Figure 1: High-throughput gene-gene, gene-drug and drug-drug interaction profiling provides novel mechanistic insights into the cellular network architecture and into drug mode-of-action (Typas et al., Nat Methods 2008; Typas et al., Cell 2010; Nichols et al., Cell 2011; Ezraty et al. Science 2013: Paradis-Bleau et al., PLoS Gen 2014).
Figure 2: A. A structure-function view of novel lipoprotein regulators controlling cell wall synthesis from the outside (Typas et al., Cell 2010; Egan et al., PNAS 2014). B. A signal transduction system for monitoring b-barrel insertion into the bacterial outer membrane (Cho et al., Cell 2014).
The Typas group develops and utilises high-throughput methods to study the cellular networks of different bacterial species, and how these bacteria interact with the environment and with each other.
Previous and current research
The recent explosion of genomic sequence information provides a first step towards better understanding diverse bacteria, but also makes it crucial to develop large-scale phenotyping approaches to characterise functions of novel genes and to map them within pathways. We are developing such high-throughput, multi-readout, automated approaches to quantitatively assess gene-gene, gene-drug and drug-drug interactions in many different bacteria and at many different levels (figure 1). We then use the data as starting points for generating new mechanistic insights into targeted cellular processes, and also for uncovering how function, regulation and cross-talk between cellular processes changes across evolution and how this impacts the phenotype.
Our biological focus is on the bacterial envelope – its mode of assembly and growth, and its ability to sense the environment. The bacterial envelope is vital for pathogenesis, cell morphogenesis and cell developmental programs. Although many envelope structural components have been characterised, we often have limited information on how their biosynthesis and transport are interconnected, regulated, or linked to the overall status of the cell, how the cell senses perturbations in these process and how signals are transduced to achieve homeostasis. Working at the intersection between genomics and mechanistic molecular biology, we have discovered key missing players of major envelope components, uncovered niche-specific regulation of conserved envelope processes, identified linking proteins that allow coordination between processes, and mapped network rewiring under different stresses (figure 2).
We are also developing large-scale automated platforms for elucidating the mode-of-action of new antibacterials, for large-scale profiling of combinatorial drug therapies and for dissecting the underlying mechanism(s), and for identifying adjuvants that re-sensitise multi-resistant bacterial pathogens or target chronic infections (persisters). Our ultimate goal is to identify rules underlying drug-drug interactions that will allow rational design, and to find solutions for difficult to kill pathogens.
Future projects and goals
We are now expanding our efforts in two directions. First, we are introducing our high-throughput screening approaches into abundant and prevalent species of the human gut microbiome. In collaboration with the Alexandrov, Bork, and Patil groups, and utilising a plethora of complementary technologies – such as imaging mass spectrometry, cutting-edge microscopy approaches, meta-omics, modeling –, we aim at understanding the dynamics of such communities, and how their composition is affected by drugs, natural and dietary compounds, physical parameters, and host molecules. Secondly, we are setting up a multi-pronged systematic approach aimed at gaining novel insights into the host-pathogen interface. Here, we combine high-throughput reverse genetics, high-content microscopy and different types of quantitative proteomics to dissect the Salmonella-host interaction.