the time after addition, and the y axis represents radiolabel incorporation as counts per minute per optical density in Klett units.
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FIG. 6. Fruiting body morphology of nalidixic acid-resistant mutant MS1701 compared to the wild type. Shown are light micrographs of the developmental morphology of wild-type DK1622 and the mutant nalidixic acid-resistant strain MS1701 after 5 days of development when fruiting bodies have fully formed. The untreated samples have no inhibitor added to the surrounding medium, while the nalidixic acid-treated samples are exposed to inhibitor at a concentration of 20 µg/ml from the onset of development.
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FIG. 7. Incorporation of radiolabeled thymidine during development. Shown are the results of three independent experiments on the incorporation of 3H-labeled thymidine by wild-type DK1622 during a developmental time course from 0 to 24 h. No DNA replication inhibitors were used. The x axis represents hours after the onset of development, and the y axis represents absolute levels of radiolabel incorporation.
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Interestingly, when radiolabel incorporation of [3H]thymidine into developing M. xanthus cells is observed, there appears to be a controlled increase in DNA synthesis early in development. This is an unexpected result because in previous studies of glycerol spores, it was shown that no new rounds of DNA replication are initiated during sporulation (18). While this may be an artifact of experimental procedures, it may in fact represent the first developmental checkpoint for chromosome replication in M. xanthus. Since DNA replication would take approximately 5 h in M. xanthus (25), cells that are to become myxospores need to initiate chromosome replication very early into development to allow for completion. Cells at this point would need to evaluate their chromosome replication status, initiating DNA replication when appropriate. Recent studies in the Kaiser laboratory using M. xanthus DNA microarrays have suggested that dnaA expression is activated three- to fourfold during the early stages of development (8), which correlates with this result. We have also proposed previously that chromosome replication during development may be directly controlled by the stringent response (24) which also occurs within this time frame, at the onset of development (19).
A possible second checkpoint in development is after completion of chromosome replication at the end of aggregation phase. This is based on the observation that DNA replication is essential for development to proceed past the aggregation phase. When DNA replication is inhibited by addition of replication inhibitors, we observed a specific block at this stage of development. It perhaps is no coincidence that a number of regulatory pathways are active during the aggregation stage of development, including the C-signal (11) and the SdeK (17) pathways and the activation of the devTRS operon (23). A checkpoint mechanism monitoring DNA replication state could easily feed into one or more of these previously described regulatory pathways, halting cells at aggregation if cells have not fully replicated their DNA or if there are errors in replication. It has been shown with B. subtilis that DnaA regulates sda expression, preventing sporulation from occurring before the completion of DNA replication (2). Although M. xanthus does not appear to possess an Sda homologue, these observations would suggest that M. xanthus, like B. subtilis, has a regulatory circuit that prevents progression of development until DNA replication functions are fully completed.
Previously, we have reported that the two populations formed at the end of development, myxospores and peripheral rods (15), have differing chromosomal copy numbers. Myxospores appear to have two copies of the chromosome, while peripheral rod cells have only one copy (24). Given our current observation that there is a general increase in DNA replication during the aggregation phase of development, how are these two distinct states established? It would be interesting to propose a model where stringent response-induced activation of dnaA expression and initiation of chromosome replication are events that occur universally across the entire developing population. At the end of aggregation phase, the integrity of chromosome replication is checked. A majority of cells may have incomplete replication or errors due to lack of energy, and these cells will abort development, either simply arresting the developmental process or undergoing autolysis. The remaining cells all contain two copies of the chromosome but contain differing levels of C signaling because of spatial distribution within the aggregating mass of cells. It has been shown previously that a key difference between peripheral rods and cells within the fruiting body (presumably fated to become myxospores) is in the level of C signaling. Peripheral rods have low levels of C signaling and low expression of C-signal-dependent genes, while cells within the fruiting body have a much higher level of expression of these genes (9). So with low levels of C signaling, we propose that cells will be induced to septate a reducing chromosomal copy number to one to become peripheral rods; however, with high levels of C signaling, cells will inhibit septation, retaining their two-chromosome state, and proceed into the later stages of development.
From our initial experiments, we proposed that the developmental block in the presence of nalidixic acid was caused specifically by the effect on DNA replication. This hypothesis is supported by the fact that a nalidixic acid-resistant mutation in gyrA is not only capable of synthesizing DNA normally but also able to grow and develop in the presence of nalidixic acid, bypassing the block in development at the aggregation stage and strongly suggesting that DNA gyrase is the primary target of the inhibitor.
All previous characterizations of chromosome replication during sporulation in M. xanthus have been based on studies of glycerol spores (10, 18, 26). The data presented here show that in terms of chromosome replication in M. xanthus development, there is a significant difference between what occurs in glycerol sporulation and what happens in fruiting body-associated sporulation, leading us to alter the basic assumptions that are currently held about when or if chromosome replication is related to development in this organism.
This work was supported by the National Institute of General Medical Sciences, U.S. Public Health Service grant GM54592, to M.S.
Present address: National Institute of Environmental Health Sciences, Laboratory of Respiratory Biology, P.O. Box 12233, Mail Stop C2-14, Research Triangle Park, NC 27709. ![]()
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