Transposition: A CRISPR Way to Get Around

This is the author accepted manuscript. The final version is available from the publisher via the DOI in this recordCRISPR-Cas systems provide sequence-specific immunity against selfish genetic elements in prokaryotes. Now, two studies show that transposon-encoded variants can guide sequence-specific transposition. These findings have important practical implications but also raise questions of why and how this strategy would benefit transposons

Genetic information transfer promotes cooperation in bacteria

Many bacterial species are social, producing costly secreted “public good” molecules that enhance the growth of neighboring cells. The genes coding for these cooperative traits are often propagated via mobile genetic elements and can be virulence factors from a biomedical perspective. Here, we present an experimental framework that links genetic information exchange and the selection of cooperative traits. Using simulations and experiments based on a synthetic bacterial system to control public good secretion and plasmid conjugation, we demonstrate that horizontal gene transfer can favor cooperation. In a well-mixed environment, horizontal transfer brings a direct infectious advantage to any gene, regardless of its cooperation properties. However, in a structured population transfer selects specifically for cooperation by increasing the assortment among cooperative alleles. Conjugation allows cooperative alleles to overcome rarity thresholds and invade bacterial populations structured purely by stochastic dilution effects. Our results provide an explanation for the prevalence of cooperative genes on mobile elements, and suggest a previously unidentified benefit of horizontal gene transfer for bacteria

Live to cheat another day: bacterial dormancy facilitates the social exploitation of beta-lactamases

The breakdown of antibiotics by β-lactamases may be cooperative, since resistant cells can detoxify their environment and facilitate the growth of susceptible neighbours. However, previous studies of this phenomenon have used artificial bacterial vectors or engineered bacteria to increase the secretion of β-lactamases from cells. Here, we investigated whether a broad-spectrum β-lactamase gene carried by a naturally occurring plasmid (pCT) is cooperative under a range of conditions. In ordinary batch culture on solid media, there was little or no evidence that resistant bacteria could protect susceptible cells from ampicillin, although resistant colonies could locally detoxify this growth medium. However, when susceptible cells were inoculated at high densities, late-appearing phenotypically susceptible bacteria grew in the vicinity of resistant colonies. We infer that persisters, cells that have survived antibiotics by undergoing a period of dormancy, founded these satellite colonies. The number of persister colonies was positively correlated with the density of resistant colonies and increased as antibiotic concentrations decreased. We argue that detoxification can be cooperative under a limited range of conditions: if the toxins are bacteriostatic rather than bacteridical; or if susceptible cells invade communities after resistant bacteria; or if dormancy allows susceptible cells to avoid bactericides. Resistance and tolerance were previously thought to be independent solutions for surviving antibiotics. Here, we show that these are interacting strategies: the presence of bacteria adopting one solution can have substantial effects on the fitness of their neighbours

