Whole Genome DNA Methylation (Methylome) Analysis of an Entomopathogenic Bacterium

Background: DNA methylation is an epigenetic mechanism involved in the pathogenicity of several major bacterial pathogens. It can decrease the affinity of some transcriptional regulators to their binding site, leading to sub-populations expressing or not various genes, depending on the DNA methylation state. Dam DNA methyltransferase is widespread in Gammaproteobacteria and methylates the adenine of GATC sites. Objectives: The role of Dam was investigated in Photorhabdus luminescens during its symbiosis with a soil nematode and during its pathogenic stage in insects.Methods: SMRT sequencing (PacBio) and Bisulfite-seq were performed to identify the DNA methylation of the whole genome (methylome). In addition, RNAseq and phenotypic analysis were performed in a P. luminescens strain overexpressing Dam.Results: Dam overexpression caused a decrease in motility whereas it increased biofilm formation. While symbiosis ability of the Dam overexpressing strain was not significantly different from that of a control strain, the nemato-bacterial complex displayed an impaired pathogenicity in insect, as also observed after direct insect injection of the bacteria alone. Transcriptomic analysis revealed that the observed phenotypes were related to differences at the transcriptional level. More than 99% of the GATC sites of the genome were found methylated and DNA methylation levels did not change over growth kinetics. However, the Dam-overexpressing strain displayed more methylated GATC sites than the control and most of these sites were located in promoter regions. These sites may be involved in the observed differences in phenotypes and gene expression and provide clues to understand the involvement of Dam DNA methylation in P. luminescens life-cycle

Plastic architecture of bacterial genome revealed by comparative genomics of Photorhabdus variants

Background: The phenotypic consequences of large genomic architecture modifications within a clonal bacterial population are rarely evaluated because of the difficulties associated with using molecular approaches in a mixed population. Bacterial variants frequently arise among Photorhabdus luminescens, a nematode-symbiotic and insect-pathogenic bacterium. We therefore studied genome plasticity within Photorhabdus variants. Results: We used a combination of macrorestriction and DNA microarray experiments to perform a comparative genomic study of different P. luminescens TT01 variants. Prolonged culturing of TT01 strain and a genomic variant, collected from the laboratory-maintained symbiotic nematode, generated bacterial lineages composed of primary and secondary phenotypic variants and colonial variants. The primary phenotypic variants exhibit several characteristics that are absent from the secondary forms. We identify substantial plasticity of the genome architecture of some variants, mediated mainly by deletions in the 'flexible' gene pool of the TT01 reference genome and also by genomic amplification. We show that the primary or secondary phenotypic variant status is independent from global genomic architecture and that the bacterial lineages are genomic lineages. We focused on two unusual genomic changes: a deletion at a new recombination hotspot composed of long approximate repeats; and a 275 kilobase single block duplication belonging to a new class of genomic duplications. Conclusion: Our findings demonstrate that major genomic variations occur in Photorhabdus clonal populations. The phenotypic consequences of these genomic changes are cryptic. This study provides insight into the field of bacterial genome architecture and further elucidates the role played by clonal genomic variation in bacterial genome evolutio

Virulence and Pathogen Multiplication: A Serial Passage Experiment in the Hypervirulent Bacterial Insect-Pathogen Xenorhabdus nematophila

The trade-off hypothesis proposes that the evolution of pathogens' virulence is shaped by a link between virulence and contagiousness. This link is often assumed to come from the fact that pathogens are contagious only if they can reach high parasitic load in the infected host. In this paper we present an experimental test of the hypothesis that selection on fast replication can affect virulence. In a serial passage experiment, we selected 80 lines of the bacterial insect-pathogen Xenorhabdus nematophila to multiply fast in an artificial culture medium. This selection resulted in shortened lag phase in our selected bacteria. We then injected these bacteria into insects and observed an increase in virulence. This could be taken as a sign that virulence in Xenorhabdus is linked to fast multiplication. But we found, among the selected lineages, either no link or a positive correlation between lag duration and virulence: the most virulent bacteria were the last to start multiplying. We then surveyed phenotypes that are under the control of the flhDC super regulon, which has been shown to be involved in Xenorhabdus virulence. We found that, in one treatment, the flhDC regulon has evolved rapidly, but that the changes we observed were not connected to virulence. All together, these results indicate that virulence is, in Xenorhabdus as in many other pathogens, a multifactorial trait. Being able to grow fast is one way to be virulent. But other ways exist which renders the evolution of virulence hard to predict

The Entomopathogenic Bacterial Endosymbionts Xenorhabdus and Photorhabdus: Convergent Lifestyles from Divergent Genomes

Members of the genus Xenorhabdus are entomopathogenic bacteria that associate with nematodes. The nematode-bacteria pair infects and kills insects, with both partners contributing to insect pathogenesis and the bacteria providing nutrition to the nematode from available insect-derived nutrients. The nematode provides the bacteria with protection from predators, access to nutrients, and a mechanism of dispersal. Members of the bacterial genus Photorhabdus also associate with nematodes to kill insects, and both genera of bacteria provide similar services to their different nematode hosts through unique physiological and metabolic mechanisms. We posited that these differences would be reflected in their respective genomes. To test this, we sequenced to completion the genomes of Xenorhabdus nematophila ATCC 19061 and Xenorhabdus bovienii SS-2004. As expected, both Xenorhabdus genomes encode many anti-insecticidal compounds, commensurate with their entomopathogenic lifestyle. Despite the similarities in lifestyle between Xenorhabdus and Photorhabdus bacteria, a comparative analysis of the Xenorhabdus, Photorhabdus luminescens, and P. asymbiotica genomes suggests genomic divergence. These findings indicate that evolutionary changes shaped by symbiotic interactions can follow different routes to achieve similar end points

Caracterisation de plasmides chez Azospirillum lipoferum bacterie associee aux racines de graminees

SIGLEAvailable from INIST (FR), Document Supply Service, under shelf-number : T 78137 / INIST-CNRS - Institut de l'Information Scientifique et TechniqueFRFranc

Les nématodes entomopathogènes (NEPs)

Les nématodes entomopathogènes (NEPs). Réunion de lancement - EMB

C39 - La place de l’individu bactérien dans l’interaction tripartite entre Xenorhabdus/Photorhabdus , les nématodes et les insectes

C39 - La place de l’individu bactérien dans l’interaction tripartite entre Xenorhabdus/Photorhabdus , les nématodes et les insectes. 4. Congrès National SF

Phenotypic Noise in Entomopathogenic Bacterial Endosymbionts Xenorhabdus

Phenotypic Noise in Entomopathogenic Bacterial Endosymbionts Xenorhabdus. Epigenetic variations in population