Nathalie Leblond-Bourget

University of Lorraine | UdL · UMR1128 UL/INRA DynAMic

Multidrug resistance, due to acquired antimicrobial resistance genes, is increasingly reported in the zoonotic pathogen Streptococcus suis. Most of these resistance genes are carried by chromosomal Mobile Genetic Elements (MGEs), in particular, Integrative and Conjugative Elements (ICEs) and Integrative and Mobilizable Elements (IMEs). ICEs and IME...

Metagenome analyses of the human microbiome suggest that horizontal gene transfer (HGT) is frequent in these rich and complex microbial communities. However, so far, only a few HGT studies have been conducted in vivo. In this work, three different systems mimicking the physiological conditions encountered in the human digestive tract were tested, i...

Tetracycline resistance in streptococci is mainly due to ribosomal protection mediated by the tet(M) gene that is usually located in the integrative and conjugative elements (ICEs) of the Tn916-family. In this study, we analyzed the genes involved in tetracycline resistance and the associated mobile genetic elements (MGEs) in Streptococcus dysgalac...

Objectives ‘Integrative and Conjugative Elements’ (ICEs) and ‘Integrative and Mobilizable Elements’ (IMEs) are two classes of mobile genetic elements that are complex to detect and delineate. Therefore, they are yet poorly annotated in bacterial genomes. FirmiData provides to the scientific community of microbiologists and bioinformaticians a refer...

Mobile Genetic Elements (MGEs) are integrated in bacterial genomes and key elements that drive prokaryote genome evolution. Among them are Integrative and Conjugative Elements (ICEs) and Integrative Mobilizable Elements (IMEs) which are important for bacterial fitness since they frequently carry genes participating in important bacterial adaptation...

Horizontal Gene Transfer (HGT) is a powerful force generating genomic diversity in bacterial populations. HGT in Streptomyces is in large part driven by conjugation thanks to plasmids, Integrative and Conjugative elements (ICEs) and Actinomycete ICEs (AICEs). To investigate the impact of ICE and AICE conjugation on Streptomyces genome evolution, we...

Integrative and conjugative elements (ICEs) are important drivers of horizontal gene transfer in prokaryotes. They are responsible for antimicrobial resistance spread, a major current health concern. ICEs are initially processed by relaxases that recognize the binding site of oriT sequence and nick at a conserved nic site. The ICESt3/Tn916/ICEBs1 s...

Conjugative transfer is mediated by specialized type IV secretion systems (T4SSs). However, their architecture and mode of function remain poorly defined in Gram-positives. In this issue of Structure, Jäger et al. reveal an exclusive assembly of PrgL and illustrate the importance of its structural organization in pCF10 conjugative transfer.

Streptococcus suis is a zoonotic pathogen causing important economic losses in swine production. The most commonly used antibiotics in swine industry are tetracyclines, beta-lactams, and macrolides. Resistance to these antibiotics has already been observed worldwide (reaching high rates for macrolides and tetracyclines) as well as resistance to ami...

Conjugative transfer is a major threat to global health since it contributes to the spread of antibiotic resistance genes and virulence factors among commensal and pathogenic bacteria. To allow their transfer, mobile genetic elements including Integrative and Conjugative Elements (ICEs) use a specialized conjugative apparatus related to Type IV sec...

A bstract Conjugative transfer is a major threat to global health since it contributes to the spread of antibiotic resistance genes and virulence factors among commensal and pathogenic bacteria. To allow their transfer, mobile genetic elements including Integrative and Conjugative Elements (ICEs) use a specialized conjugative apparatus related to T...

Integrative mobilizable elements (IMEs) are widespread but very poorly studied integrated elements that can excise and hijack the transfer apparatus of co-resident conjugative elements to promote their own spreading. Sixty-four putative IMEs, harboring closely related mobilization and recombination modules, were found in 14 Streptococcus species an...

Streptococcus salivarius is a significant contributor to the human oral, pharyngeal and gut microbiomes that contribute to the maintenance of health. The high genomic diversity observed in this species is mainly caused by horizontal gene transfer. This work aimed to evaluate the contribution of integrative and conjugative elements (ICEs) and integr...

