Lactic acid bacteria (LAB) are associated with various plant, animal, and human niches and are also present in many fermented foods and beverages. Thus, they are subjected to several stress ...conditions and have developed advanced response mechanisms to resist, adapt, and grow. This work aimed to identify the genes involved in some stress adaptation mechanisms in LAB. For this purpose, global reverse genetics was applied by screening a library of 1287
transposon mutants for mild monofactorial stresses. This library was submitted independently to heat (52°C, 30 min), ethanol (170 g.L
, 30 min), salt (NaCl 0.8 M, 24 h), acid (pH 4.5, 24 h), and oxidative (2 mM H
O
, 24 h) perturbations which trigger mild monofactorial stresses compatible with bacterial adaptation. Stress sensitivity of mutants was determined either by evaluating viability using propidium iodide (PI) staining, or by following growth inhibition through turbidity measurement. The screening for heat and ethanol stresses lead respectively to the identification of 63 and 27 genes/putative promoters whose disruption lead to an increased sensitivity. Among them, 14 genes or putative promoters were common for both stresses. For salt, acid and oxidative stresses, respectively 8, 6, and 9 genes or putative promoters were identified as essential for adaptation to these unfavorable conditions, with only three genes common to at least two stresses. Then, RT-qPCR was performed on selected stress response genes identified by mutant screenings in order to evaluate if their expression was modified in response to stresses in the parental strain. Eleven genes (membrane, transposase, chaperone, nucleotide and carbohydrate metabolism, and hypothetical protein genes) were upregulated during stress adaptation for at least two stresses. Seven genes, encoding membrane functions, were upregulated in response to a specific stress and thus could represent potential transcriptomic biomarkers. The results highlights that most of the genes identified by global reverse genetics are specifically required in response to one stress and that they are not differentially transcribed during stress in the parental strain. Most of these genes have not been characterized as stress response genes and provide new insights into the adaptation of lactic acid bacteria to their environment.
Although the composition of the gut microbiota and its symbiotic contribution to key host physiological functions are well established, little is known as yet about the bacterial factors that account ...for this symbiosis. We selected Lactobacillus casei as a model microorganism to proceed to genomewide identification of the functions required for a symbiont to establish colonization in the gut. As a result of our recent development of a transposon-mutagenesis tool that overcomes the barrier that had prevented L. casei random mutagenesis, we developed a signature-tagged mutagenesis approach combining whole-genome reverse genetics using a set of tagged transposons and in vivo screening using the rabbit ligated ileal loop model. After sequencing transposon insertion sites in 9,250 random mutants, we assembled a library of 1,110 independent mutants, all disrupted in a different gene, that provides a representative view of the L. casei genome. By determining the relative quantity of each of the 1,110 mutants before and after the in vivo challenge, we identified a core of 47 L. casei genes necessary for its establishment in the gut. They are involved in housekeeping functions, metabolism (sugar, amino acids), cell wall biogenesis, and adaptation to environment. Hence we provide what is, to our knowledge, the first global functional genomics analysis of L. casei symbiosis.
The cell surface is the primary recognition site between the bacterium and the host. An operon of three genes, LSEI_0219 (
), LSEI_0220 (
), and LSEI_0221 (
), has been previously identified as ...required for the establishment of
in the gut. The genes
and
encode a predicted two-component system (TCS) and
a predicted D-alanyl-D-alanine carboxypeptidase which is a peptidoglycan (PG) biosynthesis enzyme. We explored the functionality and the physiological role of these three genes, particularly their impact on the bacterial cell wall architecture and on the bacterial adaptation to environmental perturbations in the gut. The functionality of CwaS/R proteins as a TCS has been demonstrated by biochemical analysis. It is involved in the transcriptional regulation of several genes of the PG biosynthesis. Analysis of the muropeptides of PG in mutants allowed us to re-annotate LSEI_0221 as a putative L,D-carboxypeptidase (LdcA). The absence of this protein coincided with a decrease of two surface antigens: LSEI_0020, corresponding to p40 or msp2 whose implication in the host epithelial homeostasis has been recently studied, and LSEI_2029 which has never been functionally characterized. The inactivation of each of these three genes induces susceptibility to antimicrobial peptides (hBD1, hBD2, and CCL20), which could be the main cause of the gut establishment deficiency. Thus, this operon is necessary for the presence of two surface antigens and for a suitable cell wall architecture.
Random transposon mutagenesis followed by adequate screening methods is an unavoidable procedure to characterize genetics of bacterial adaptation to environmental changes. We have recently ...constructed a mutant library of Lactobacillus casei and we aimed to fully annotate it. However, we have observed that, for L. casei which is a difficult to lyse bacterium, methods used to identify the transposon insertion site in a few mutants (transposon rescue by restriction and recircularization or PCR-based methods) were not transposable for a larger number because they are too time-consuming and sometimes not reliable. Here, we describe a method for large-scale and reliable identification of transposon insertion sites in a L. casei mutant library of 9250 mutants. DNA extraction procedure based on silica membranes in 96-column format was optimized to obtain genomic DNA from a large number of mutants. Then reliable direct genomic sequencing was improved to fit the obtained genomic DNA extracts. Using this procedure, readable and identifiable sequences were obtained for 87% of the L. casei mutants. This method extends the applications of a library of this type, reduces the number of insertions needed to be screened, and allows selection of specific mutants from an arrayed and stored mutant library. This method is applicable to any already existing mutant library (obtained by transposon or insertional mutagenesis) and could be useful for other bacterial species, especially for highly lysis-resistant bacteria species such as lactic acid bacteria.
