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. 2017 Apr 25;199(10):e00788-16.
doi: 10.1128/JB.00788-16. Print 2017 May 15.

The dev Operon Regulates the Timing of Sporulation during Myxococcus xanthus Development

Affiliations

The dev Operon Regulates the Timing of Sporulation during Myxococcus xanthus Development

Ramya Rajagopalan et al. J Bacteriol. .

Abstract

Myxococcus xanthus undergoes multicellular development when starved. Thousands of rod-shaped cells coordinate their movements and aggregate into mounds in which cells differentiate into spores. Mutations in the dev operon impair development. The dev operon encompasses a clustered regularly interspaced short palindromic repeat-associated (CRISPR-Cas) system. Null mutations in devI, a small gene at the beginning of the dev operon, suppress the developmental defects caused by null mutations in the downstream devR and devS genes but failed to suppress defects caused by a small in-frame deletion in devT We provide evidence that the original mutant has a second-site mutation. We show that devT null mutants exhibit developmental defects indistinguishable from devR and devS null mutants, and a null mutation in devI suppresses the defects of a devT null mutation. The similarity of DevTRS proteins to components of the CRISPR-associated complex for antiviral defense (Cascade), together with our molecular characterization of dev mutants, support a model in which DevTRS form a Cascade-like subcomplex that negatively autoregulates dev transcript accumulation and prevents DevI overproduction that would strongly inhibit sporulation. Our results also suggest that DevI transiently inhibits sporulation when regulated normally. The mechanism of transient inhibition may involve MrpC, a key transcription factor, whose translation appears to be weakly inhibited by DevI. Finally, our characterization of a devI devS mutant indicates that very little exo transcript is required for sporulation, which is surprising since Exo proteins help form the polysaccharide spore coat.IMPORTANCE CRISPR-Cas systems typically function as adaptive immune systems in bacteria. The dev CRISPR-Cas system of M. xanthus has been proposed to prevent bacteriophage infection during development, but how dev controls sporulation has been elusive. Recent evidence supported a model in which DevR and DevS prevent overproduction of DevI, a predicted 40-residue inhibitor of sporulation. We provide genetic evidence that DevT functions together with DevR and DevS to prevent DevI overproduction. We also show that spores form about 6 h earlier in mutants lacking devI than in the wild type. Only a minority of natural isolates appear to have a functional dev promoter and devI, suggesting that a functional dev CRISPR-Cas system evolved recently in niches where delayed sporulation and/or protection from bacteriophage infection proved advantageous.

Keywords: CRISPR-Cas; Myxococcus xanthus; bacterial development; dev operon; gene regulation; signaling; sporulation.

