@article{avEQ5:DELAVAT:2019aab,

title = {Transient Replication in Specialized Cells Favors Transfer of an Integrative and Conjugative Element},

author = {François Delavat and Roxane Moritz and Jan Roelof van der Meer},

doi = {10.1128/mBio.01133-19},

year  = {2019},

date = {2019-01-01},

journal = {mBio},

volume = {10},

number = {3},

abstract = {Integrative and conjugative elements (ICEs) are widespread mobile DNA within bacterial genomes, whose lifestyle is relatively poorly understood. ICEs transmit vertically through donor cell chromosome replication, but in order to transfer, they have to excise from the chromosome. The excision step makes ICEs prone to loss, in case the donor cell divides and the ICE is not replicated. By adapting the system of LacI-cyan fluorescent protein (CFP) binding to lacO operator arrays, we analyze here the process of excision and transfer of the ICE for 3-chlorobenzoate degradation (ICEclc) in individual cells of the bacterium Pseudomonas putida We provide evidence that ICEclc excises exclusively in a subset of specialized transfer-competent cells. ICEclc copy numbers in transfer-competent cells were higher than in regular nontransferring cells but were reduced in mutants lacking the ICE oriT1 origin of transfer, the ICE DNA relaxase, or the excision recombination sites. Consistently, transfer-competent cells showed a higher proportion without any observable LacI-CFP foci, suggesting ICEclc loss, but this proportion was independent of the ICE relaxase or the ICE origins of transfer. Our results thus indicated that the excised ICE becomes transiently replicated in transfer-competent cells, with up to six observable copies from LacI-CFP fluorescent focus measurements. Most of the observed ICEclc transfer to ICE-free P. putida recipients occurred from donors displaying 3 to 4 ICE copies, which constitute a minority among all transfer-competent cells. This finding suggests, therefore, that replication of the excised ICEclc in donors is beneficial for transfer fitness to recipient cells.IMPORTANCE Bacterial evolution is driven to a large extent by horizontal gene transfer (HGT)-the processes that distribute genetic material between species rather than by vertical descent. The different elements and processes mediating HGT have been characterized in great molecular detail. In contrast, very little is known on adaptive features selecting HGT evolvability and fitness optimization. By studying the molecular behavior of an integrated mobile DNA of the class of integrative and conjugative elements in individual Pseudomonas putida donor bacteria, we report here how transient replication of the element after its excision from the chromosome is favorable for its transfer success. Since successful transfer into a new recipient is a measure of the element's fitness, transient replication may have been selected as an adaptive benefit for more-optimal transfer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DELAVAT20181,

title = {Rapid and efficient protocol to introduce exogenous DNA in Vibrio harveyi and Pseudoalteromonas sp.},

author = {François Delavat and Adeline Bidault and Vianney Pichereau and Christine Paillard},

url = {https://www.sciencedirect.com/science/article/pii/S0167701218306870},

doi = {https://doi.org/10.1016/j.mimet.2018.09.022},

issn = {0167-7012},

year  = {2018},

date = {2018-01-01},

journal = {Journal of Microbiological Methods},

volume = {154},

pages = {1-5},

abstract = {Vibrio campbellii BAA-1116 is renowned for its bioluminescence properties, and genetic tools are available to genetically track this strain. However, many other ecologically important V. harveyi strains exist, for which only few genetic tools are available. In this study, a rapid electroporation protocol was developed to transform replicative plasmids in various environmental V. harveyi and Pseudoalteromonas strains. Moreover, a mini-Tn7 delivery system was modified to site-specifically integrate mini-transposons in the genome of V. harveyi ORM4. As a proof-of-principle, replicative plasmids carrying bioreporters were introduced by electroporation in V. harveyi ORM4 cells, and gene expression was followed at the single cell level. We could demonstrate that a flagellar gene is subjected to bimodal gene expression in V. harveyi ORM4, being highly expressed in 10% of the population in stationary phase. This study extends the possibilities to study environmental Vibrio strains and uncovers the occurrence of phenotypic heterogeneity in flagellar expression in Vibrio.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{avEQ5:DELAVAT:2017aa,

title = {The hidden life of integrative and conjugative elements},

author = {François Delavat and Ryo Miyazaki and Nicolas Carraro and Nicolas Pradervand and Jan Roelof van der Meer},