Coévolution entre mobilité des gènes et comportements sociaux chez les bactéries

Bacteria are social organisms which participate in multiple cooperative and group behaviours. They moreover have peculiar genetic systems, as they often bear mobile genetic elements like plasmids, molecular symbionts that are the cause of widespread horizontal gene transfer and play a large role in bacterial evolution. Both cooperation and horizontal transfer have consequences for human health: cooperative behaviours are very often involved in the virulence of pathogens, and horizontal gene transfer leads to the spread of antibiotic resistance. The evolution of plasmid transfer has mainly been analyzed in terms of infectious benefits for selfish mobile elements. However, chromosomal genes can also modulate horizontal transfer. A huge diversity in transfer rates is observed among bacterial isolates, suggesting a complex co-evolution between plasmids and hosts. Moreover, plasmids are enriched in genes involved in social behaviours, and so could play a key role in bacterial cooperative behaviours. We study here the coevolution of gene mobility and sociality in bacteria. To investigate the selective pressures acting on plasmid transfer and public good production, we use both mathematical modelling and a synthetic system that we constructed where we can independently control public good cooperation and plasmid conjugation in Escherichia coli. We first show experimentally that horizontal transfer allows the specific maintenance of public good alleles in a structured population by increasing relatedness at the gene-level. We further demonstrate experimentally and theoretically that this in turn allows for second-order selection of transfer ability: when cooperation is needed, alleles promoting donor and recipient abilities for public good traits can be selected both on the plasmid and on the chromosome in structured populations. Moreover, donor ability for private good traits can also be selected on the chromosome, provided that transfer happens towards kin. The interactions between transfer and cooperation can finally lead to an association between transfer and public good production alleles, explaining the high frequency of genes related to cooperation that are located on plasmids. Globally, these results provide insight into the mechanisms maintaining cooperation in bacteria, and may suggest ways to target cooperative virulence.Les bactéries sont des organismes extrêmement sociaux, qui présentent de multiples comportements de coopération. De plus, les génomes bactériens sont caractérisés par la présence de nombreux éléments génétiques mobiles, tels que les plasmides. Ces éléments mobiles sont la cause de transferts génétiques horizontaux, et jouent un rôle important dans l'évolution bactérienne. La coopération et le transfert horizontal ont tous deux des conséquences importantes sur la santé humaine: des comportements coopératifs sont souvent à l'origine de propriétés de virulence chez les bactéries pathogènes, et le transfert horizontal entraîne la dissémination de gènes de résistance aux antibiotiques. L'évolution du transfert horizontal a jusqu'ici été analysée essentiellement en termes de bénéfices infectieux apportés à des éléments génétiques égoïstes. Cependant, le taux de transfert des plasmides est extrêmement variable et partiellement contrôlé par les gènes des bactéries hôtes, suggérant une co-évolution complexe entre hôtes et plasmides. De plus, les plasmides sont particulièrement riches en gènes liés à des comportements coopératifs, et semblent donc jouer un rôle-clé dans les phénomènes de socialité bactérienne. Ce travail porte sur la coévolution entre mobilité génétique et socialité chez les bactéries. Nous analysons ici les pressions de sélection agissant sur le transfert de plasmides et la production de biens publics, à l'aide de modèles mathématiques et d'un système synthétique que nous avons construit chez Escherichia coli, dans lequel nous pouvons contrôler indépendamment la coopération et la conjugaison. Dans un premier temps, nous montrons expérimentalement que le transfert horizontal favorise le maintien de la coopération dans une population structurée, en augmentant la sélection de parentèle agissant au niveau des gènes transférés. Dans un second temps, nous montrons expérimentalement et théoriquement que l'échange génétique lui-même peut être sélectionné: les bactéries transférant des plasmides codant pour des biens publics sont favorisées dans une population structurée. Le transfert de gènes codant pour des biens privés peut également être sélectionné, à condition que ce transfert s'effectue entre bactéries apparentées. Finalement, ces interactions entre transfert horizontal et coopération peuvent mener à une association entre allèles de coopération et de transfert, expliquant la fréquence élevée de gènes sociaux situés sur des plasmides.Ces résultats permettent de mieux comprendre le maintien de comportements coopératifs chez les bactéries, et suggèrent des moyens de cibler certains cas de virulence bactérienne

Coévolution entre mobilité des gènes et comportements sociaux chez les bactéries

Les bactéries sont des organismes extrêmement sociaux, qui présentent de multiples comportements de coopération. De plus, les génomes bactériens sont caractérisés par la présence de nombreux éléments génétiques mobiles, tels que les plasmides. Ces éléments mobiles sont la cause de transferts génétiques horizontaux, et jouent un rôle important dans l'évolution bactérienne. La coopération et le transfert horizontal ont tous deux des conséquences importantes sur la santé humaine: des comportements coopératifs sont souvent à l'origine de propriétés de virulence chez les bactéries pathogènes, et le transfert horizontal entraîne la dissémination de gènes de résistance aux antibiotiques. L'évolution du transfert horizontal a jusqu'ici été analysée essentiellement en termes de bénéfices infectieux apportés à des éléments génétiques égoïstes. Cependant, le taux de transfert des plasmides est extrêmement variable et partiellement contrôlé par les gènes des bactéries hôtes, suggérant une co-évolution complexe entre hôtes et plasmides. De plus, les plasmides sont particulièrement riches en gènes liés à des comportements coopératifs, et semblent donc jouer un rôle-clé dans les phénomènes de socialité bactérienne. Ce travail porte sur la coévolution entre mobilité génétique et socialité chez les bactéries. Nous analysons ici les pressions de sélection agissant sur le transfert de plasmides et la production de biens publics, à l'aide de modèles mathématiques et d'un système synthétique que nous avons construit chez Escherichia coli, dans lequel nous pouvons contrôler indépendamment la coopération et la conjugaison. Dans un premier temps, nous montrons expérimentalement que le transfert horizontal favorise le maintien de la coopération dans une population structurée, en augmentant la sélection de parentèle agissant au niveau des gènes transférés. Dans un second temps, nous montrons expérimentalement et théoriquement que l'échange génétique lui-même peut être sélectionné: les bactéries transférant des plasmides codant pour des biens publics sont favorisées dans une population structurée. Le transfert de gènes codant pour des biens privés peut également être sélectionné, à condition que ce transfert s'effectue entre bactéries apparentées. Finalement, ces interactions entre transfert horizontal et coopération peuvent mener à une association entre allèles de coopération et de transfert, expliquant la fréquence élevée de gènes sociaux situés sur des plasmides.Ces résultats permettent de mieux comprendre le maintien de comportements coopératifs chez les bactéries, et suggèrent des moyens de cibler certains cas de virulence bactérienne.Bacteria are social organisms which participate in multiple cooperative and group behaviours. They moreover have peculiar genetic systems, as they often bear mobile genetic elements like plasmids, molecular symbionts that are the cause of widespread horizontal gene transfer and play a large role in bacterial evolution. Both cooperation and horizontal transfer have consequences for human health: cooperative behaviours are very often involved in the virulence of pathogens, and horizontal gene transfer leads to the spread of antibiotic resistance. The evolution of plasmid transfer has mainly been analyzed in terms of infectious benefits for selfish mobile elements. However, chromosomal genes can also modulate horizontal transfer. A huge diversity in transfer rates is observed among bacterial isolates, suggesting a complex co-evolution between plasmids and hosts. Moreover, plasmids are enriched in genes involved in social behaviours, and so could play a key role in bacterial cooperative behaviours. We study here the coevolution of gene mobility and sociality in bacteria. To investigate the selective pressures acting on plasmid transfer and public good production, we use both mathematical modelling and a synthetic system that we constructed where we can independently control public good cooperation and plasmid conjugation in Escherichia coli. We first show experimentally that horizontal transfer allows the specific maintenance of public good alleles in a structured population by increasing relatedness at the gene-level. We further demonstrate experimentally and theoretically that this in turn allows for second-order selection of transfer ability: when cooperation is needed, alleles promoting donor and recipient abilities for public good traits can be selected both on the plasmid and on the chromosome in structured populations. Moreover, donor ability for private good traits can also be selected on the chromosome, provided that transfer happens towards kin. The interactions between transfer and cooperation can finally lead to an association between transfer and public good production alleles, explaining the high frequency of genes related to cooperation that are located on plasmids. Globally, these results provide insight into the mechanisms maintaining cooperation in bacteria, and may suggest ways to target cooperative virulence.PARIS5-Bibliotheque electronique (751069902) / SudocSudocFranceF

