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Ankur B. Dalia - One of the best experts on this subject based on the ideXlab platform.
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prophage dependent neighbor predation fosters horizontal gene transfer by Natural Transformation
mSphere, 2020Co-Authors: Roberto C Molinaquiroz, Ankur B. Dalia, Andrew Camilli, Triana N. Dalia, Cecilia A SilvavalenzuelaAbstract:ABSTRACT Natural Transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits. Recent work has established that neighbor predation via type VI secretion systems, bacteriocins, and virulent phages plays an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of nonlysogens to enhance HGT. Through predation of nonlysogens, K139 lysogens also have a fitness advantage under these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their Natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes. IMPORTANCE Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by Natural Transformation in the waterborne pathogen Vibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of Naturally competent bacteria in their Natural environment.
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prophage dependent neighbor predation fosters horizontal gene transfer by Natural Transformation
bioRxiv, 2020Co-Authors: Roberto C Molinaquiroz, Ankur B. Dalia, Andrew Camilli, Triana N. Dalia, Cecilia A SilvavalenzuelaAbstract:ABSTRACT Natural Transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria (1) that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits (2). Recent work has established that neighbor predation via Type VI secretion systems (3), bacteriocins (4) and virulent phages (5), play an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of non-lysogens to enhance HGT. Through predation of non-lysogens, K139 lysogens also have a fitness advantage in these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their Natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes. IMPORTANCE Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by Natural Transformation in the water-borne pathogen Vibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of Naturally competent bacteria in their Natural environment.
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Diversity in Natural Transformation Frequencies and Regulation across Vibrio Species.
mBio, 2019Co-Authors: Chelsea A. Simpson, Ankur B. Dalia, Ram Podicheti, Douglas B. Rusch, Julia C. Van KesselAbstract:In Vibrio species, chitin-induced Natural Transformation enables bacteria to take up DNA from the external environment and integrate it into their genome. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in Vibrio campbellii strains DS40M4 and NBRC 15631 enables high Natural Transformation frequencies. Conversely, Transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for Transformation in V. campbellii DS40M4 or Vibrio parahaemolyticus in contrast to the established regulatory pathway in Vibrio cholerae in which quorum sensing is required to activate the competence regulator QstR. Similar to V. cholerae, expression of both QstR and TfoX is necessary for Transformation in DS40M4. There is a wide disparity in Transformation frequencies among even closely related Vibrio strains, with V. vulnificus having the lowest functional Transformation frequency. Ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in Transformation frequency in Vibrio vulnificus To explore differences in competence regulation, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. We find that Transformation capability cannot necessarily be predicted by the level of gene conservation but rather correlates with competence gene expression following TfoX induction. Thus, we have uncovered notable species- and strain-level variations in the competence gene regulation pathway across the Vibrio genus.IMPORTANCE Naturally transformable, or competent, bacteria are able to take up DNA from their environment, a key method of horizontal gene transfer for acquisition of new DNA sequences. Our research shows that Vibrio species that inhabit marine environments exhibit a wide diversity in Natural Transformation capability ranging from nontransformability to high Transformation rates in which 10% of cells measurably incorporate new DNA. We show that the role of regulatory systems controlling the expression of competence genes (e.g., quorum sensing) differs throughout both the species and strain levels. We explore Natural Transformation capabilities of Vibrio campbellii species which have been thus far uncharacterized and find novel regulation of competence. Expression of two key transcription factors, TfoX and QstR, is necessary to stimulate high levels of Transformation in Vibrio campbellii and recover low rates of Transformation in Vibrio vulnificus.
