To kill but not be killed: a delicate balance

Pleiomorphism in Mycobacterium

Morphological variants in mycobacterial cultures under different growth conditions, including aging of the culture, have been shown to include fibrous aggregates, biofilms, coccoids, and spores. Here we discuss the diversity in shape and size changes demonstrated by bacterial cells with special reference to pleiomorphism observed in Mycobacterium spp. in response to nutritional and other environmental stresses. Inherent asymmetry in cell division and compartmentalization of cell interior under different growth conditions might contribute toward the observed pleiomorphism in mycobacteria. The regulatory genes comprising the bacterial signaling pathway responsible for initiating morphogenesis are speculated upon from bioinformatic identifications of genes for known sensors, kinases, and phosphatases existing in mycobacterial genomes as well as on the basis of what is known in other bacteria.

Time-related transcriptome analysis of B. subtilis 168 during growth with glucose

Gene expression in Bacillus subtilis from late exponential to stationary phase was monitored by DNA microarrays with samples taken from the culture in LB broth with glucose supplement to prevent sporulation. Three major patterns of gene expression as revealed in this study were consistent to the expression profiling of PerR/Spx regulons and three major sigma factors-SigA, SigB, and SigW. Expression of most SigA-dependent house-keeping genes was significantly decreased and remained at low levels in the stationary phase. The sigB gene and additional genes of the SigB regulon for stress response exhibited a distinct pattern of transient induction with a peak in transition phase. The majority of induced genes after cessation of SigB-dependent surge were subjected to regulation by SigW, PerR, and Spx in response to oxidative stress. No induction of spo0A and skfA regulons supports the suppression of sporulation and cannibalism processes in the stationary phase by glucose supplement. In summary, these results depicted complicated strategies by cells to adapt changes from the fast growing exponential phase toward the stationary phase. The absence of programmed cell death and sporulation greatly facilitated data analysis and the identification of distinct expression patterns in the stationary phase of growth in B. subtilis.

A genome-wide transcriptional profiling of sporulating Bacillus subtilis strain lacking PrpE protein phosphatase

The sporulation process is a complex genetic developmental program leading to profound changes in global gene expression profile. In this work, we have applied genome-wide microarray approach for transcriptional profiling of Bacillus subtilis strain lacking a gene coding for PrpE protein phosphatase. This protein was previously shown to be involved in the regulation of germination of B. subtilis spores. Moreover, the deletion of prpE gene resulted in changing the resistance properties of spores. Our results provide genome-wide insight into the influence of this protein phosphatase on the physiology of B. subtilis cells. Although the precise role of PrpE in shaping the observed phenotype of ΔprpE mutant strain still remains beyond the understanding, our experiments brought observations of possible indirect implication of this protein in the regulation of cell motility and chemotaxis, as well as the development of competence. Surprisingly, prpE-deleted cells showed elevated level of general stress response, which turned out to be growth medium specific.

Culture history and population heterogeneity as determinants of bacterial adaptation: the adaptomics of a single environmental transition

Diversity in adaptive responses is common within species and populations, especially when the heterogeneity of the frequently large populations found in environments is considered. By focusing on events in a single clonal population undergoing a single transition, we discuss how environmental cues and changes in growth rate initiate a multiplicity of adaptive pathways. Adaptation is a comprehensive process, and stochastic, regulatory, epigenetic, and mutational changes can contribute to fitness and overlap in timing and frequency. We identify culture history as a major determinant of both regulatory adaptations and microevolutionary change. Population history before a transition determines heterogeneities due to errors in translation, stochastic differences in regulation, the presence of aged, damaged, cheating, or dormant cells, and variations in intracellular metabolite or regulator concentrations. It matters whether bacteria come from dense, slow-growing, stressed, or structured states. Genotypic adaptations are history dependent due to variations in mutation supply, contingency gene changes, phase variation, lateral gene transfer, and genome amplifications. Phenotypic adaptations underpin genotypic changes in situations such as stress-induced mutagenesis or prophage induction or in biofilms to give a continuum of adaptive possibilities. Evolutionary selection additionally provides diverse adaptive outcomes in a single transition and generally does not result in single fitter types. The totality of heterogeneities in an adapting population increases the chance that at least some individuals meet immediate or future challenges. However, heterogeneity complicates the adaptomics of single transitions, and we propose that subpopulations will need to be integrated into future population biology and systems biology predictions of bacterial behavior.

