W. Seth Childers

An intriguing question with roots in the origin of life is how matter transitioned from Darwin’s warm pond to the last universal common ancestor. Impossible to address directly, scientists can still provide insights into these issues by asking questions about life today. For example, how do the simplest modern cells orchestrate the location and activity of millions of molecules like organized nano-sized factories? And how do molecules work as systems make complex decisions? Understanding these questions can also advance the design of intelligent materials, new synthetic biology technologies for health applications, and reveal antibiotic targets. Since establishing my independent career at the University of Pittsburgh in 2015, has investigated biomolecular condensates as a compartmentalization strategy in bacteria, biomolecular condensates as a  reaction crucible in the origins of life and the design of intelligent nanomaterials.  In addition, we develop synthetic biology tools and biosensors to study bacterial signaling mechanisms in how bacterial cells develop and how they impact the gut-brain axis. To investigate these questions, we apply interdisciplinary approaches that include synthetic biology, biophysical chemistry, chemical biology, mechanistic biochemistry and microbial genetics.  

Biomolecular condensates as compartments in bacteria

Recently in eukaryotes, a new type of “membraneless organelles” formed from liquid-liquid phase separation of scaffolding proteins has been realized as a fundamental way eukaryotes organize biochemistry. In fact, in the 1920s, Alexander Oparin postulated that similar coacervate assemblies were critical precursors to the first cells. However, before 2015, “membraneless organelles” were curiously absent in the bacterial kingdom. If membraneless organelles were abundant in all kingdoms of life, that would strengthen the potential role of these compartments in life’s beginnings. Moreover, it would radically change our view of bacteria that notably lack typical membrane-bound organelles.

Sparked by this curiosity, our lab co-discovered that biomolecular condensates organize and regulate global RNA decay and signaling pathways in bacteria. We’ve also found biomolecular condensates chemical environment uniquely stimulates the ribonuclease functions of PNPase and the kinase-to-phosphatase activity switch of the histidine kinase PleC. These findings are significant in showing that biomolecular condensates act as a compartmentalization strategy in bacteria. Critically, we  have developed a new FRET biosensor approach that reported how biomolecular condensates impact signaling enzymes in vivo. Motivated by the roles of biomolecular condensates in physiology, our lab identified an inhibitor to disrupt the phase separation of an essential bacterial protein. Combined with contemporaneous discoveries from peers, these results suggest phase separation as a fundamental way bacteria organize biochemistry into organelle-like structures—a cytoplasm more organized than the classic textbook view.  Moreover, these assemblies present new antibiotic targets.  

Development of bacterial synthetic biology tools for signaling proteins and biomolecular condensates

Figure 2: Development of Synthetic Biology Tools for signal transduction and compartmentalization in bacterial.  New tools opened the door to decode bacterial ,

We also aim to translate our discovered knowledge into synthetic biology tools that can be applied to address health challenges (Figure 2). We are actively building tools that will allow us to understand how gut microbial signaling and metabolism contribute to conditions ranging from Crohn’s Disease to depression. This includes new protein engineering strategies that will help unlock the functions of cryptic signaling proteins and catalytically dead pseudokinases that control development, pathogenesis, and gut-brain-axis dysregulation. We are also developing methods that will ultimately allow us to sense and potentially one-day correct dysregulation within the gut microbiome that leads to mental health diseases. Towards these goals, we have developed biosensors to detect microbially produced indole metabolites that impact mental health. We have also repurposed peptide nanomaterials as synthetic membraneless organelles that we aim to use to produce therapeutic metabolites and proteins. These synthetic biology advances lay the foundation for studying aspects of the gut-brain axis involved in mental health issues.