Genomic conflicts are major drivers of evolutionary innovation and play an increasingly recognized role in human disease. Intra-genomic conflicts arise because self-promoting elements such as driving centromeres or transposable elements (TEs) can spread in a population without increasing the fitness of their carriers. Inter-genomic conflicts arise when genes have opposite fitness effects in different carriers, as is the case for genes underlying traits with distinct optimal values in males and females. Here I propose to use asexual species as a novel system to studying intra- and inter-genomic conflicts. Because there is no recombination or segregation under asexual reproduction, intra-genomic conflict disappears as the interests of all genetic elements become aligned with those of their host. This allows us to test the predictions that intra-genomic conflict drives the evolution of TE virulence, centromeres, and centromere-binding proteins. Furthermore, because asexual species are comprised of only females, male phenotypes are no longer under selection and sexual conflict over optimal trait values therefore disappears. This proposal leverages the replicated loss of conflicts in independently evolved asexual lineages of Timema stick insects to identify conflict driven aspects of genomic and phenotypic evolution in sexual species. Because Timema have an XX:XO sex determination system, males can be recovered from asexual lineages via X-chromosome losses. This allows for the study of male reproductive traits, sexual dimorphism and sex-biased gene expression in species where selection has been acting solely on females for prolonged time periods, and for the identification of traits and biological processes subject to sexual conflict. By combining phenotypic, experimental and next-generation sequencing approaches, we will generate a cohesive understanding of how intra- and inter-genomic conflict shape phenotype and genome evolution.

Plants are sessile photosynthetic organisms, which adapt their growth and development according to their light environment. The reduction in red/far-red ratio (low R/FR), caused by absorption of red light and reflection of far-red radiation by canopy leaves, signals the proximity of neighboring plants and triggers the shade avoidance syndrome (SAS). The SAS consists in large changes in plant body form, in particular rapid elongation of selected organs providing enhanced access to sunlight. Shade-induced elongation is triggered by a rapid and transient burst in the production of the phyto-hormone auxin (IAA). However, elongation growth persists way beyond the initial increase in IAA levels and it is currently not understood how this initial signal leads to long-term growth. This project aims to identify epigenetic reprogramming events caused by reduction in R/FR and the pulse of IAA production, to allow a rapid and persistent growth response in Arabidopsis thaliana. The chromatin state of shade-grown seedlings will be analyzed by combining two novel approaches: INTACT nuclei purification and ATAC-sequencing providing information about chromatin accessibility. This data will be integrated with genome-wide expression and transcription factor binding sites enabling us to relate transcription factor binding, chromatin state and gene expression. The relevance of shade-induced changes in chromatin modification will be tested functionally by mutational analyses. This project will provide important information about the regulation of gene expression by changes in the environment and how these are mediated by hormonal cues and light-regulated chromatin organization. More broadly, understanding the response to shade has an agricultural relevance. Crops grown at high density display the SAS leading to the reallocation of resources towards fast growing stems and causing a reduction in biomass of storage organs that are important for agricultural yield.

When the Noble Prize-winning Alexandre Fleming discovered antibiotics, he already noticed that microorganisms developed resistance mechanisms to survive. Therefore, he anticipated that a misuse of antimicrobial compounds to treat infections will drive the selection of hyper-resistant strains and the resurgence of almost-eradicated infectious diseases. Nowadays, the problem is so critical that the World Health Organization foresees that superbugs will outcompete cancer and cardiovascular diseases to become the first cause of mortality on the planet in less than 30 years (horizon 2050). Recently, the international organization drew a list of 10 priority pathogens that includes Streptococcus pneumoniae, a bacterium notorious in pneumonia (major upper respiratory tract infections), endocarditis, meningitis and brain abscess. To replace or restore antibiotic action, we thus need to find alternative strategies. In this proposal, I aim to use bacteriocins, small antimicrobial peptides secreted by bacteria, to kill S. pneumoniae. They are currently underexploited for human need but feature many valuable characteristics (e.g., efficiency, evolvability, specific spectrum, cheap/easy production, high sequence diversity, stability) complementary to antibiotics. I will test a collection of hundreds of bacteriocins and, according to their mode of action, will rationally assemble “overwhelming” bacteriocin cocktails to prevent emergence of resistance. In parallel, a tantalizing idea would be to exploit the beneficial bacteria of our microbiota and mobilize their bacteriocins to treat local infections. So, I will perform ex vivo infection of human epithelia with S. pneumoniae and test how bacteriocin-induced S. salivarius, a commensal bacterium of our gut, influences it. Besides generating valuable fundamental insight into the S. pneumoniae resistance mechanisms and infection cycle, the results of this project will also pave the way to fight against other notorious pathogens.

There is much truth in the ancient Chinese saying; “if you want to win the battle, you have to know your enemy”. When it comes to bacterial infections, we often don’t know our enemy very well and we are losing. Despite our best efforts to combat Streptococcus pneumoniae infections, this opportunistic pathogen remains a serious threat to human health, killing over 826 000 children each year and causing severe illness in 14 million more. Mankind is therefore in desperate need of novel therapies that can eradicate S. pneumoniae infections. The search for these therapies, however, is impeded by the lack of insight into the life cycle of this important pathogen. In this proposal, I therefore aim to generate unprecedented insight into the S. pneumoniae cell cycle. I will do so by performing an innovative pooled CRISPRi (Clustered Regularly Interspaced Short Palindromic Repeats Interference) screen combined with FACS (Fluorescence Activated Cell Sorting) to assess the effect of downregulation of all S. pneumoniae genes on important cell cycle parameters such as cell morphology, DNA content and the formation of the Z-ring that is required for cell division. This genome-wide screen will reveal several gene products that are important for the correct progression of the S. pneumoniae cell cycle. I will further characterize the most promising targets to unravel their cell cycle-related function at the molecular level. Moreover, newly-identified gene products that are important for cell cycle progression could be interesting novel drug targets. The efficacy of these prospective targets will be validated in an in vivo infection model in Galleria mellonella (wax moth) larvae. In the future, these candidates can be used as a starting point for the development of novel and effective therapies. Besides generating valuable fundamental insight into the S. pneumoniae cell cycle, the results of this project will thus also assist in our fight against this notorious pathogen.