- C. Francke (1)
- H.M.S. Gaballo (1)
- M. Herber (1)
- M. Kleerebezem (1)
- O.P. Kuipers (1)
- R.E. Lenski (1)
- A.J. Maris van (1)
- R. Moezelaar (1)
- W. Overkamp (1)
- N. Philippe (1)
- D.E. Rozen (1)
- D. Schneider (1)
- R.J. Siezen (1)
- J.A.G.M. Visser de (1)
- M.H. Zwietering (1)
Physiological and cell morphology adaptation of Bacillus subtilis at near-zero specific growth rates: a transcriptome analysis
Overkamp, W. ; Ercan, O. ; Herber, M. ; Maris, A.J. van; Kleerebezem, M. ; Kuipers, O.P. - \ 2015
Environmental Microbiology 17 (2015)2. - ISSN 1462-2912 - p. 346 - 363.
stationary-phase mutagenesis - limiting bacterial-growth - general stress-response - gram-positive bacteria - escherichia-coli - slow growth - stringent response - maintenance energy - continuous-culture - population heterogeneity
Nutrient scarcity is a common condition in nature, but the resulting extremely low growth rates (below 0.025 h-1) are an unexplored research area in B. subtilis. To understand microbial life in natural environments, studying the adaptation of B. subtilis to near-zero growth conditions is relevant. To this end, a chemostat modified for culturing an asporogenous B. subtilis sigF mutant strain at extremely low growth rates (also named a retentostat) was set up and biomass accumulation, culture viability, metabolite production and cell morphology were analysed. During retentostat culturing the specific growth rate decreased to a minimum of 0.00006 h-1, corresponding to a doubling time of 470 days. The energy distribution between growth- and maintenance-related processes showed that a state of near-zero growth was reached. Remarkably, a filamentous cell morphology emerged, suggesting that cell separation is impaired under near-zero growth conditions. To evaluate the corresponding molecular adaptations to extremely low specific growth, transcriptome changes were analysed. These revealed that cellular responses to near-zero growth conditions share several similarities with those of cells during the stationary phase of batch-growth. However, fundamental differences between these two non-growing states are apparent by their high viability and absence of stationary phase mutagenesis under near-zero growth conditions.
Novel SigB regulation modules of Gram-positive bacteria involve the use of complex hybrid histidine kinases
Been, M.W.H.J. de; Francke, C. ; Siezen, R.J. ; Abee, T. - \ 2011
Microbiology 157 (2011)1. - ISSN 1350-0872 - p. 3 - 12.
general stress-response - 2-component signal-transduction - bacillus-subtilis - streptomyces-coelicolor - transcription factor - energy stress - phosphatase 2c - osmotic-stress - pathway - protein
A common bacterial strategy to cope with stressful conditions is the activation of alternative sigma factors that control specific regulons enabling targeted responses. In the human pathogen Bacillus cereus, activation of the major stress-responsive sigma factor sB is controlled by a signalling route that involves the multi-sensor hybrid histidine kinase RsbK. RsbK-type kinases are not restricted to the B. cereus group, but occur in a wide variety of other bacterial species, including members of the the low-GC Gram-positive genera Geobacillus and Paenibacillus as well as the high-GC actinobacteria. Genome context and protein sequence analyses of 118 RsbK homologues revealed extreme variability in N-terminal sensory as well as C-terminal regulatory domains and suggested that RsbK-type kinases are subject to complex fine-tuning systems, including sensitization and desensitization via methylation and demethylation within the helical domain preceding the H-box. The RsbK-mediated stress-responsive sigma factor activation mechanism that has evolved in B. cereus and the other species differs markedly from the extensively studied and highly conserved RsbRST-mediated sB activation route found in Bacillus subtilis and other low-GC Gram-positive bacteria. Implications for future research on sigma factor control mechanisms are presented and current knowledge gaps are briefly discussed.
