Fimbrial phase variation: stochastic or cooperative?

Khandige, Surabhi; Møller‐Jensen, Jakob

doi:10.1007/s00294-015-0529-3

Cited by 6 publications

(1 citation statement)

References 43 publications

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“…While switching is considered a stochastic process, environmental factors such as temperature, amino acids, carbon sources, osmolarity and iron limitation can influence inversion frequencies [ 7 – 10 ]. Additionally, an alternative model where cooperation rather than stochasticity is the driving force behind the switching has been proposed recently [ 11 ]. Recent evidence of lipoprotein phase variation in Mycoplasma gallisepticum and M .…”

Section: Introductionmentioning

confidence: 99%

Genome-wide detection of conservative site-specific recombination in bacteria

et al. 2018

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The ability of clonal bacterial populations to generate genomic and phenotypic heterogeneity is thought to be of great importance for many commensal and pathogenic bacteria. One common mechanism contributing to diversity formation relies on the inversion of small genomic DNA segments in a process commonly referred to as conservative site-specific recombination. This phenomenon is known to occur in several bacterial lineages, however it remains notoriously difficult to identify due to the lack of conserved features. Here, we report an easy-to-implement method based on high-throughput paired-end sequencing for genome-wide detection of conservative site-specific recombination on a single-nucleotide level. We demonstrate the effectiveness of the method by successfully detecting several novel inversion sites in an epidemic isolate of the enteric pathogen Clostridium difficile. Using an experimental approach, we validate the inversion potential of all detected sites in C. difficile and quantify their prevalence during exponential and stationary growth in vitro. In addition, we demonstrate that the master recombinase RecV is responsible for the inversion of some but not all invertible sites. Using a fluorescent gene-reporter system, we show that at least one gene from a two-component system located next to an invertible site is expressed in an on-off mode reminiscent of phase variation. We further demonstrate the applicability of our method by mining 209 publicly available sequencing datasets and show that conservative site-specific recombination is common in the bacterial realm but appears to be absent in some lineages. Finally, we show that the gene content associated with the inversion sites is diverse and goes beyond traditionally described surface components. Overall, our method provides a robust platform for detection of conservative site-specific recombination in bacteria and opens a new avenue for global exploration of this important phenomenon.

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Section: Introductionmentioning

confidence: 99%

Genome-wide detection of conservative site-specific recombination in bacteria

et al. 2018

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(Actino)Bacterial “intelligence”: using comparative genomics to unravel the information processing capacities of microbes

Pinto

Mascher

2016

Curr Genet

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Bacterial genomes encode numerous and often sophisticated signaling devices to perceive changes in their environment and mount appropriate adaptive responses. With their help, microbes are able to orchestrate specific decision-making processes that alter the cellular behavior, but also integrate and communicate information. Moreover and beyond, some signal transducing systems also enable bacteria to remember and learn from previous stimuli to anticipate environmental changes. As recently suggested, all of these aspects indicate that bacteria do, in fact, exhibit cognition remarkably reminiscent of what we refer to as intelligent behavior, at least when referred to higher eukaryotes. In this essay, comprehensive data derived from comparative genomics analyses of microbial signal transduction systems are used to probe the concept of cognition in bacterial cells. Using a recent comprehensive analysis of over 100 actinobacterial genomes as a test case, we illustrate the different layers of the capacities of bacteria that result in cognitive and behavioral complexity as well as some form of 'bacterial intelligence'. We try to raise awareness to approach bacteria as cognitive organisms and believe that this view would enrich and open a new path in the experimental studies of bacterial signal transducing systems.

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Classical chaperone-usher (CU) adhesive fimbriome: uropathogenic Escherichia coli (UPEC) and urinary tract infections (UTIs)

Behzadi

2019

Folia Microbiol

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Fimbrial phase variation: stochastic or cooperative?

Cited by 6 publications

References 43 publications

Genome-wide detection of conservative site-specific recombination in bacteria

Genome-wide detection of conservative site-specific recombination in bacteria

(Actino)Bacterial “intelligence”: using comparative genomics to unravel the information processing capacities of microbes

Classical chaperone-usher (CU) adhesive fimbriome: uropathogenic Escherichia coli (UPEC) and urinary tract infections (UTIs)

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