doi = {10.1093/femsre/fux008},

year  = {2017},

date = {2017-01-01},

journal = {FEMS Microbiol Rev},

volume = {41},

number = {4},

pages = {512-537},

abstract = {Integrative and conjugative elements (ICEs) are widespread mobile DNA that transmit both vertically, in a host-integrated state, and horizontally, through excision and transfer to new recipients. Different families of ICEs have been discovered with more or less restricted host ranges, which operate by similar mechanisms but differ in regulatory networks, evolutionary origin and the types of variable genes they contribute to the host. Based on reviewing recent experimental data, we propose a general model of ICE life style that explains the transition between vertical and horizontal transmission as a result of a bistable decision in the ICE-host partnership. In the large majority of cells, the ICE remains silent and integrated, but hidden at low to very low frequencies in the population specialized host cells appear in which the ICE starts its process of horizontal transmission. This bistable process leads to host cell differentiation, ICE excision and transfer, when suitable recipients are present. The ratio of ICE bistability (i.e. ratio of horizontal to vertical transmission) is the outcome of a balance between fitness costs imposed by the ICE horizontal transmission process on the host cell, and selection for ICE distribution (i.e. ICE 'fitness'). From this emerges a picture of ICEs as elements that have adapted to a mostly confined life style within their host, but with a very effective and dynamic transfer from a subpopulation of dedicated cells.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{avEQ5:DELAVAT:2016aab,

title = {Highly variable individual donor cell fates characterize robust horizontal gene transfer of an integrative and conjugative element},

author = {François Delavat and Sara Mitri and Serge Pelet and Jan Roelof van der Meer},

doi = {10.1073/pnas.1604479113},

year  = {2016},

date = {2016-01-01},

journal = {Proc Natl Acad Sci U S A},

volume = {113},

number = {24},

pages = {E3375-83},

abstract = {Horizontal gene transfer is an important evolutionary mechanism for bacterial adaptation. However, given the typical low transfer frequencies in a bacterial population, little is known about the fate and interplay of donor cells and the mobilized DNA during transfer. Here we study transfer of an integrative and conjugative element (ICE) among individual live bacterial cells. ICEs are widely distributed mobile DNA elements that are different than plasmids because they reside silent in the host chromosome and are maintained through vertical descent. Occasionally, ICEs become active, excise, and transmit their DNA to a new recipient, where it is reintegrated. We develop a fluorescent tool to differentiate excision, transfer, and reintegration of a model ICE named ICEclc (for carrying the clc genes for chlorocatechol metabolism) among single Pseudomonas cells by using time-lapse microscopy. We find that ICEclc activation is initiated in stationary phase cells, but excision and transfer predominantly occur only when such cells have been presented with new nutrients. Donors with activated ICE develop a number of different states, characterized by reduced cell division rates or growth arrest, persistence, or lysis, concomitant with ICE excision, and likely, ICE loss or replication. The donor cell state transitions can be described by using a stochastic model, which predicts that ICE fitness is optimal at low initiation rates in stationary phase. Despite highly variable donor cell fates, ICE transfer is remarkably robust overall, with 75% success after excision. Our results help to better understand ICE behavior and shed a new light on bacterial cellular differentiation during horizontal gene transfer.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{Pradervand3971,

title = {The TetR-Type MfsR Protein of the Integrative and Conjugative Element (ICE) ICEclc Controls both a Putative Efflux System and Initiation of ICE Transfer},

author = {Nicolas Pradervand and François Delavat and Sandra Sulser and Ryo Miyazaki and Jan Roelof van der Meer},

url = {https://jb.asm.org/content/196/22/3971},

doi = {10.1128/JB.02129-14},

issn = {0021-9193},

year  = {2014},

date = {2014-01-01},

journal = {Journal of Bacteriology},

volume = {196},

number = {22},

pages = {3971--3979},

publisher = {American Society for Microbiology Journals},

abstract = {Integrative and conjugating elements (ICE) are self-transferable DNAs widely present in bacterial genomes, which often carry a variety of auxiliary genes of potential adaptive benefit. One of the model ICE is ICEclc, an element originally found in Pseudomonas knackmussii B13 and known for its propensity to provide its host with the capacity to metabolize chlorocatechols and 2-aminophenol. In this work, we studied the mechanism and target of regulation of MfsR, a TetR-type repressor previously found to exert global control on ICEclc horizontal transfer. By using a combination of ICEclc mutant and transcriptome analysis, gene reporter fusions, and DNA binding assays, we found that MfsR is a repressor of both its own expression and that of a gene cluster putatively coding for a major facilitator superfamily efflux system on ICEclc (named mfsABC). Phylogenetic analysis suggests that mfsR was originally located immediately adjacent to the efflux pump genes but became displaced from its original cis target DNA by a gene insertion. This resulted in divergence of the original bidirectional promoters into two separated individual regulatory units. Deletion of mfsABC did not result in a strong phenotype, and despite screening a large number of compounds and conditions, we were unable to define the precise current function or target of the putative efflux pump. Our data reconstruct how the separation of an ancestor mfsR-mfsABC system led to global control of ICEclc transfer by MfsR.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{pradervand2014operon,