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Figures

FIG 1
FIG 1
Map of the dev operon. The operon includes eight genes and the downstream CRISPR (8). The devR and devS products negatively autoregulate the dev promoter (7, 8, 10).
FIG 2
FIG 2
Development of devT mutants under submerged culture conditions. (A) Fruiting body formation by wild-type DK1622 and development of the indicated devT mutants. DK1622 formed dark fruiting bodies by 72 h poststarvation (an arrow points to one), as did the ΔdevT13–541 ΔPdev and ΔdevT13–541 ΔdevI mutants, but the original ΔdevT408–502 mutant failed to form mounds, and the mounds formed by the reconstructed ΔdevT408–502 mutant and the ΔdevT13–541 mutant failed to darken. Scale bar, 100 μm. Similar results were observed in at least two biological replicates. (B) Cellular shape change by wild-type DK1622 and the indicated devT mutants. DK1622 formed ovoid spores by 48 h poststarvation (an arrow points to one), but shape change was delayed in the devT mutants (arrows point to thickened rods at 48 h and ovoid spores at 72 h). Scale bar, 5 μm. Similar results were observed in at least two biological replicates.
FIG 3
FIG 3
FruA (A) and MrpC (B) levels during development of devT mutants. The indicated strains were starved under submerged culture conditions. Samples were collected at the indicated times (in hours), and equal amounts of protein (1 μg) were analyzed by immunoblotting using anti-FruA or anti-MrpC antibodies. Representative immunoblots are shown from two or three biological replicates. The graph below the immunoblots shows quantification of signal intensities relative to a 15-h sample of wild-type DK1622 on the same immunoblot. Values are the average of the results from the replicates, and error bars indicate one standard deviation from the mean.
FIG 4
FIG 4
Levels of dev transcripts in ΔdevT13–541 and Δcas mutants. The indicated strains were starved under submerged culture conditions. At 24 h poststarvation, cultures were harvested, RNA was isolated, and the RNA was subjected to RT-qPCR analysis using primers PdevF-2 and PdevR-3. Values are the averages of the results from three biological replicates relative to wild-type DK1622, and error bars indicate one standard deviation from the mean.
FIG 5
FIG 5
Timing of sporulation in mutants that fail to express devI. (A) Cellular shape change. The indicated strains were starved under submerged culture conditions and samples were collected, gently dispersed, and examined microscopically at the times indicated. Photos show densely packed cell aggregates presumed to be nascent fruiting bodies. Arrows indicate thickened rods or ovoid spores. Scale bar, 5 μm. Similar results were observed in at least two biological replicates. (B) Sonication-resistant spores. The indicated strains were starved under submerged culture conditions and samples were collected at the indicated times (in hours) for the measurement of sonication-resistant spores. Values (log10) are the averages of the results from at least three biological replicates, and error bars represent one standard deviation from the mean.
FIG 6
FIG 6
MrpC (A) and FruA (B) levels during development in the absence of devI. The indicated strains were starved under submerged culture conditions. Samples were collected at the indicated times (in hours), and equal amounts of protein (1 μg) were analyzed by immunoblotting using anti-MrpC or anti-FruA antibodies. Representative immunoblots are shown from two or three biological replicates. The graph below the immunoblots shows quantification of signal intensities relative to a 15-h sample of wild-type DK1622 on the same immunoblot. Values are the averages of the results from replicates, and error bars indicate one standard deviation from the mean.
FIG 7
FIG 7
Levels of exo transcripts during development in the absence of devI. (A) exo transcripts at 30 h poststarvation. The indicated strains were starved under submerged culture conditions. At 30 h poststarvation, cultures were harvested, RNA was isolated, and the RNA was subjected to RT-pPCR analysis using primers Pexo-F-3 and Pexo-R to determine the exo transcript level relative to one of the biological replicates of wild-type DK1622. Values are the averages of the results from three biological replicates, and error bars indicate one standard deviation from the mean. (B) exo transcripts earlier during development of wild-type DK1622 and the ΔdevI mutant. Samples were collected at the indicated times and analyzed as described for panel A, except the exo transcript level was determined relative to the 12-h sample of wild-type DK1622 in the same experiment. Values are the averages of the results from three biological replicates, and error bars indicate one standard deviation from the mean.
FIG 8
FIG 8
Model of the gene regulatory network governing M. xanthus sporulation. Starvation and C-signal (the product of csgA) enhance the activity of transcription factors MrpC and FruA, respectively, which exert positive regulation, indicated by black arrows, including combinatorial control of dev transcription. DevTRS are proposed to negatively autoregulate dev transcript accumulation, and DevI is proposed to strongly inhibit spore formation when overproduced in devT, devR, or devS null mutants (red lines). DevI is proposed to transiently inhibit spore formation when produced normally (as in wild-type strain DK1622) by the same mechanism as when overproduced and/or by weak negative regulation of MrpC (solid blue line) at the level of translation. DevTRS also exert weak negative regulation of MrpC, which has no apparent impact on sporulation (dashed blue line). Also dispensable for sporulation are strong and weak positive regulation of exo that appears to be mediated by DevTRS and DevI, respectively (thick and thin green arrows, respectively).

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