Dissecting bacterial lifestyle and interspecies interactions with systems approaches
The Typas group develops and utilises high-throughput methods to study the cellular networks of different species of bacteria, and how these bacteria interact with the environment and with each other.
Figure 1: High-throughput phenotypic screens are used to identify gene function and map pathway architecture (Typas et al., Nat Methods 2008; Nichols et al., Cell 2011).
Figure 2: Two novel niche-specific lipoproteins control peptidoglycan synthesis from the outside of the sacculus (Typas et al., Cell 2010).
Figure 3: Integration of different large-scale datasets.
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. Research pioneered in yeast indicates that some of the most powerful global phenotyping approaches are based on scaling up long-standing concepts in biology. Epistasis-genetic interactions, for instance, assess how the function of one gene depends on the function of another, while chemical genetic interactions measure how the function of one gene affects cellular responses to chemical stress. We have developed quantitative high-throughput versions of these approaches in E. coli, and used them to obtain a mechanistic understanding of key aspects of its envelope function and architecture.
The bacterial envelope is sandwiched between two membranes in gram-negative bacteria and constitutes the interface of the bacterium to the environment. This compartment acts as a protective barrier, but also allows bacteria to sense changes in, and communicate with, their environment and 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 they sense perturbations, and how signals are transduced to achieve homeostasis.
Working at the intersection between systems genomic biology 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. Specific examples of the biological stories we have uncovered include: i) identification of the first regulators controlling peptidoglycan synthesis outside of the cell, thereby providing an opportunity for outer membrane status to influence the fundamental shape-forming structure in bacterial cells (see figure 2); ii) discovery of a new player that orchestrates outer membrane constriction during cell division; iii) a mechanism to transduce information about cell size/shape to the transcriptional machinery; iv) a mechanism to control the activity of lipoproteins.
Future projects and goals
Our main goal is to expand our efforts in two directions. First, we want to develop analogous high-throughput methods for other bacteria. This will enable us to generate comprehensive interaction datasets in different bacteria, enrich them with other available genome-wide resources, and ultimately use them to create inferences about common and individual characteristics of biology in those organisms. Second, we plan to expand this technology to report on more social characteristics of bacteria. This will enable us to probe interspecies interactions and interactions with the host, shedding light on different mechanistic aspects of these interactions. Our specific aims include: i) generation of global genetic and chemical genetic interaction profiles for different pathogen and commensal bacteria and integration with other available global phenotyping data; ii) cross-species comparisons to map key features of divergence in the organisation of the bacterial envelope; iii) development of high-throughput approaches to study bacterial interspecies interactions and bacterial-host interactions.