Speaker: Prof. Roy D. Welch
From: Department of Biology, Syracuse University
Date/Room/Time: Tuesday, December 7, 2004 /129 DeBartolo/ 4-5 PM

Tea begins at 3:30 PM in Room 257 of Hurley Hall

Title: Functional genomics of the self-organizing prokaryote Myxococcus xanthus

Abstract:
Myxococcus xanthus is a delta proteobacterium that can exist as both a free-living cell and single-species biofilm called a swarm. Though each bacterium is autonomous with respect to metabolism and reproduction, M. xanthus has many characteristics of a multicellular organism; a swarm is a predatory collective that moves and feeds cooperatively, hunting together and pooling extracellular enzymes when digesting prey bacteria. The millions of cells within a swarm also exhibits a unified starvation stress-response, synchronizing a change in behavior and initiating a complex program of self-organization that culminates in the transition from an evenly distributed population of cells to densely packed aggregates called fruiting bodies – spherical structures of approximately 1X10E5 cells that contain stress-resistant spores. The purpose of forming fruiting bodies prior to sporulating can be inferred from a fruiting body’s physical properties; it is small (1/10 mm), tightly packed and sticky. If a moving object, such as the leg of an insect, comes in contact with a fruiting body, all of the M. xanthus spores will likely be transported as a unit. This way, if carried to a new food source, the thousands of M. xanthus spores can emerge as an “instant’ swarm, rather than having to re-establish a swarm from a single cell. For this reason, M. xanthus’ collective hunting behavior makes fruiting body development highly advantageous.

The construction of fruiting bodies is complicated from an engineering standpoint, and even more complex when considering the requisite behavioral genetics. A swarm represents a distributed system, a dispersed collection of (genetically) computing entities that must function together and coordinate their behavior through a communication network. As a swarm develops to form fruiting bodies, self-organization occurs in stages that produce different patterns of behavior; complexity is added stepwise so that the order imposed by each pattern can add to the final structure. Therefore, much of process that guides development can be observed by watching the emergence, propagation, and transition of dynamic patterns within a developing swarm.

The ultimate goal of the Welch Lab is to recapitulate the genetic networks that produce swarm patterns and, ultimately, guide the self-assembly of fruiting bodies. To accomplish this goal, we must exploit the M. xanthus genome sequence to understand the behavioral genetics of cells within a swarm. We have initiated a project to develop tools for genome visualization and functional annotation. Proteins with shared evolutionary histories were grouped together, placed on a three dimensional map, and visualized as a topological landscape. The resulting phylogenomic map is a useful tool for functional genomics and module discovery. The map recapitulates known and studied subsystems of M. xanthus, identifies clusters of novel biological function and suggests linkages between genes and gene clusters, identifies clusters of novel biological function, and successfully predicts swarm phenotypes of deletion mutants.