Low Efficiency of Homology-Facilitated Illegitimate Recombination during Conjugation in Escherichia coli

Amarir-Bouhram, Jihane; Goin, Mélodie; Petit, Marie‐Agnès

doi:10.1371/journal.pone.0028876

Cited by 9 publications

(8 citation statements)

References 17 publications

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“…Sak4 being similar to the central domain of RecA, we asked whether Sak4 could complete cross-over recombination in vivo , in a recombination conjugation assay. For this, a CmR suicide plasmid pJA3 (Amarir-Bouhram et al, 2011 ) was used, which depends for its replication and conjugation on genes introduced into the chromosome of the donor strain MFD pir (Ferrières et al, 2010 ). Upon conjugation with a recipient strain devoid of the pir plasmid replication protein, the only way for the cat gene to be maintained is to recombine by single or double cross-over with the lacZ gene of the recipient, as pJA3 contains two 1 kb regions spanning the 5′ and 3′ end of lacZ and flanking the cat gene (Supplementary Figure S8 ).…”

Section: Resultsmentioning

confidence: 99%

“…Conjugations were performed between the MAC1628 donor strain containing the pJA3 plasmid (Amarir-Bouhram et al, 2011 ) and various recipient strains corresponding to MG1655 recA mutant strains containing L-arabinose inducible genes on pKD46 derivative plasmids (see Supplementary Tables S1 , S4 ). Expression of these genes was induced by adding 0.2% of L-arabinose in exponentially growing cultures (OD 600nm = 0.1) of the recipient strains in LB medium at 30°C for 1 h. Recipient cells (1 mL, OD 600nm = 0.4) were then mixed with exponentially growing culture of the donor strain (OD 600nm = 0.4) using a ratio of 2 recipient cells per donor cell.…”

Section: Methodsmentioning

confidence: 99%

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Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein

et al. 2018

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Bacteriophages are remarkable for the wide diversity of proteins they encode to perform DNA replication and homologous recombination. Looking back at these ancestral forms of life may help understanding how similar proteins work in more sophisticated organisms. For instance, the Sak4 family is composed of proteins similar to the archaeal RadB protein, a Rad51 paralog. We have previously shown that Sak4 allowed single-strand annealing in vivo, but only weakly compared to the phage λ Redβ protein, highlighting putatively that Sak4 requires partners to be efficient. Here, we report that the purified Sak4 of phage HK620 infecting Escherichia coli is a poorly efficient annealase on its own. A distant homolog of SSB, which gene is usually next to the sak4 gene in various species of phages, highly stimulates its recombineering activity in vivo. In vitro, Sak4 binds single-stranded DNA and performs single-strand annealing in an ATP-dependent way. Remarkably, the single-strand annealing activity of Sak4 is stimulated by its cognate SSB. The last six C-terminal amino acids of this SSB are essential for the binding of Sak4 to SSB-covered single-stranded DNA, as well as for the stimulation of its annealase activity. Finally, expression of sak4 and ssb from HK620 can promote low-level of recombination in vivo, though Sak4 and its SSB are unable to promote strand exchange in vitro. Regarding its homology with RecA, Sak4 could represent a link between two previously distinct types of recombinases, i.e., annealases that help strand exchange proteins and strand exchange proteins themselves.

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Section: Resultsmentioning

confidence: 99%

Section: Methodsmentioning

confidence: 99%

Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein

et al. 2018

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“…However, sexual isolation can impact the creation of ecological divergence by limiting the opportunities for HGT. This is because bacteria are much more likely to acquire genes through HGT from close relatives, both because lower sequence divergence will foster homology-facilitated illegitimate recombination (117) and because closer relatives are more likely to share habitats (109).…”

Section: The Genetic Basis Of Early Diversificationmentioning

confidence: 99%

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

Cohan

2019

Microbial Transmission

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Any two lineages, no matter how distant they are now, began their divergence as one population splitting into two lineages that could coexist indefinitely. The rate of origin of higher-level taxa is therefore the product of the rate of speciation times the probability that two new species coexist long enough to reach a particular level of divergence. Here I have explored these two parameters of disparification in bacteria. Owing to low recombination rates, sexual isolation is not a necessary milestone of bacterial speciation. Rather, irreversible and indefinite divergence begins with ecological diversification, that is, transmission of a bacterial lineage to a new ecological niche, possibly to a new microhabitat but at least to new resources. Several algorithms use sequence data from a taxon of focus to identify phylogenetic groups likely to bear the dynamic properties of species. Identifying these newly divergent lineages allows us to characterize the genetic bases of speciation, as well as the ecological dimensions upon which new species diverge. Speciation appears to be least frequent when a given lineage has few new resources it can adopt, as exemplified by photoautotrophs, C1 heterotrophs, and obligately intracellular pathogens; speciation is likely most rapid for generalist heterotrophs. The genetic basis of ecological divergence may determine whether ecological divergence is irreversible and whether lineages will diverge indefinitely into the future. Long-term coexistence is most likely when newly divergent lineages utilize at least some resources not shared with the other and when the resources themselves will coexist into the remote future.

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“…It has been shown experimentally that V. cholerae can maintain R-plasmids received via conjugative transfer from V. anguillarum [56], indicating that V. cholerae and V. anguillarum have the potential to share DNA. While R-plasmids have a broad host range, it is interesting to note that V. cholerae cannot stably maintain R-plasmids received from Enterobacteraceae [56].…”

Section: Discussionmentioning

confidence: 99%

PandemicVibrio choleraeAcquired Competitive Traits from an EnvironmentalVibrioSpecies

Santoriello

Boucher

et al. 2021

Preprint

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Background: Vibrio cholerae, the causative agent of cholera, is a human pathogen that thrives in estuarine environments. V. cholerae competes with neighboring microbes by the contact-dependent translocation of toxic effectors with the type VI secretion system (T6SS). Effector types are highly variable across V. cholerae strains, but all pandemic isolates encode the same set of distinct effectors. It is possible that acquisition of these effectors via horizontal gene transfer played a role in the development of pandemic V. cholerae. Results: We assessed the distribution of V. cholerae T6SS loci across multiple Vibrio species. We showed that the fish-pathogen V. anguillarum encodes all three V. cholerae core loci as well as two of the four additional auxiliary clusters. We further demonstrated that V. anguillarum shares T6SS effectors with V. cholerae, including every pandemic-associated V. cholerae effector. We identified a novel T6SS cluster (Accessory Aux1) that is widespread in V. anguillarum and encodes the pandemic V. cholerae effector TseL. We highlighted potential gene transfer events of Accessory Aux1 from V. anguillarum to V. cholerae. Finally, we showed that TseL from V. cholerae can be neutralized by the V. anguillarum Accessory Aux1 immunity protein and vice versa, indicating V. anguillarum as the donor of tseL to the V. cholerae species. Conclusions: V. anguillarum constitutes an environmental reservoir of pandemic-associated V. cholerae T6SS effectors. V. anguillarum and V. cholerae likely share an environmental niche, compete, and exchange T6SS effectors. Further, our findings highlight the fish as a potential reservoir of pandemic V. cholerae.

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Low Efficiency of Homology-Facilitated Illegitimate Recombination during Conjugation in Escherichia coli

Cited by 9 publications

References 17 publications

Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein

Sak4 of Phage HK620 Is a RecA Remote Homolog With Single-Strand Annealing Activity Stimulated by Its Cognate SSB Protein

Transmission in the Origins of Bacterial Diversity, From Ecotypes to Phyla

PandemicVibrio choleraeAcquired Competitive Traits from an EnvironmentalVibrioSpecies

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