Background Conjugative spread of antibiotic resistance and virulence genes in bacteria constitutes an important threat to public health. Beyond the well-known conjugative plasmids, recent genome analyses have shown that integrative and conjugative elements (ICEs) are the most widespread conjugative elements, even if their transfer mechanism has bee...

The adhesion properties of 14 Streptococcus salivarius strains to mucus (HT29-MTX) and non-mucus secreting (Caco-2/TC7) human intestinal epithelial cells were investigated. Ability to adhere to these two eukaryotic cell lines greatly differs between strains. The presence of mucus played a major factor in adhesion, likely due to high adhesiveness to...

Conjugation is a key mechanism of bacterial evolution that involves mobile genetic elements. Recent findings indicated that the main actors of conjugative transfer are not the well-known conjugative or mobilizable plasmids but are the integrated elements. This paper reviews current knowledge on “integrative and mobilizable elements” (IMEs) that hav...

Integrative and conjugative elements (ICEs) are widespread chromosomal mobile genetic elements which can transfer autonomously by conjugation in bacteria. Thirteen ICEs with a conjugation module closely related to that of ICESt3 of Streptococcus thermophilus were characterized in Streptococcus salivarius by whole-genome sequencing. Sequence compari...

Recent analyses of bacterial genomes have shown that integrated elements that transfer by conjugation play an essential role in horizontal gene transfer. Among these elements, the integrative and mobilizable elements (IMEs) are known to encode their own excision and integration machinery, and to carry all the sequences or genes necessary to hijack...

Phylogenetic tree of Rel_PF02486/MobT relaxases. All the Rel_PF02486/MobT relaxases from IMEs (in black) and only one representative of each 90% protein identity cluster of MobT relaxases from ICEs (in mauve and underlined) are presented in the ML tree. Bootstrap values (BioNJ/ML) are given only when they exceed 50 for both analyses. Relaxases shar...

Phylogenetic tree of Rel_PF01719 relaxases. All the Rel_PF01719 relaxases are presented in the ML tree. Bootstrap values (BioNJ/ML) are given only when they exceed 50 for both analyses. All these relaxases share more than 40% sequence identity and therefore belong to a unique family. The TcpA family associated with each relaxase is indicated.

Phylogenetic tree of serine integrases. One representative of each 90% protein identity cluster from IMEs (in black) and one representative of each 90% protein identity cluster of serine integrases from ICEs targeting the same site as IMEs (in mauve and underlined) are presented in the ML tree. Bootstrap values (BioNJ/ML) are given only when they e...

Phylogenetic tree of Rel_PF01719-PF00910 relaxases. All the Rel_PF01719-PF00910 relaxases are presented in the ML tree. Bootstrap values (BioNJ/ML) are given only when they exceed 50 for both analyses. The relaxases sharing more than 40% sequence identity and therefore belonging to the same family are merged with brackets. These families are distin...

Phylogenetic tree of TcpA proteins. All the TcpA CPs from IMEs (in black) and one of each 90% protein identity cluster of TcpA from ICEs (in mauve and underlined) are presented in the BioNJ tree. Bootstrap values are given only when they exceed 50. The TcpA CPs sharing more than 40% sequence identity and therefore belonging to the same family are m...

Phylogenetic tree of Rel_PHA00330 relaxases. All the Rel_PHA00330 relaxases are presented in the ML tree. Bootstrap values (BioNJ/ML) are given only when they exceed 50 for both analyses. The relaxases sharing more than 40% sequence identity and therefore belonging to the same family are merged with brackets. These families are distinguished with a...

Recent genome analyses suggest that integrative and conjugative elements (ICEs) are widespread in bacterial genomes and therefore play an essential role in horizontal transfer. However, only a few of these elements are precisely characterized and correctly delineated within sequenced bacterial genomes. Even though previous analysis showed the prese...

The diversity of clinical (n=92) and oral and digestive commensal isolates (n=120) of Streptococcus salivarius was analysed by Multilocus Sequence Typing (MLST). No clustering of clinical or commensal strains can be observed in the phylogenetic tree. Selected strains (92 clinical and 46 commensal strains) were then examined for their susceptibility...