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Diversity in Natural Transformation frequencies and regulation across Vibrio species
2019Co-Authors: Chelsea A. Simpson, Ankur B. Dalia, Ram Podicheti, Douglas B. Rusch, Julia C. Van KesselAbstract:Abstract In marine Vibrio species, chitin-induced Natural Transformation enables bacteria to take up DNA from the external environment and integrate it into their genome via homologous recombination. Expression of the master competence regulator TfoX bypasses the need for chitin induction and drives expression of the genes required for competence in several Vibrio species. Here, we show that TfoX expression in two Vibrio campbellii strains, DS40M4 and NBRC 15631, enables high frequencies of Natural Transformation. Conversely, Transformation was not achieved in the model quorum-sensing strain V. campbellii BB120 (previously classified as Vibrio harveyi). Surprisingly, we find that quorum sensing is not required for Transformation in V. campbellii DS40M4. This result is in contrast to Vibrio cholerae that requires the quorum-sensing regulator HapR to activate the competence regulator QstR. However, similar to V. cholerae, QstR is necessary for Transformation in DS40M4. To investigate the difference in Transformation frequencies between BB120 and DS40M4, we used previously studied V. cholerae competence genes to inform a comparative genomics analysis coupled with transcriptomics. BB120 encodes homologs of all known competence genes, but most of these genes were not induced by ectopic expression of TfoX, which likely accounts for the non-functional Natural Transformation in this strain. Comparison of Transformation frequencies among Vibrio species indicates a wide disparity among even closely related strains, with Vibrio vulnificus having the lowest functional Transformation frequency. We show that ectopic expression of both TfoX and QstR is sufficient to produce a significant increase in Transformation frequency in Vibrio vulnificus. Significance Naturally transformable or competent bacteria are able to take up DNA from their environment, a key method of horizontal gene transfer for acquisition of new DNA sequences. Our research shows that Vibrio species that inhabit marine environments exhibit a wide diversity in Natural Transformation capability ranging from non-transformable to high Transformation rates in which 10% of cells measurably incorporate new DNA. We show that the role of regulatory systems controlling the expression of competence genes (e.g., quorum sensing) is conserved among closely related species but differs throughout the genus. Expression of two key transcription factors, TfoX and QstR, are necessary and sufficient to stimulate high levels of Transformation in Vibrio campbellii and recover low rates of Transformation in Vibrio vulnificus.
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comm is a hexameric helicase that promotes branch migration during Natural Transformation in diverse gram negative species
Nucleic Acids Research, 2018Co-Authors: Thomas M Nero, Triana N. Dalia, Joseph Cheyen Wang, David T Kysela, Matthew L Bochman, Ankur B. DaliaAbstract:Acquisition of foreign DNA by Natural Transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in Naturally competent Gram-negative bacterial species. In vivo, we found that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration. Also, ComM was particularly important for integration of tDNA with increased sequence heterology, suggesting that its activity promotes the acquisition of novel DNA sequences. In vitro, we showed that purified ComM binds ssDNA, oligomerizes into a hexameric ring, and has bidirectional helicase and branch migration activity. Based on these data, we propose a model for tDNA integration during Natural Transformation. This study provides mechanistic insight into the enigmatic steps involved in tDNA integration and uncovers the function of a protein required for this conserved mechanism of horizontal gene transfer.
Franck Bertolla - One of the best experts on this subject based on the ideXlab platform.
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Influence of DNA conformation and role of comA and recA on Natural Transformation in Ralstonia solanacearum.
Canadian journal of microbiology, 2009Co-Authors: Anne Mercier, Franck Bertolla, Eugenie Passelegue-robe, Pascal SimonetAbstract:Naturally competent bacteria such as the plant pathogen Ralstonia solanacearum are characterized by their ability to take up free DNA from their surroundings. In this study, we investigated the efficiency of various DNA types including chromosomal linear DNA and circular or linearized integrative and (or) replicative plasmids to Naturally transform R. solanacearum. To study the respective regulatory role of DNA transport and maintenance in the definite acquisition of new DNA by bacteria, the Natural Transformation frequencies were compared with those obtained when the bacterial strain was transformed by electroporation. An additional round of electroTransformation and Natural Transformation was carried out with the same set of donor DNAs and with R. solanacearum disrupted mutants that were potentially affected in competence (comA gene) and recombination (recA gene) functions. Our results confirmed the critical role of the comA gene for Natural Transformation and that of recA for recombination and, more surprisingly, for the maintenance of an autonomous plasmid in the host cell. Finally, our results showed that homologous recombination of chromosomal linear DNA fragments taken up by Natural Transformation was the most efficient way for R. solanacearum to acquire new DNA, in agreement with previous data showing competence development and Natural Transformation between R. solanacearum cells in plant tissues.