Genome-scale genetic manipulation methods for exploring bacterial molecular biology

Bacteria are diverse and abundant, playing key roles in human health and disease, the environment, and biotechnology. Despite progress in genome sequencing and bioengineering, much remains unknown about the functional organization of prokaryotes. For instance, roughly a third of the protein-coding genes of the best-studied model bacterium, Escherichia coli, currently lack experimental annotations. Systems-level experimental approaches for investigating the functional associations of bacterial genes and genetic structures are essential for defining the fundamental molecular biology of microbes, preventing the spread of antibacterial resistance in the clinic, and driving the development of future biotechnological applications. This review highlights recently introduced large-scale genetic manipulation and screening procedures for the systematic exploration of bacterial gene functions, molecular relationships, and the global organization of bacteria at the gene, pathway, and genome levels.

Integration of σB activity into the decision-making process of sporulation initiation in Bacillus subtilis

Spo0A∼P is the master regulator of sporulation in Bacillus subtilis. Activity of Spo0A is regulated by a phosphorelay integrating multiple positive and negative signals by the action of kinases and phosphatases. The phosphatase Spo0E specifically inactivates the response regulator Spo0A∼P by dephosphorylation. We identified a σ(B)-type promoter adjacent to spo0E that is activated by the general stress response sigma factor σ(B) and is responsible for spo0E induction in vivo. Ectopic expression of σ(B) and subsequent induction of spo0E cause a σ(B)-dependent block of sporulation-specific transcription of the spo0A and spoIIE genes and produces a sporulation-deficient phenotype. This effect could be erased by a deletion of the σ(B) promoter of spo0E and thus solely addresses σ(B) activity. Here, a molecular mechanism is shown that integrates σ(B) activity into the decision-making process of sporulation and provides a link to interconnect these two dominant and probably mutually exclusive adaptive responses in the regulatory network of B. subtilis.

Adaptation in bacterial flagellar and motility systems: from regulon members to 'foraging'-like behavior in E. coli

Bacterial flagellar motility and chemotaxis help cells to reach the most favorable environments and to successfully compete with other micro-organisms in response to external stimuli. Escherichia coli is a motile gram-negative bacterium, and the flagellar regulon in E. coli is controlled by a master regulator FlhDC as well as a second regulator, flagellum-specific sigma factor, σ^F. To define the physiological role of these two regulators, we carried out transcription profiling experiments to identify, on a genome-wide basis, genes under the control of these two regulators. In addition, the synchronized pattern of increasing CRP activity causing increasing FlhDC expression with decreasing carbon source quality, together with the apparent coupling of motility activity with the activation of motility and chemotaxis genes in poor quality carbon sources, highlights the importance of CRP activation in allowing E. coli to devote progressively more of its limited reserves to search out better conditions. In adaptation to a variety of carbon sources, the motile bacteria carry out tactical responses by increasing flagellar operation but restricting costly flagellar synthesis, indicating its capability of strategically using the precious energy in nutrient-poor environments for maximizing survival.

Cannibalism and fratricide: mechanisms and raisons d'être

Cannibalism and fratricide refer to the killing of genetically identical cells (siblings) that was recently documented in two Gram-positive species, Bacillus subtilis and Streptococcus pneumoniae, respectively. Cannibalism occurs during the early stages of sporulation in B. subtilis, whereas fratricide occurs in S. pneumoniae during natural genetic transformation. Here, we compare and contrast these two phenomena and discuss whether these processes are fundamentally different from the more traditional 'chemical warfare' among bacteria.