Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin

Slager, Jelle; Kjos, Morten; Attaiech, Laetitia; Veening, Jan‐Willem

doi:10.1016/j.cell.2014.01.068

Cited by 223 publications

(347 citation statements)

References 70 publications

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“…The increase in gene dosage is sufficient to trigger the competent state (137). The origin-proximal location of early com genes thus constitutes a sensory mechanism that enables cells to activate competence in response to antibiotics interfering with DNA replication (137). In contrast, the SOS response mediated by HdiR and competence are antagonistic processes in S. thermophilus (138).…”

Section: The Sos Response In Lab: Dna As a Sensormentioning

confidence: 99%

“…This results in a higher copy number of genes close to the replication origin, including the comCDE operon. The increase in gene dosage is sufficient to trigger the competent state (137). The origin-proximal location of early com genes thus constitutes a sensory mechanism that enables cells to activate competence in response to antibiotics interfering with DNA replication (137).…”

Section: The Sos Response In Lab: Dna As a Sensormentioning

confidence: 99%

“…It now appears that it is caused by the chromosomal location of early competence genes. Slager et al (137) showed that antibiotics targeting DNA replication cause replication to stall while initiation of DNA replication continues. This results in a higher copy number of genes close to the replication origin, including the comCDE operon.…”

Section: The Sos Response In Lab: Dna As a Sensormentioning

confidence: 99%

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Stress Physiology of Lactic Acid Bacteria

Papadimitriou

Alegría

Bron

et al. 2016

Microbiol Mol Biol Rev

521

404

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SUMMARYLactic acid bacteria (LAB) are important starter, commensal, or pathogenic microorganisms. The stress physiology of LAB has been studied in depth for over 2 decades, fueled mostly by the technological implications of LAB robustness in the food industry. Survival of probiotic LAB in the host and the potential relatedness of LAB virulence to their stress resilience have intensified interest in the field. Thus, a wealth of information concerning stress responses exists today for strains as diverse as starter (e.g.,Lactococcus lactis), probiotic (e.g., severalLactobacillusspp.), and pathogenic (e.g.,EnterococcusandStreptococcusspp.) LAB. Here we present the state of the art for LAB stress behavior. We describe the multitude of stresses that LAB are confronted with, and we present the experimental context used to study the stress responses of LAB, focusing on adaptation, habituation, and cross-protection as well as on self-induced multistress resistance in stationary phase, biofilms, and dormancy. We also consider stress responses at the population and single-cell levels. Subsequently, we concentrate on the stress defense mechanisms that have been reported to date, grouping them according to their direct participation in preserving cell energy, defending macromolecules, and protecting the cell envelope. Stress-induced responses of probiotic LAB and commensal/pathogenic LAB are highlighted separately due to the complexity of the peculiar multistress conditions to which these bacteria are subjected in their hosts. Induction of prophages under environmental stresses is then discussed. Finally, we present systems-based strategies to characterize the “stressome” of LAB and to engineer new food-related and probiotic LAB with improved stress tolerance.

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Section: The Sos Response In Lab: Dna As a Sensormentioning

confidence: 99%

Section: The Sos Response In Lab: Dna As a Sensormentioning

confidence: 99%

Section: The Sos Response In Lab: Dna As a Sensormentioning

confidence: 99%

See 1 more Smart Citation

Stress Physiology of Lactic Acid Bacteria

Papadimitriou

Alegría

Bron

et al. 2016

Microbiol Mol Biol Rev

521

404

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“…Replication stress is defined here as the slowing of replication fork progression during DNA synthesis (Zeman and Cimprich 2014) which, in next-generation sequencing data, has been associated with a progressive, directional decrease in DNA copy number along the genome (Slager et al 2014). We therefore compared ptDNA coverage curves for each mutant line to the WT.…”