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Natural Transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred.
FEMS microbiology ecology, 2008Co-Authors: Bénédicte Coupat, Xavier Nesme, Pascal Simonet, Fanny Chaumeille-dole, Saliou Fall, Philippe Prior, Franck BertollaAbstract:Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. Reference strain GMI1000 is Naturally transformable at in vitro and also in planta conditions and thus has the ability to acquire free exogenous DNA. We tested the ubiquity and variability of Natural Transformation in the four phylotypes of this species complex using 55 strains isolated from different hosts and geographical regions. Eighty per cent of strains distributed in all the phylotypes were Naturally transformable by plasmids and/or genomic DNA. Transformability can be considered as a ubiquitous physiological trait in the R. solanacearum species complex. Transformation performed with two independent DNA donors showed that multiple integration events occurred simultaneously in two distant genomic regions. We also engineered a fourfold-resistant R. solanacearum GMI1000 mutant RS28 to evaluate the size of DNA exchanged during Natural Transformation. The results demonstrated that this bacterium was able to exchange large DNA fragments ranging from 30 to 90 kb by DNA replacement. The combination of these findings indicated that the Natural Transformation mechanism could be the main driving force of genetic diversification of the R. solanacearum species complex.
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Natural Transformation in the Ralstonia solanacearum species complex: numberand size of DNA that can be transferred
FEMS Microbiology Ecology, 2008Co-Authors: Bénédicte Coupat, Xavier Nesme, Pascal Simonet, Fanny Chaumeille-dole, Saliou Fall, Philippe Prior, Franck BertollaAbstract:Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. Reference strain GMI1000 is Naturally transformable at in vitro and also in planta conditions and thus has the ability to acquire free exogenous DNA.We tested the ubiquity and variability of Natural Transformation in the four phylotypes of this species complex using 55 strains isolated from different hosts and geographical regions. Eighty per cent of strains distributed in all the phylotypes were Naturally transformable by plasmids and/or genomic DNA. Transformability can be considered as a ubiquitous physiological trait in the R. solanacearum species complex. Transformation performed with two independent DNA donors showed that multiple integration events occurred simultaneously in two distant genomic regions. We also engineered a fourfold-resistant R. solanacearum GMI1000 mutant RS28 to evaluate the size of DNA exchanged during Natural Transformation. The results demonstrated that this bacterium was able to exchange large DNA fragments ranging from 30 to 90 kb by DNA replacement. The combination of these findings indicated that the Natural Transformation mechanism could be the main driving force of genetic diversification of the R. solanacearum species complex.
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Conditions for Natural Transformation of Ralstonia solanacearum
Applied and Environmental Microbiology, 1997Co-Authors: Franck Bertolla, Xavier Nesme, Frédérique Van Gijsegem, Pascal SimonetAbstract:The development of competence allowing Natural Transformation of Ralstonia solanacearum was found to occur during exponential growth and not in response to any excreted factors. Linear DNAs were effectively integrated by recombination requiring a minimum of 50 bp of homologous DNA. Therefore, DNA from other genera and species were ineffective.
Pascal Simonet - One of the best experts on this subject based on the ideXlab platform.
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Influence of DNA conformation and role of comA and recA on Natural Transformation in Ralstonia solanacearum.
Canadian journal of microbiology, 2009Co-Authors: Anne Mercier, Franck Bertolla, Eugenie Passelegue-robe, Pascal SimonetAbstract:Naturally competent bacteria such as the plant pathogen Ralstonia solanacearum are characterized by their ability to take up free DNA from their surroundings. In this study, we investigated the efficiency of various DNA types including chromosomal linear DNA and circular or linearized integrative and (or) replicative plasmids to Naturally transform R. solanacearum. To study the respective regulatory role of DNA transport and maintenance in the definite acquisition of new DNA by bacteria, the Natural Transformation frequencies were compared with those obtained when the bacterial strain was transformed by electroporation. An additional round of electroTransformation and Natural Transformation was carried out with the same set of donor DNAs and with R. solanacearum disrupted mutants that were potentially affected in competence (comA gene) and recombination (recA gene) functions. Our results confirmed the critical role of the comA gene for Natural Transformation and that of recA for recombination and, more surprisingly, for the maintenance of an autonomous plasmid in the host cell. Finally, our results showed that homologous recombination of chromosomal linear DNA fragments taken up by Natural Transformation was the most efficient way for R. solanacearum to acquire new DNA, in agreement with previous data showing competence development and Natural Transformation between R. solanacearum cells in plant tissues.