Horizontal transfer of genomic islands (GEIs), i.e. chromosomal regions encoding functions that can be advantageous for the host, plays a key role in bacterial evolution, but their mechanisms of transfer remained elusive for a long time. Recent data suggest that numerous GEIs belong to non-canonical classes of mobile genetic elements (MGEs) that ca...

The physicochemical determinants governing the temperature-dependent adhesion of Streptococcus thermophilus to abiotic surfaces are identified under physiological condition for cells lacking or not the Rgg0182 transcriptional regulator involved in their thermal adaptation. For that purpose, the wild type LMG18311 strain and Δrgg0182 mutant were ima...

Streptococcus thermophilus is an important starter strain for the production of yogurt and cheeses. The analysis of sequenced genomes of four strains of S. thermophilus indicates that they contain several genes of the rgg familly potentially encoding transcriptional regulators. Some of the Rgg proteins are known to be involved in bacterial stress a...

We identified a genetic context encoding a transcriptional regulator of the Rgg family and a small hydrophobic peptide (SHP) in nearly all streptococci and suggested that it may be involved in a new quorum-sensing mechanism, with SHP playing the role of a pheromone. Here, we provide further support for this hypothesis by constructing a phylogenetic...

Cell separation is dependent on cell wall hydrolases that cleave the peptidoglycan shared between daughter cells. In Streptococcus thermophilus, this step is performed by the Cse protein whose depletion resulted in the formation of extremely long chains of cells. Cse, a natural chimeric enzyme created by domain shuffling, carries at least two impor...

Within Streptococcus thermophilus, Cse was identified as the major cell disconnecting peptidoglycan hydrolase (PGH) and was demonstrated to be species-specific. To identify cell disconnecting PGHs encoded by other Streptococcus genomes, we explored the diversity of domains carried by Firmicutes PGHs, and especially that of enzymes involved in daugh...

Cell division is a dynamic process ending by separation of the daughter cells. This final step requires the cleavage of the murein septum synthetized during cell division. In Streptococcus thermophilus, cse plays an important role in cell separation. Cse protein contains, at its N-terminal end, a signal peptide and a putative LysM motif suggesting...

The cse gene of Streptococcus thermophilus encodes an extracytoplasmic protein involved in cell segregation. The Cse protein consists of two putative domains: a cell wall attachment LysM domain and a catalytic CHAP domain. These two domains are spaced by an interdomain linker, known as Var-Cse, previously reported to be highly divergent between two...

In Streptococcus thermophilus, the locus rggC contains a frameshift mutation and thus consists of two open reading frames (ORFs), rggC 1 and rggC 2, which encode proteins exhibiting similarity with the Rgg transcriptional regulator family. In this work, mutants showing a partial deletion of rggC 1 and rggC 2 were constructed and their response to m...

Streptococcus thermophilus is a major dairy starter used for the manufacture of yoghurt and cheese. The access to three genome sequences, comparative genomics and multilocus sequencing analyses suggests that this species recently emerged and is still undergoing a process of regressive evolution towards a specialised bacterium for growth in milk. No...

The isolation of a Streptococcus thermophilus CNRZ368 mutant displaying a long-chain phenotype allowed us to identify the cse gene (for cellular segregation). The N terminus of Cse exhibits high similarity to Streptococcus agalactiae surface immunogenic protein (SIP), while its C terminus exhibits high similarity to S. thermophilus PcsB. In CNRZ368...

During industrial processes, the dairy organism Streptococcus thermophilus is exposed to stress conditions. Its ability to survive and grow in an aerobic environment indicates that it must possess defensive mechanisms against reactive oxygen species. To identify the genes involved in oxidative stress defence, a collection of mutants was generated b...

To better understand the defense mechanism of Streptococcus thermophilus against superoxide stress, molecular analysis of 10 menadione-sensitive mutants, obtained by insertional mutagenesis, was undertaken. This analysis allowed the identification of 10 genes that, with respect to their putative functions, were classified into five categories: (i)...