Short- and Long-Term Biomarkers for Bacterial Robustness: A Framework for Quantifying Correlations between Cellular Indicators and Adaptive Behavior
Besten, H.M.W. den; Arvind, A. ; Gaballo, H.M.S. ; Moezelaar, R. ; Zwietering, M.H. ; Abee, T. - \ 2010
PLoS One 5 (2010)10. - ISSN 1932-6203 - 10 p.
gram-positive bacteria - general stress-response - bacillus-cereus atcc-14579 - listeria-monocytogenes - hydrogen-peroxide - environmental-changes - staphylococcus-aureus - food preservation - sigma(b) regulon - salt stress
The ability of microorganisms to adapt to changing environments challenges the prediction of their history-dependent behavior. Cellular biomarkers that are quantitatively correlated to stress adaptive behavior will facilitate our ability to predict the impact of these adaptive traits. Here, we present a framework for identifying cellular biomarkers for mild stress induced enhanced microbial robustness towards lethal stresses. Several candidate-biomarkers were selected by comparing the genome-wide transcriptome profiles of our model-organism Bacillus cereus upon exposure to four mild stress conditions (mild heat, acid, salt and oxidative stress). These candidate-biomarkers—a transcriptional regulator (activating general stress responses), enzymes (removing reactive oxygen species), and chaperones and proteases (maintaining protein quality)—were quantitatively determined at transcript, protein and/or activity level upon exposure to mild heat, acid, salt and oxidative stress for various time intervals. Both unstressed and mild stress treated cells were also exposed to lethal stress conditions (severe heat, acid and oxidative stress) to quantify the robustness advantage provided by mild stress pretreatment. To evaluate whether the candidate-biomarkers could predict the robustness enhancement towards lethal stress elicited by mild stress pretreatment, the biomarker responses upon mild stress treatment were correlated to mild stress induced robustness towards lethal stress. Both short- and long-term biomarkers could be identified of which their induction levels were correlated to mild stress induced enhanced robustness towards lethal heat, acid and/or oxidative stress, respectively, and are therefore predictive cellular indicators for mild stress induced enhanced robustness. The identified biomarkers are among the most consistently induced cellular components in stress responses and ubiquitous in biology, supporting extrapolation to other microorganisms than B. cereus. Our quantitative, systematic approach provides a framework to search for these biomarkers and to evaluate their predictive quality in order to select promising biomarkers that can serve to early detect and predict adaptive traits.
Death and cannibalism in a seasonal environment facilitate bacterial coexistence
Rozen, D.E. ; Philippe, N. ; Visser, J.A.G.M. de; Lenski, R.E. ; Schneider, D. - \ 2009
Ecology Letters 12 (2009)1. - ISSN 1461-023X - p. 34 - 44.
term experimental evolution - escherichia-coli mutants - general stress-response - stationary-phase - adaptive radiation - balanced polymorphism - constant environment - microbial microcosms - prolonged starvation - niche construction
Bacterial populations can evolve and adapt to become diverse niche specialists, even in seemingly homogeneous environments. One source of this diversity arises from newly 'constructed' niches that result from the activities of the bacteria themselves. Ecotypes specialized to exploit these distinct niches can subsequently coexist via frequency-dependent interactions. Here, we describe a novel form of niche construction that is based upon differential death and cannibalism, and which evolved during 20 000 generations of experimental evolution in Escherichia coli in a seasonal environment with alternating growth and starvation. In one of 12 populations, two monophyletic ecotypes, S and L, evolved that stably coexist with one another. When grown and then starved in monoculture, the death rate of S exceeds that of L, whereas the reverse is observed in mixed cultures. As shown by experiments and numerical simulations, the competitive advantage of S cells is increased by extending the period of starvation, and this advantage results from their cannibalization of the debris of lysed L cells, which allows the S cells to increase both their growth rate and total cell density. At the molecular level, the polymorphism is associated with divergence in the activity of the alternative sigma factor RpoS, with S cells displaying no detectable activity, while L cells show increased activity relative to the ancestral genotype. Our results extend the repertoire of known cross-feeding mechanisms in microbes to include cannibalism during starvation, and confirm the central roles for niche construction and seasonality in the maintenance of microbial polymorphisms