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Natural Transformation in the Ralstonia solanacearum species complex: number and size of DNA that can be transferred.
FEMS microbiology ecology, 2008Co-Authors: Bénédicte Coupat, Xavier Nesme, Pascal Simonet, Fanny Chaumeille-dole, Saliou Fall, Philippe Prior, Franck BertollaAbstract:Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. Reference strain GMI1000 is Naturally transformable at in vitro and also in planta conditions and thus has the ability to acquire free exogenous DNA. We tested the ubiquity and variability of Natural Transformation in the four phylotypes of this species complex using 55 strains isolated from different hosts and geographical regions. Eighty per cent of strains distributed in all the phylotypes were Naturally transformable by plasmids and/or genomic DNA. Transformability can be considered as a ubiquitous physiological trait in the R. solanacearum species complex. Transformation performed with two independent DNA donors showed that multiple integration events occurred simultaneously in two distant genomic regions. We also engineered a fourfold-resistant R. solanacearum GMI1000 mutant RS28 to evaluate the size of DNA exchanged during Natural Transformation. The results demonstrated that this bacterium was able to exchange large DNA fragments ranging from 30 to 90 kb by DNA replacement. The combination of these findings indicated that the Natural Transformation mechanism could be the main driving force of genetic diversification of the R. solanacearum species complex.
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Strategy for in situ detection of Natural Transformation-based horizontal gene transfer events
Applied and Environmental Microbiology, 2008Co-Authors: Aurora Rizzi, Pascal Simonet, Alessandra Pontiroli, Lorenzo Brusetti, Sara Borin, Claudia Sorlini, Alessandro Abruzzese, Gian Sacchi, Timothy Vogel, Marco BazzicalupoAbstract:A strategy is described that enables the in situ detection of Natural Transformation in Acinetobacter baylyi BD413 by the expression of a green fluorescent protein. Microscale detection of bacterial transformants growing on plant tissues was shown by fluorescence microscopy and indicated that cultivation-based selection of transformants on antibiotic-containing agar plates underestimates Transformation frequencies.
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Natural Transformation in the Ralstonia solanacearum species complex: numberand size of DNA that can be transferred
FEMS Microbiology Ecology, 2008Co-Authors: Bénédicte Coupat, Xavier Nesme, Pascal Simonet, Fanny Chaumeille-dole, Saliou Fall, Philippe Prior, Franck BertollaAbstract:Ralstonia solanacearum is a widely distributed phytopathogenic bacterium that is known to invade more than 200 host species, mainly in tropical areas. Reference strain GMI1000 is Naturally transformable at in vitro and also in planta conditions and thus has the ability to acquire free exogenous DNA.We tested the ubiquity and variability of Natural Transformation in the four phylotypes of this species complex using 55 strains isolated from different hosts and geographical regions. Eighty per cent of strains distributed in all the phylotypes were Naturally transformable by plasmids and/or genomic DNA. Transformability can be considered as a ubiquitous physiological trait in the R. solanacearum species complex. Transformation performed with two independent DNA donors showed that multiple integration events occurred simultaneously in two distant genomic regions. We also engineered a fourfold-resistant R. solanacearum GMI1000 mutant RS28 to evaluate the size of DNA exchanged during Natural Transformation. The results demonstrated that this bacterium was able to exchange large DNA fragments ranging from 30 to 90 kb by DNA replacement. The combination of these findings indicated that the Natural Transformation mechanism could be the main driving force of genetic diversification of the R. solanacearum species complex.