data for "Indirect fitness benefits enable the spread of host genes promoting costly transfer of beneficial plasmids"

This folder contains raw data from the publication “Indirect fitness benefits enable the spread of host genes promoting costly transfer of beneficial plasmids.” <br>The excel file contains experimental data, ordered per figure. <br>Text files contain simulation data (raw data for Fig 6 and Fig S7 are in file “plasmid_linkage.txt”; raw data for Fig 4, Fig S5 and Fig S10 are in file “poisson.txt”). <br

data_procb_trakin

This file contains the data ordered by figure from the main text. All sheets except "genetic distances" contain conjugation data ordered by figure, including identity of the donor and recipient strains, densities of donor, recipient and transconjugants (CFUs per mL) obtained by selective plating, and computed conjugation rates. "genetic distances" contains a matrix of pairwise genetic distances for E. coli isolates, obtained with 3 genes or 2 genes as described in the methods

Group selection as a basis for screening mutagenized libraries of public goods (bacillus thuringiensis cry toxins)

The pesticidal toxins of Bacillus thuringiensis (Bt) supply the active proteins for genetically modified insect-resistant crops. There is therefore keen interest in finding new toxins, or improving known toxins, in order to increase the mortality of various targets. The production and screening of large libraries of mutagenized toxins are among the means of identifying improved toxins. Since Cry toxins are public goods, and do not confer advantages to producers in competition, conventional directed evolution approaches cannot be used here. Instead, thousands of individual mutants have to be sequenced and assayed individually, a costly and time-consuming process. In this study, we tested a group selection-based approach that could be used to screen an uncharacterized pool of Cry toxin mutants. This involved selecting for infectivity between subpopulations of Bt clones within metapopulations of infected insects in three rounds of passage. We also tested whether additional mutagenesis from exposure to ethyl methanesulfonate could increase infectivity or supply additional Cry toxin diversity during passage. Sequencing of pools of mutants at the end of selection showed that we could effectively screen out Cry toxin variants that had reduced toxicity with our group selection approach. The addition of extra mutagenesis during passage decreased the efficiency of selection for infectivity and did not produce any additional novel toxin diversity. Toxins with loss-of-function mutations tend to dominate mutagenized libraries, and so a process for screening out these mutants without time-consuming sequencing and characterization steps could be beneficial when applied to larger libraries. IMPORTANCE Insecticidal toxins from the bacterium Bacillus thuringiensis are widely exploited in genetically modified plants. This application creates a demand for novel insecticidal toxins that can be used to better manage resistant pests or control new or recalcitrant target species. An important means of producing novel toxins is via high-throughput mutagenesis and screening of existing toxins, a lengthy and resource-intensive process. This study describes the development and testing of an efficient means of screening a test library of mutagenized insecticidal toxins. Here, we showed that it is possible to screen out loss-of-function mutations with low infectivity within a pool without the need to characterize and sequence each mutant individually. This has the potential to improve the efficiency of processes used to identify novel proteins