Section: U-turn-like Rearrangements Are Associated With Replication Smentioning

confidence: 99%

Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans

et al. 2015

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Failure to maintain organelle genome stability has been linked to numerous phenotypes, including variegation and cytosolic male sterility (CMS) in plants, as well as cancer and neurodegenerative diseases in mammals. Here we describe a next-generation sequencing approach that precisely maps and characterizes organelle DNA rearrangements in a single genome-wide experiment. In addition to displaying global portraits of genomic instability, it surprisingly unveiled an abundance of shortrange rearrangements in Arabidopsis thaliana and human organelles. Among these, short-range U-turn-like inversions reach 25% of total rearrangements in wild-type Arabidopsis plastids and 60% in human mitochondria. Furthermore, we show that replication stress correlates with the accumulation of this type of rearrangement, suggesting that U-turn-like rearrangements could be the outcome of a replication-dependent mechanism. We also show that U-turn-like rearrangements are mostly generated using microhomologies and are repressed in plastids by Whirly proteins WHY1 and WHY3. A synergistic interaction is also observed between the genes for the plastid DNA recombinase RECA1 and those encoding plastid Whirly proteins, and the triple mutant why1why3reca1 accumulates almost 60 times the WT levels of U-turn-like rearrangements. We thus propose that the process leading to U-turn-like rearrangements may constitute a RecA-independent mechanism to restart stalled forks. Our results reveal that short-range rearrangements, and especially U-turn-like rearrangements, are a major factor of genomic instability in organelles, and this raises the question of whether they could have been underestimated in diseases associated with mitochondrial dysfunction.

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“…[15] A recent study revealed that antibiotics targeting DNA replication activate competence in Streptococcus pneumonia, which leads to increased uptake of foreign DNA. [16] AMCRA: Center of Expertise on Antimicrobial Consumption and Resistance in Animals in Belgium Mission, objectives, and achievements AMCRA, a Belgian initiative, was launched in January 2012. From the One World, One Health perspective, AMCRA proposes guidelines to direct the entire animal industry towards responsible and reduced antibiotic use, thereby limiting the selection and spread of antibiotic-resistant bacteria (www.amcra.be).…”

Section: Transfer Of Resistance and Environmental Resistance Reservoirmentioning

confidence: 99%

Antibiotic use and resistance in animals: Belgian initiatives

Daeseleire¹,

Graef

Rasschaert³

et al. 2016

Drug Testing and Analysis

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The widespread use of antibiotics in animals is causing concerns about the growing risk for development and the spread of antibiotic-resistant bacteria. Antibiotic consumption is higher in animals than in humans as reported in a joint publication of EFSA (European Food Safety Agency), ECDC (European Centre for Disease Prevention and Control), and EMA (European Medicines Agency) using data from 2011 and 2012. Both in humans and animals, positive associations between the consumption of antibiotics and resistant bacteria are observed. Responsible use of antibiotics in humans and animals should therefore be promoted. In this paper some general aspects of antibiotic resistance such as microbiological versus clinical resistance, intrinsic versus acquired resistance, resistance mechanisms, and transfer of resistance are briefly introduced. In 2012, the Belgian Center of Expertise on Antimicrobial Consumption and Resistance in Animals (AMCRA) was founded. Its mission is to collect and analyze all data related to antibiotic use and resistance in animals in Belgium and to communicate these findings in a neutral and objective manner. One of AMCRA's 10 objectives is a 50% reduction in antibiotic consumption in veterinary medicine in Belgium by 2020. The aim of this paper is to report on the achievements of this national project. The Institute for Agricultural and Fisheries Research (ILVO, Merelbeke-Melle), in collaboration with Ghent University, is currently working on three nationally funded projects on antibiotic resistance in animal husbandry. In the first project, an in vitro model is used to study the influence of low antibiotic concentrations due to carry-over after production and usage of medicated feed on the development of resistance in the pig gut. Part of that project is to develop a quantitative risk assessment model. A second project focuses on tracking excreted antibiotics used in pig rearing and their influence on the development of antibiotic resistance in pig manure and the environment. In the last project, the relation between the use of biocides in animal husbandry and antibiotic resistance development are being studied. Copyright

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Antibiotic-Induced Replication Stress Triggers Bacterial Competence by Increasing Gene Dosage near the Origin

Cited by 223 publications

References 70 publications

Stress Physiology of Lactic Acid Bacteria

Stress Physiology of Lactic Acid Bacteria

Organelle DNA rearrangement mapping reveals U-turn-like inversions as a major source of genomic instability in Arabidopsis and humans

Antibiotic use and resistance in animals: Belgian initiatives

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