Eight mutants of Streptococcus thermophilus CNRZ368 presenting a menadione-resistant phenotype were selected and the locus mutated in each mutant was identified. Among these clones, 5 were disrupted in a gene of unknown function, 2 were impaired in genes involved in cellular metabolism and the last one (the mutant 15H7) was disrupted in rgg encodin...

Streptococcus thermophilus bacteria are used as a starter in the fermentation of yogurts and many cheeses. To construct mutants of S. thermophilus CNRZ368, the use of the plasmid pGh9:ISS1 was considered. This plasmid is known to be a good tool for insertional mutagenesis in gram-positive bacteria, owing to its ability to integrate in the genome by...

Insertional mutagenesis was used to isolate clones from Streptococcus thermophilus CNRZ368 that were modified in their abilities to tolerate oxidative stress. During this process, two menadione-sensitive clones (6G4 and 18C3) were found to display abnormal cell morphologies and distorted chain topologies and were further studied. Molecular characte...

In Streptococcus thermophilus CNRZ368, two mutants of the peptidoglycan biosynthesis have been isolated and characterised. The mutation in the rodA or in the pbp2b gene results in spherical cells instead of ovoid associated with a reduction of the cell length. This altered cell morphology suggests that these genes are implicated in the control of t...

Streptococcus thermophilus CNRZ368 is an anaerobic aerotolerant bacteria and its ability to survive under aerobic growth conditions raises the question of the existence of a putative defence system against oxidative stress. Thus, survival of CNRZ368 in the presence of increasing concentrations of hydrogen peroxide was studied. Moreover, the influen...

The aerotolerance of Streptococcus thermophilus raises the question of the existence of a defence system against oxidative stress. This work, focused on the strain CNRZ368, provides evidence that such a system actually exists and characterises its inducible and adaptative character. Besides, it shows that survival depends on the physiological state...

Nhlh1 is a basic helix-loop-helix (bHLH) gene that has been implicated in mouse neurogenesis. Previous studies have shown it to be expressed in regions in which there are differentiating neurons during late embryonic and fetal development, but detailed studies of the role of Nhlh1 earlier in embryonic development have not been performed. In this pa...

Ribosomal DNA polymorphism was studied in order to demonstrate intra- and interspecies differentiation of 42 Bifidobacterium strains. DNA from these strains was digested with the endonucleases BamHI, EcoRV, HindIII and PvuII and then analysed by Southern blotting. Ribosomal patterns using a part of an rRNA 23S gene as a probe clearly differentiated...

In the last few years many attempts have been made to differentiate more than 20 Bifidobacterium species. It has been recognized that identification of bifidobacterial species is problematic because of phenetic and genetic heterogeneities. In order to contribute to our understanding of Bifidobacterium taxonomy, we studied Bifidobacterium phylogeny...

Randomly cloned fragments (in a size range 1 to 2.5 kb) of DNA from Bifidobacterium longum ATCC 15707, B. adolescentis CIP 64.59T, B. bifidum CIP 64.65 and B. animalis ATCC 25527 were used as hybridization probes to characterize strains of these species and distinguish them from closely related Bifidobacterium species. The fragments were screened f...

Total DNA from 21 collection or industrial Bifidobacterium strains was cleaved with various restriction endonucleases. Following electrophoresis, the fragments were subjected to Southern blot hybridization with a heterologous [alpha-32P]dCTP-labeled rDNA (genes coding for rRNA) 23S gene probe. The ribosomal patterns allowed all tested strains to be...

Global gene expression is dramatically altered by genomic rearrangements in Streptomyces ambofaciens RP181110. Partial genome mapping of two derivatives of strain RP181110 (strains NSA205 and NSA228) revealed rearrangements located in the unstable region of the genome (deletion in strain NSA228; deletion and amplification in strain NSA205). Compute...

Streptomyces ambofaciens RP181110 produces the macrolide antibiotic spiramycin. After treatment with ethidium bromide, 7 strains presenting an amplified sequence of DNA (ADS) were found in its progeny. These ADS were localized within the same amplifiable region of the RP181110 genome. It has been established that these amplified strains were non-pr...