Biology subjects

Bonneaud, C.

Publications and source records attributed to Bonneaud, C..

4 recordsLinked to original sources

bioRxiv2023

Evolution of the CRISPR-Cas9 defence system following a bacterial host shift

CRISPR-Cas systems are bacterial defences that target bacteriophages and mobile genetic elements. How these defences evolve in novel host environments remains, however, unknown. We studied the evolution of the CRISPR-Cas system in Mycoplasma gallisepticum, a bacterial pathogen of poultry that jumped into a passerine host [~]30 years ago. Over the decade following the host shift, all isolates displayed a functional CRISPR-Cas system were found not only to harbour completely new sets of spacers, but the DNA protospacer adjacent motif (PAM) recognised by the main effector MgCas9 was also different. These changes in CRISPR-Cas diversity and specificity are consistent with a change in the community of phages and mobile elements infecting M. gallisepticum as it colonised the novel host. In the years following the host shift, we also detected a gradual rise in isolates displaying non-functional MgCas9. After 12 years, all circulating isolates harboured inactive forms only. This loss of CRISPR-Cas function comes at a time when the passerine host is known to have evolved widespread resistance, which in turn drove the evolution of increasing M. gallisepticum virulence through antagonistic coevolution. Such striking concordance in the rise of inactivated forms of CRISPR-Cas and the evolution of host resistance suggests that inactivation of the CRISPR-Cas system was necessary for enabling adaptive bacterial responses to host-driven selection. We highlight the need to consider both host and pathogen selection pressures on bacteria for understanding the evolution of CRISPR-Cas systems and the key factors driving the emergence of a pathogenic bacterium in a novel host. Data summaryThe authors confirm all supporting data and protocols have been provided within the article or through supplementary data files available in the online version of this article. GenBank accession numbers of all publicly available M. gallisepticum genomes are listed in Table S3. Sequences of the CRISPR locus of other strains are also provided in Table S3. Impact statementMycoplasma are minimal bacteria involved in many diseases affecting humans and a wide diversity of animals. In this paper, we report the evolution of the Type II CRISPR-Cas system of the bird pathogen, Mycoplasma gallisepticum, following an host jump from its original poultry host into its novel house finch host in the early 90s. Instances in which bacterial pathogens have been documented to jump into and subsequently adapt to a new host are rare, and the well documented case of M. gallisepticum is a unique model to evaluate the effect of any dramatic host environmental change on bacterial CRISPR-Cas defence systems. First, we performed in silico analyses on an extended set of 98 M. gallisepticum genomes to better understand the evolution of the CRISPR-Cas9 system in the novel finch host. We documented several evolutionary events leading to the drastic divergence of spacer sets present in poultry and house finch arrays, as well as the progressive inactivation of the CRISPR-Cas system after 12 years in the novel finch host. Second, using in vitro and in vivo assays, we demonstrated that the evolution of the MgCas9 PI domain, involved in the protospacer adjacent motif (PAM) recognition has led to a major change in the defence system, with a modification of the recognized PAM in the novel host. Such radical change in the CRISPR-Cas defence system of M. gallisepticum may have implications for the its rapid adaptation to its novel host. Together, our results highlight the need to consider not only the host-driven selection pressures a bacterium experiences, but also the complex interplay between phages and defence systems for better understanding the key factors driving the emergence of a pathogenic bacterium in a novel host.

microbiology↗

bioRxiv2020

Sex identification in embryos and adults of Darwins finches

Darwins finches, endemic to the Galapagos and Cocos islands, are an iconic example of adaptive radiation and evolution under natural selection. Comparative genetic studies using embryos of Darwins finches have shed light on the possible evolutionary processes underlying the speciation of this clade. Molecular identification of the sex of embryonic samples is important for such studies, where this information often cannot be inferred otherwise. We tested a fast and simple chicken embryo protocol for extraction of genomic DNA on Darwins finch embryos. In addition, we suggest modifications to two of the previously reported PCR primer sets for CHD1, a gene used for sexing in adult passerine birds. The sex of all 29 tested embryos of six species of Darwins finches was determined successfully by PCR, using both primer sets. Hatchlings/nestlings and fledglings are also impossible to distinguish visually. This includes juveniles of sexually dimorphic species which are yet to moult in adult-like plumage and beak colouration. Furthermore, four species of Darwins finches are monomorphic, males and females looking alike. Therefore, sex assessment in the field can be a source of error, especially with respect to juveniles and mature monomorphic birds outside of the mating season. We caught 567 juveniles and adults belonging to six species of Darwins finches and only 44% had unambiguous sex-specific morphology. We sexed 363 birds by PCR, including individuals sexed based on marginal sex specific morphological traits (N=278) and birds which were impossible to classify in the field (N=39). For birds with marginal sex specific traits, PCR results revealed a 13% sexing error rate. This demonstrates that PCR based sexing can improve field studies on Darwins finches, especially when individuals with unclear sex-related morphology are involved. The protocols used here provide an easy and reliable way to sex Darwins finches throughout ontogeny, from embryos to adults.