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Conditions for Natural Transformation of Ralstonia solanacearum
Applied and Environmental Microbiology, 1997Co-Authors: Franck Bertolla, Xavier Nesme, Frédérique Van Gijsegem, Pascal SimonetAbstract:The development of competence allowing Natural Transformation of Ralstonia solanacearum was found to occur during exponential growth and not in response to any excreted factors. Linear DNAs were effectively integrated by recombination requiring a minimum of 50 bp of homologous DNA. Therefore, DNA from other genera and species were ineffective.
Melanie Blokesch - One of the best experts on this subject based on the ideXlab platform.
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overexpression of the tcp gene cluster using the t7 rna polymerase promoter system and Natural Transformation mediated genetic engineering of vibrio cholerae
PLOS ONE, 2013Co-Authors: Sandrine Borgeaud, Melanie BlokeschAbstract:The human pathogen and aquatic bacterium Vibrio cholerae belongs to the group of Naturally competent bacteria. This developmental program allows the bacterium to take up free DNA from its surrounding followed by a homologous recombination event, which allows integration of the transforming DNA into the chromosome. Taking advantage of this phenomenon we genetically engineered V. cholerae using Natural Transformation and FLP recombination. More precisely, we adapted the T7 RNA polymerase/promoter system in this organism allowing expression of genes in a T7 RNA polymerase-dependent manner. We Naturally transformed V. cholerae by adding a T7-specific promoter sequence upstream the toxin-coregulated pilus (tcp) gene cluster. In a V. cholerae strain, which concomitantly produced the T7 RNA polymerase, this genetic manipulation resulted in the overexpression of downstream genes. The phenotypes of the strain were also in line with the successful production of TCP pili. This provides a proof-of-principle that the T7 RNA polymerase/promoter system is functional in V. cholerae and that genetic engineering of this organism by Natural Transformation is a straightforward and efficient approach.
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A quorum sensing-mediated switch contributes to Natural Transformation of Vibrio cholerae
Mobile genetic elements, 2012Co-Authors: Melanie BlokeschAbstract:There is a fundamental gap in our understanding of how horizontal gene transfer contributes to the enormous range of genetic variations that are observed among bacteria. The objective of our study was to better understand how the acquisition of genetic material by Natural Transformation is regulated within a population of Vibrio cholerae cells. V. cholerae is an aquatic bacterium and a facultative human pathogen. It acquires Natural competence for Transformation in response to changing environmental signals, such as the presence of chitinous surfaces, the absence of monomeric sugars and quorum sensing-linked autoinducers. The latter play a distinctive role in V. cholerae as they fine-tune a switch from the degradation of extracellular DNA toward the uptake of intact DNA strands in competence-induced cells. The link between quorum sensing and Natural competence for Transformation will be discussed. Furthermore, we speculate on the overrepresentation of Transformation-negative strains of V. cholerae in patient-derived culture collections, which might be the result of a biased sampling strategy as virulence and Natural Transformation are contrarily regulated by the quorum sensing network.
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quorum sensing contributes to Natural Transformation of vibrio cholerae in a species specific manner
Journal of Bacteriology, 2011Co-Authors: Gaia Suckow, Patrick Seitz, Melanie BlokeschAbstract:Although it is a human pathogen, Vibrio cholerae is a regular member of aquatic habitats, such as coastal regions and estuaries. Within these environments, V. cholerae often takes advantage of the abundance of zooplankton and their chitinous molts as a nutritious surface on which the bacteria can form biofilms. Chitin also induces the developmental program of Natural competence for Transformation in several species of the genus Vibrio. In this study, we show that V. cholerae does not distinguish between species-specific and non-species-specific DNA at the level of DNA uptake. This is in contrast to what has been shown for other Gram-negative bacteria, such as Neisseria gonorrhoeae and Haemophilus influenzae. However, species specificity with respect to Natural Transformation still occurs in V. cholerae. This is based on a positive correlation between quorum sensing and Natural Transformation. Using mutant-strain analysis, cross-feeding experiments, and synthetic cholera autoinducer-1 (CAI-1), we provide strong evidence that the species-specific signaling molecule CAI-1 plays a major role in Natural competence for Transformation. We suggest that CAI-1 can be considered a competence pheromone.
