After >50 years of molecular biology research, the genetic tractability of a few model systems has established itself as the principal pillar of functional genome analyses. As the analysis of many sequenced genomes is still hampered by their genetic intractability, new alternative and broadly applicable procedures are needed to permit functional in vivo studies, particularly in pathogens whose biology is poorly understood. Pharmacological methods present an appealing alternative to inactivate (or enhance the activity of) a client protein in vivo. We will test a novel, interdisciplinary and broadly applicable pharmacogenetic strategy to conduct functional genome analyses in the genetically intractable bacterium Waddlia chondrophila, a strict intracellular pathogen and member of the phylum Chlamydiae. Like the etiological agent of trachoma (Chlamydia trachomatis,) the most prevalent sexually transmitted bacterial disease worldwide that causes blindness, infertility and extra-uterine pregnancy, W. chondrophila features the typical chlamydial differentiation cycle - from an infectious cell type to a replicative one and back - whose genetic basis is unknown.
As W. chondrophila is much easier to cultivate in the laboratory than C. trachomatis, our interdisciplinary team of three distinct university research units (led by two PhDs and a clinician MD-PhD) in the Arc Lémanique will explore the function of 10 W. chondrophila regulatory genes using a simple three-step strategy. First, we will design a functional readout (reporter assay) by heterologous expression of W. chondrophila target protein(s) in the genetically tractable surrogate host Escherichia coli (UNIGE: CMU). Next, we will screen small molecule libraries for compounds that inactivate/enhance the target protein in the E. coli reporter and determine their cytotoxicity on human/amoeba cells (UNIGE: PHARM). Finally, we will use these compounds to inactivate/enhance the native target proteins in W. chondrophila and other Chlamydiae within human/amoeba cells and infer their function by evaluating the consequences of administering the compounds to Chlamydia (UNIL: CHUV).
By targeting regulatory proteins in. W. chondrophila that are conserved among the Chlamydiae, we anticipate a) defining the genetic basis of the mysterious chlamydial differentiation program and b) illuminating the underlying molecular mechanisms, while also c) discovering new potential antibiotics that could be used to treat chlamydial (or other bacterial) infections.