Spatiotemporal trascriptomics of Bacillus subtilis swarming colony
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ABSTRACT: Using transcriptomics, we studied the spatiotemporal dynamics of B. subtilis swarming colonies on soft-agar surface and identified functional subpopulations.
Project description:Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviated ribosome pausing at sequences encoding tandem prolines, and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.
Project description:Translation elongation factor P (EF-P) alleviates ribosome pausing at a subset of motifs encoding consecutive proline residues and is required for growth in many organisms. Here we show that Bacillus subtilis EF-P also alleviated ribosome pausing at sequences encoding tandem prolines, and ribosomes paused within several essential genes without a corresponding growth defect in an efp mutant. The B. subtilis efp mutant is instead impaired for flagellar biosynthesis which results in the abrogation of a form of motility called swarming. We isolate swarming suppressors of efp and identify mutations in 8 genes that suppressed the efp mutant swarming defect, many of which encode conserved ribosomal proteins or ribosome-associated factors. One mutation abolished a translational pause site within the flagellar C-ring component FliY to increase flagellar number and restore swarming motility in the absence of EF-P. Our data support a model wherein EF-P-alleviation of ribosome pausing may be particularly important for macromolecular assemblies like the flagellum that require precise protein stoichiometries.
Project description:Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions.
Project description:The natural biotope of Bacillus subtilis is the upper layer of soil where it grows as a biofilm. To mimic this physiological development and study the impact of nanoparticles during the formation of a biofilm in a contaminated soil, we have studied the proteomic response of the ancestral strain Bacillus subtilis 3610, which is able to form biofilm contrary to the 168 laboratory strain. The bacteria were grown on soft agar plates containing n-ZnO, n-TiO2 or ZnSO4 metal ion.
Project description:Salmonella 14028 time course on swarming agar (0.6%) plates mRNA from 3 h time point on swarming plates used as reference for all the time course arrays Keywords: other
Project description:Transcriptome comparison of Bacillus subtilis Natto under sliding permissive (0.7% agar) and restrictive (1.5% agar or spo0A mutant strain) conditions. B subtilis Natto wild type cells were grown on the top of LB solid medium with 1.5% and 0.7% agar concentration (samples 1-4). B subtilis Natto wild type and spo0A derivative were grown on top of LB solid medium with 0.7% agar concentration (Sample 5-7). In first experiment, 4 biological replicates were used, while in the second experiment 3 biological replicates included. Dye swaps are included in both experiments.
Project description:Bacillus subtilis has been extensively used as a model for molecular studies on biofilm formation. These studies encompassed the development of complex macro-colonies on agar, the formation of pellicles at the air-liquid interface, and lately the formation of submerged architectural biofilms at the solid-liquid interface. Beside similarities, these multicellular communities also display considerable heterogeneity at the structural, chemical and biological levels. Here we use RNA-seq to analyze nine different spatio-physiological conditions, including the three biofilm populations (colony, pellicle, and submerged).
Project description:Salmonella strain 14028, time course, on non-swarming agar plates (1.5%), array were done between reference mRNA (from swarmer cells at 3 hour) and mRNA from various time points on non-swarming plates. Keywords: other
Project description:Transcriptome comparison of Bacillus subtilis 168 grown on solid agar (sample 1-3) or aerated liquid (sample 4-7) 2xSG medium with and without of 0.1 mM manganese.