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genetic manipulation of vibrio cholerae by combining Natural Transformation with flp recombination
Plasmid, 2010Co-Authors: Olga De Souza Silva, Melanie BlokeschAbstract:Even though Vibrio cholerae is a well-known human pathogen, it is also a normal member of aquatic habitats. Within this environment it often forms biofilms on the chitin-containing exoskeleton of crustaceans and their molts. Chitin not only serves as nutrient source but also induces a developmental program called Natural competence. Naturally competent bacteria take up free DNA and integrate it into their genome by homologous recombination, thereby becoming Naturally transformed. In this study, we made use of the knowledge on the environmental lifestyle of V. cholerae to genetically manipulate its genome. We achieved this by combining the methods of chitin-induced Natural Transformation and Flp recombination. Using this approach, we disrupted several genes by insertion of FRT-site-flanked antibiotic-resistance cassettes. The cassettes were subsequently excised by induction of the Flp recombinase, which acts on the FRT sites. This method represents a simplified and faster alternative to standard gene deletion techniques, which often depend on bacterial conjugation and the availability of suicide vectors.
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Natural Transformation of vibrio cholerae as a tool optimizing the procedure
BMC Microbiology, 2010Co-Authors: Rasmus L Marvig, Melanie BlokeschAbstract:Background: Vibrio cholerae gains Natural competence upon growth on chitin. This allows the organism to take up free DNA from the environment and to incorporate it into its genome by homologous recombination. Results: Making use of this developmental program in order to use it as a tool to genetically manipulate V. cholerae and potentially also others Vibrio species was envisaged. Therefore, we re-investigated the experimental design for Natural Transformation of V. cholerae and tested different donor DNA fragments with respect to their source (genomic versus PCR-derived), quantity, and homologous flanking regions. Furthermore, we simplified the procedure in terms of the chitin source used as inducer of Natural competence and the composition of the growth medium. Conclusions: The current study allows us to recommend a standard protocol to genetically manipulate V. cholerae using commercially available sources of chitin and minimal medium, respectively, as well as PCR-derived donor DNA as transforming material.
Triana N. Dalia - One of the best experts on this subject based on the ideXlab platform.
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prophage dependent neighbor predation fosters horizontal gene transfer by Natural Transformation
mSphere, 2020Co-Authors: Roberto C Molinaquiroz, Ankur B. Dalia, Andrew Camilli, Triana N. Dalia, Cecilia A SilvavalenzuelaAbstract:ABSTRACT Natural Transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits. Recent work has established that neighbor predation via type VI secretion systems, bacteriocins, and virulent phages plays an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of nonlysogens to enhance HGT. Through predation of nonlysogens, K139 lysogens also have a fitness advantage under these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their Natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes. IMPORTANCE Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by Natural Transformation in the waterborne pathogen Vibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of Naturally competent bacteria in their Natural environment.
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prophage dependent neighbor predation fosters horizontal gene transfer by Natural Transformation
bioRxiv, 2020Co-Authors: Roberto C Molinaquiroz, Ankur B. Dalia, Andrew Camilli, Triana N. Dalia, Cecilia A SilvavalenzuelaAbstract:ABSTRACT Natural Transformation is a broadly conserved mechanism of horizontal gene transfer (HGT) in bacteria (1) that can shape their evolution through the acquisition of genes that promote virulence, antibiotic resistance, and other traits (2). Recent work has established that neighbor predation via Type VI secretion systems (3), bacteriocins (4) and virulent phages (5), play an important role in promoting HGT. Here, we demonstrate that in chitin estuary microcosms, Vibrio cholerae K139 lysogens exhibit prophage-dependent neighbor predation of non-lysogens to enhance HGT. Through predation of non-lysogens, K139 lysogens also have a fitness advantage in these microcosm conditions. The ecological strategy revealed by our work provides a better understanding of the evolutionary mechanisms used by bacteria to adapt in their Natural setting and contributes to our understanding of the selective pressures that may drive prophage maintenance in bacterial genomes. IMPORTANCE Prophages are nearly ubiquitous in bacterial species. These integrated phage elements have previously been implicated in horizontal gene transfer (HGT) largely through their ability to carry out transduction (generalized or specialized). Here, we show that prophage-encoded viral particles promote neighbor predation leading to enhanced HGT by Natural Transformation in the water-borne pathogen Vibrio cholerae. Our findings contribute to a comprehensive understanding of the dynamic forces involved in prophage maintenance which ultimately drive the evolution of Naturally competent bacteria in their Natural environment.