title = {An operon of three transcriptional regulators controls horizontal gene transfer of the integrative and conjugative element ICE clc in Pseudomonas knackmussii B13},

author = {Nicolas Pradervand and Sandra Sulser and François Delavat and Ryo Miyazaki and Iker Lamas and Jan Roelof van der Meer},

url = {https://doi.org/10.1371/journal.pgen.1004441},

doi = {10.1371/journal.pgen.1004441},

year  = {2014},

date = {2014-01-01},

journal = {PLoS Genet},

volume = {10},

number = {6},

pages = {e1004441},

publisher = {Public Library of Science},

abstract = {The integrative and conjugative element ICEclc is a mobile genetic element in Pseudomonas knackmussii B13, and an experimental model for a widely distributed group of elements in Proteobacteria. ICEclc is transferred from specialized transfer competent cells, which arise at a frequency of 3-5% in a population at stationary phase. Very little is known about the different factors that control the transfer frequency of this ICE family. Here we report the discovery of a three-gene operon encoded by ICEclc, which exerts global control on transfer initiation. The operon consists of three consecutive regulatory genes, encoding a TetR-type repressor MfsR, a MarR-type regulator and a LysR-type activator TciR. We show that MfsR autoregulates expression of the operon, whereas TciR is a global activator of ICEclc gene expression, but no clear role was yet found for MarR. Deletion of mfsR increases expression of tciR and marR, causing the proportion of transfer competent cells to reach almost 100% and transfer frequencies to approach 1 per donor. mfsR deletion also caused a two orders of magnitude loss in population viability, individual cell growth arrest and loss of ICEclc. This indicates that autoregulation is an important feature maintaining ICE transfer but avoiding fitness loss. Bioinformatic analysis showed that the mfsR-marR-tciR operon is unique for ICEclc and a few highly related ICE, whereas tciR orthologues occur more widely in a large variety of suspected ICE among Proteobacteria.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{DELAVAT2013823,

title = {Yeast and bacterial diversity along a transect in an acidic, As–Fe rich environment revealed by cultural approaches},

author = {François Delavat and Marie-Claire Lett and Didier Lièvremont},

url = {https://www.sciencedirect.com/science/article/pii/S004896971300675X},

doi = {https://doi.org/10.1016/j.scitotenv.2013.06.023},

issn = {0048-9697},

year  = {2013},

date = {2013-01-01},

journal = {Science of The Total Environment},

volume = {463-464},

pages = {823-828},

abstract = {Acid mine drainages (AMDs) are often thought to harbour low biodiversity, yet little is known about the diversity distribution along the drainages. Using culture-dependent approaches, the microbial diversity from the Carnoulès AMD sediment was investigated for the first time along a transect showing progressive environmental stringency decrease. In total, 20 bacterial genera were detected, highlighting a higher bacterial diversity than previously thought. Moreover, this approach led to the discovery of 16 yeast species, demonstrating for the first time the presence of this important phylogenetic group in this AMD. All in all, the location of the microbes along the transect helps to better understand their distribution in a pollution gradient.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{delavat2012amylases,

title = {Amylases without known homologues discovered in an acid mine drainage: significance and impact},

author = {François Delavat and Vincent Phalip and Anne Forster and Frédéric Plewniak and Marie-Claire Lett and Didier Lievremont},

url = {https://doi.org/10.1038/srep00354},

doi = {https://doi.org/10.1038/srep00354},

year  = {2012},

date = {2012-01-01},

journal = {Scientific Reports},

volume = {2},

number = {1},

pages = {1--6},

publisher = {Nature Publishing Group},

abstract = {Acid Mine Drainages (AMDs) are extreme environments characterized by acidic and oligotrophic conditions and by metal contaminations. A function-based screening of an AMD-derived metagenomic library led to the discovery and partial characterization of two non-homologous endo-acting amylases sharing no sequence similarity with any known amylase nor glycosidase. None carried known amylolytic domains, nor could be assigned to any GH-family. One amylase displayed no similarity with any known protein, whereas the second one was similar to TraC proteins involved in the bacterial type IV secretion system. According to the scarce similarities with known proteins, 3D-structure modelling using I-TASSER was unsuccessful. This study underlined the utility of a function-driven metagenomic approach to obtain a clearer image of the bacterial community enzymatic landscape. More generally, this work points out that screening for microorganisms or biomolecules in a priori incongruous environments could provide unconventional and new exciting ways for bioprospecting.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{delavat2012deciphering,

title = {Deciphering the role of Paenibacillus strain Q8 in the organic matter recycling in the acid mine drainage of Carnoules},

author = {François Delavat and Vincent Phalip and Anne Forster and Marie-Claire Lett and Didier Lièvremont},

url = {https://doi.org/10.1186/1475-2859-11-16},

doi = {https://doi.org/10.1186/1475-2859-11-16},

year  = {2012},

date = {2012-01-01},

journal = {Microbial cell factories},

volume = {11},

number = {1},

pages = {1--10},

abstract = {BACKGROUD. The recycling of the organic matter is a crucial function in any environment, especially in oligotrophic environments such as Acid Mine Drainages (AMDs). Polymer-degrading bacteria might play an important role in such ecosystem, at least by releasing by-products useful for the rest of the community. In this study, physiological, molecular and biochemical experiments were performed to decipher the role of a Paenibacillus strain isolated from the sediment of Carnoulès AMD. 