•Our aim was to sequence a library of 9250 mutants of L. casei•DNA extraction procedure was optimized in a 96-well plate format•Protocol was optimized for direct sequencing of gDNA by Sanger method•This method is time and cost effective•This method is applicable to any transposon library
Chez les bactéries en contact direct avec leur milieu, la transcription des gènes et la synthèse des protéines sont régulées de manière efficace à chaque changement des paramètres environnementaux ...afin de permettre la survie cellulaire. Dans le cas des bactéries commensales de l’intestin, ces régulations doivent aussi permettre les interactions symbiotiques et la colonisation dont les mécanismes moléculaires, encore peu connus, sont probablement liés, entre autres, à la surface des bactéries (molécules exposées et sécrétées…). Lactobacillus casei, bactérie commensale, possède environ 330 gènes prédits comme intervenant dans la composition et la fonctionnalité de la surface cellulaire. Afin d’avoir une vue globale de la totalité des gènes qui interviennent dans l’établissement de L. casei dans l’intestin, une approche de génétique inverse a été réalisée. Pour cela, une banque de mutants aléatoires étiquetés de L. casei par « Signature-Tagged Mutagenesis » a été créée puis annotée et réorganisée grâce au séquençage des régions d’insertion du transposon. Les mutants ont été criblés quant à leur capacité à s’établir dans l’anse iléale ligaturée de lapin et quantifiés par qPCR. Parmi les 47 gènes identifiés comme étant impliqués dans l’établissement in vivo, trois gènes en opéron codant pour un système à deux composants et une « penicillin-binding protein » ont été caractérisés. Ces trois gènes sont impliqués dans la modulation de la surface cellulaire et plus particulièrement dans la régulation des hydrolases du peptidoglycane qui sont nécessaires à la protection de la bactérie dans l’environnement intestinal.
In bacteria which are in direct contact with their environment, genes transcription and proteins synthesis are efficiently regulated at each change of environmental parameters to allow cell survival. For intestinal commensal bacteria, these regulations must also allow symbiotic interactions and colonization whose molecular mechanisms, so far little known, are probably related, among others, to the bacteria surface (molecules exposed and secreted…). Lactobacillus casei, a commensal bacterium, has about 330 predicted genes involved in the composition and functionality of the cell surface. To have a global view of the whole genes involved in the establishment of L. casei in the gut, a reverse genetics approach was performed. For that, a library of L. casei random labeled-mutants by Signature-Tagged Mutagenesis was generated then annotated and reassembled thanks to the sequencing of transposon insertion sites. Mutants were screened for their ability to establish themselves in the rabbit ligated ileal loop and quantified by qPCR. Among the 47 genes identified as involved in the in vivo establishment, three genes in an operon encoding a two-component system and a penicillin-binding protein were characterized. These three genes are involved in the cell surface modulation and particularly in the regulation of peptidoglycan hydrolases which are required for the bacteria protection in the intestinal environment.
Lactobacillus pentosus is one of the few lactic acid bacteria (LAB) species capable of surviving in olive brine, and thus desirable during table olive fermentation. We have recently generated mutants ...of the efficient strain L. pentosus C11 by transposon mutagenesis and identified five mutants unable to survive and adapt to olive brine conditions. Since biofilm formation represents one of the main bacterial strategy to survive in stressful environments, in this study, the capacity of adhesion and formation of biofilm on olive skin was investigated for this strain and five derivative mutants which are interrupted in metabolic genes (enoA1 and gpi), and in genes of unknown function (“oba” genes). Confocal microscopy together with bacteria count revealed that the sessile state represented the prevailing L. pentosus C11 life-style during table olive fermentation. The characterization of cell surface properties showed that mutants present less hydrophobic and basic properties than the wild type (WT). In fact, their ability to adhere to both abiotic (polystyrene plates) and biotic (olive skin) surfaces was lower than that of the WT. Confocal microscopy revealed that mutants adhered sparsely to the olive skin instead of building a thin, multilayer biofilm. Moreover, RT-qPCR showed that the three genes enoA1, gpi and obaC were upregulated in the olive biofilm compared to the planktonic state. Thus enoA1, gpi and “oba” genes are necessary in L. pentosus to form an organized biofilm on the olive skin.
•L. pentosus C11 prevails in sessile state during olive fermentation.•Mutants were impaired in adhesion to abiotic and biotic surfaces.•oba, enoA1 and gpi genes are required for biofilm formation on the olive skin.•Olive surface is a biotic support for L. pentosus C11 adhesion and biofilm formation.
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