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comm is a hexameric helicase that promotes branch migration during Natural Transformation in diverse gram negative species
Nucleic Acids Research, 2018Co-Authors: Thomas M Nero, Triana N. Dalia, Joseph Cheyen Wang, David T Kysela, Matthew L Bochman, Ankur B. DaliaAbstract:Acquisition of foreign DNA by Natural Transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in Naturally competent Gram-negative bacterial species. In vivo, we found that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration. Also, ComM was particularly important for integration of tDNA with increased sequence heterology, suggesting that its activity promotes the acquisition of novel DNA sequences. In vitro, we showed that purified ComM binds ssDNA, oligomerizes into a hexameric ring, and has bidirectional helicase and branch migration activity. Based on these data, we propose a model for tDNA integration during Natural Transformation. This study provides mechanistic insight into the enigmatic steps involved in tDNA integration and uncovers the function of a protein required for this conserved mechanism of horizontal gene transfer.
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retraction of dna bound type iv competence pili initiates dna uptake during Natural Transformation in vibrio cholerae
Nature microbiology, 2018Co-Authors: Courtney K Ellison, Triana N. Dalia, Joseph Cheyen Wang, Alfredo Vidal Ceballos, Nicolas Biais, Yves V Brun, Ankur B. DaliaAbstract:Natural Transformation is a broadly conserved mechanism of horizontal gene transfer in bacterial species that can shape evolution and foster the spread of antibiotic resistance determinants, promote antigenic variation and lead to the acquisition of novel virulence factors. Surface appendages called competence pili promote DNA uptake during the first step of Natural Transformation1; however, their mechanism of action has remained unclear owing to an absence of methods to visualize these structures in live cells. Here, using the model Naturally transformable species Vibrio cholerae and a pilus-labelling method, we define the mechanism for type IV competence pilus-mediated DNA uptake during Natural Transformation. First, we show that type IV competence pili bind to extracellular double-stranded DNA via their tip and demonstrate that this binding is critical for DNA uptake. Next, we show that type IV competence pili are dynamic structures and that pilus retraction brings tip-bound DNA to the cell surface. Finally, we show that pilus retraction is spatiotemporally coupled to DNA internalization and that sterically obstructing pilus retraction prevents DNA uptake. Together, these results indicate that type IV competence pili directly bind to DNA via their tip and mediate DNA internalization through retraction during this conserved mechanism of horizontal gene transfer. Live-cell imaging reveals that type IV competence pili from Naturally competent Vibrio cholerae are dynamic structures that bind to exogenous DNA via their tips. Pilus retraction pulls DNA to the cell surface and across the outer membrane to initiate DNA uptake.
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comm is a hexameric helicase that promotes branch migration during Natural Transformation in diverse gram negative species
bioRxiv, 2017Co-Authors: Thomas M Nero, Triana N. Dalia, Joseph Cheyen Wang, David T Kysela, Matthew L Bochman, Ankur B. DaliaAbstract:Acquisition of foreign DNA by Natural Transformation is an important mechanism of adaptation and evolution in diverse microbial species. Here, we characterize the mechanism of ComM, a broadly conserved AAA+ protein previously implicated in homologous recombination of transforming DNA (tDNA) in Naturally competent Gram-negative bacterial species. In vivo, we find that ComM was required for efficient comigration of linked genetic markers in Vibrio cholerae and Acinetobacter baylyi, which is consistent with a role in branch migration. Also, ComM was particularly important for integration of tDNA with increased sequence heterology, suggesting that this branch migration promotes the acquisition of novel DNA sequences. In vitro, we show that purified ComM binds ssDNA, oligomerizes into a hexameric ring, and has 5′ to 3′ helicase activity. Based on these data, we propose a model for tDNA integration during Natural Transformation. This study provides mechanistic insight into the enigmatic steps involved in tDNA integration and uncovers the function of a protein required for this conserved mechanism of horizontal gene transfer.