 RESULTS. Even though Paenibacillus sp. strain Q8 was isolated from an oligotrophic AMD showing an acidic pH, it developed under both acidic and alkaline conditions and showed a heterotrophic metabolism based on the utilization of a broad range of organic compounds. It resisted to numerous metallic stresses, particularly high arsenite (As(III)) concentrations (> 1,800 mg/L). Q8 was also able to efficiently degrade polymers such as cellulose, xylan and starch. Function-based screening of a Q8 DNA-library allowed the detection of 15 clones with starch-degrading activity and 3 clones with xylan-degrading activity. One clone positive for starch degradation carried a single gene encoding a "protein of unknown function". Amylolytic and xylanolytic activities were measured both in growing cells and with acellular extracts of Q8. The results showed the ability of Q8 to degrade both polymers under a broad pH range and high As(III) and As(V) concentrations. Activity measurements allowed to point out the constitutive expression of the amylase genes and the mainly inducible expression of the xylanase genes. PACE demonstrated the endo-acting activity of the amylases and the exo-acting activity of the xylanases. 

 CONCLUSIONS. AMDs have been studied for years especially with regard to interactions between bacteria and the inorganic compartment hosting them. To date, no study reported the role of microorganisms in the recycling of the organic matter. The present work suggests that the strain Q8 might play an important role in the community by recycling the scarce organic matter (cellulose, hemicellulose, starch...), especially when the conditions change. Furthermore, function-based screening of a Q8 DNA library allowed to assign an amylolytic function to a gene previously unknown. AMDs could be considered as a reservoir of genes with potential biotechnological properties.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}

@article{delavat2012novel,

title = {Novel and unexpected bacterial diversity in an arsenic-rich ecosystem revealed by culture-dependent approaches},

author = {François Delavat and Marie-Claire Lett and Didier Lièvremont},

url = {https://doi.org/10.1186/1745-6150-7-28},

doi = {https://doi.org/10.1186/1745-6150-7-28},

year  = {2012},

date = {2012-01-01},

journal = {Biology Direct},

volume = {7},

number = {1},

pages = {1--14},

publisher = {BioMed Central},

abstract = {BACKGROUND 

Acid Mine Drainages (AMDs) are extreme environments characterized by very acid conditions and heavy metal contaminations. In these ecosystems, the bacterial diversity is considered to be low. Previous culture-independent approaches performed in the AMD of Carnoulès (France) confirmed this low species richness. However, very little is known about the cultured bacteria in this ecosystem. The aims of the study were firstly to apply novel culture methods in order to access to the largest cultured bacterial diversity, and secondly to better define the robustness of the community for 3 important functions: As(III) oxidation, cellulose degradation and cobalamine biosynthesis. 

 

RESULTS 

Despite the oligotrophic and acidic conditions found in AMDs, the newly designed media covered a large range of nutrient concentrations and a pH range from 3.5 to 9.8, in order to target also non-acidophilic bacteria. These approaches generated 49 isolates representing 19 genera belonging to 4 different phyla. Importantly, overall diversity gained 16 extra genera never detected in Carnoulès. Among the 19 genera, 3 were previously uncultured, one of them being novel in databases. This strategy increased the overall diversity in the Carnoulès sediment by 70% when compared with previous culture-independent approaches, as specific phylogenetic groups (e.g. the subclass Actinobacteridae or the order Rhizobiales) were only detected by culture. Cobalamin auxotrophy, cellulose degradation and As(III)-oxidation are 3 crucial functions in this ecosystem, and a previous meta- and proteo-genomic work attributed each function to only one taxon. Here, we demonstrate that other members of this community can also assume these functions, thus increasing the overall community robustness. 

 

CONCLUSIONS 

This work highlights that bacterial diversity in AMDs is much higher than previously envisaged, thus pointing out that the AMD system is functionally more robust than expected. The isolated bacteria may be part of the rare biosphere which remained previously undetected due to molecular biases. No matter their current ecological relevance, the exploration of the full diversity remains crucial to decipher the function and dynamic of any community. This work also underlines the importance to associate culture-dependent and -independent approaches to gain an integrative view of the community function.},

keywords = {},

pubstate = {published},

tppubtype = {article}

}