molecular biology↗

bioRxiv2018

Evolution of host resistance and damage-limiting mechanisms to an emerging bacterial pathogen

Understanding how hosts minimise the cost of emerging infections has fundamental implications for epidemiological dynamics and the evolution of pathogen virulence. Despite this, few experimental studies conducted in natural populations have explicitly tested whether hosts evolve resistance, which prevents infections or reduces pathogen load through immune activation, or tolerance, which limits somatic damages without decreasing pathogen load. In addition, none have done so controlling for the virulence of the pathogen isolate used, despite critical effects on host responses to infection. Here, we conducted an experimental inoculation study to test whether eastern North American house finches (Haemorrhous mexicanus) have evolved resistance or tolerance to their emerging bacterial pathogen, Mycoplasma gallisepticum, using 55 distinct isolates of varying virulence. First, we show that peak pathogen loads, which occurred around 8 days post-inoculation, did not differ between experimentally inoculated finches from disease-exposed (eastern) versus unexposed (western) population. However, pathogen loads subsequently decreased faster and to a greater extent in finches from exposed populations, indicating that they were able to clear the infection through adaptive immune processes. Second, we found no between-population difference in the regression of clinical symptom severity on pathogen load; if tolerance had evolved then the slope of this regression is predicted to be shallower (less negative) in the exposed population. However, finches from exposed populations displayed lower symptom severity for a given pathogen load, suggesting that damage-limitation mechanisms have accompanied the evolution of immune clearance. These observations show that resistance and damage-limitation mechanisms - including, but not limited to the standard conceptualisation of tolerance - should not be seen as mutually exclusive. Nevertheless, we propose that host resistance is especially likely to evolve in response to pathogens such as M. gallisepticum that require virulence for successful infection and transmission.

evolutionary biology↗

bioRxiv2016

Characterizing Xenopus tropicalis endurance capacities with multilevel transcriptomics

Vertebrate endurance capacity is a phenotype with considerable genetic heterogeneity. RNA-Seq technologies are an ideal tool to investigate the involved genes and processes, but several challenges exist when the phenotype of interest has a complex genetic background. Difficulties manifest at the level of results interpretation because commonly used statistical methods are designed to identify strongly associated genes. If an observed phenotype can be achieved though multiple distinct genetic mechanisms then typical gene-centric methods come with the attached risk that signal may be lost or misconstrued.\n\nGene set analysis (GSA) methods are now widely accepted as a means to address some of the shortcomings of gene-by-gene analysis methods. We carry out both gene level and gene set level analyses on Xenopus tropicalis to identify the genetic factors that contribute to endurance heterogeneity. A typical workflow might consider gene level and pathway level analyses, but in this work we propose an additional focus at the intermediate level of functional modules. We generate functional modules for GSA testing in order to be explicit in how ontology information is used with respect to the functional genomics of Xenopus. Additionally, we make use of multiple assemblies to corroborate implicated genes and processes.\n\nWe identified 42 core genes, 10 functional modules, and 14 pathways based on gene expression differences between endurant and non-endurant frogs. The majority of the genes and processes are readily associated with muscle contraction or catabolism. A substantial number of these genes are involved in lipid metabolic processes, suggesting an important role in frog endurance heterogeneity. Unsurprisingly, many of the gene expression differences between endurant and non-endurant frogs can be distilled down to the capacity to utilize substrate for energy, but at the individual level frogs appear to make use of diverse machinery to achieve these differences.

bioinformatics↗