Daniel Kearns

Daniel Kearns

Professor, Biology

  • dbkearns@indiana.edu
  • (812) 856-2523
  • Jordan Hall 469
  • Office Hours
    M-F
    By Appointment Only

Education

  • Postdoctoral Fellow, Harvard University, 2000-2004
  • Ph.D., University of Georgia, 2000

About

Multicellular behavior and bacterial domestication. Bacteria were long thought to take up nutrients, grow, and divide as individual unicellular organisms. However, this strict unicellular view has been challenged by the discovery of bacterial cell-to-cell communication systems and the observation of rudimentary multicellular behaviors. Perhaps one reason that bacterial multicellularity had gone unnoticed was the fact our cultivation techniques have selected against cell-cell interactions in favor of rapid growth as dispersed cells. Such is the case for our model system of choice, Bacillus subtilis. Laboratory strains of B. subtilis have been selected for ease of manipulation to create a powerful model genetic system at the expense of more complex biology. Our research returns to the study of wild strains of B. subtilis and two of the multicellular behaviors that were lost during laboratory strain domestication: swarming motility and biofilm formation. Each behavior appears to be an opposing and exclusive multicellular state in which swarming favors population dispersal while biofilm formation favors persistence.

Swarming motility. Swarming motility is a social form of migration in which cells associate in multicellular clusters to cooperatively propel a population over solid surfaces. Swarming is similar to swimming motility in that both motile behaviors are powered by rotating flagella. However, unlike swimming, swarming requires a solid surface, surfactant secretion, and a critical cell density. We have identified a variety of mutations that specifically impair swarming motility and many of these mutations are within genes of previously unknown function. Our lab uses a combination classical genetics, molecular genetics, and biochemistry to dissect the function of these unusual swarming specific genes.

Bistability and motility development. Through the study of swarming motility genes we discovered that B. subtilis grows a heterogeneous mixed population of short motile cells and long non-motile chains. This heterogeneity is a form of development that is governed by a bistable regulatory switch that turns motility gene expression ON in motile cells and OFF in chains. Proteins required for swarming motility, SwrA and SwrB, bias the switch in favor of the motile ON state. SwrA is of particular interest as the swrA gene is mutated in laboratory strains and contributes to the inability of domesticated strains to swarm. Future work will focus on investigating the molecular mechanisms of SwrA, SwrB, and the bistable switch that controls motility. In addition, we would like to explore the distribution of swarming motility genes in other wild isolates to assess the prevalence of swarming in the environment. By determining the presence and functionality of such genes in different natural isolates, we hope to gain insight into the evolutionary benefits and ecological roles of swarming motility.

Transition from motility to biofilm formation.  B. subtilis creates architecturally complex, sessile aggregates called biofilms and like swarming motility, biofilm formation is robust in undomesticated strains but severely attenuated in laboratory strains. Of critical importance to biofilm architecture is the master transcriptional regulator SinR. SinR mediates the transition from motility to biofilm formation by directly repressing the 15 gene eps operon required for the synthesis of a biofilm-stabilizing extracellular polysaccharide matrix. Also encoded within the eps operon is a protein, EpsE, that acts like a clutch on the flagellar motor. Thus the transition from motility to biofilm formation is determined at a single locus: when biofilm formation is initiated, SinR derepresses the eps operon, the matrix EPS is synthesized, and flagellar rotation is simultaneously inhibited.

Clutch control. Flagella are composed of nearly 40 proteins that cooperate to assemble a long helical filament. The cells rotate the filament like a propeller to push themselves through the environment. At the base of the flagellum is a series of proton channels (made of MotA and MotB) that interact with a wheel-like rotor (made of FliG). As protons flow through the channels, conformational changes in MotA cause FliG to turn and cause rotation of the flagellum. The motility inhibitor protein EpsE interacts with FliG to disrupt interaction with MotA, and like a clutch, disconnects the drive train from the power source to arrest flagellar rotation. We study the mechanistic basis of the EpsE clutch protein and the consequence of clutch activity on biofilm formation. Biofilm formation of pathogens is often an important stage in virulence and if we can trick pathogenic bacteria into remaining motile by targeting clutching mechanisms, their biofilms might be destabilized.

Goal. The overall goal of the lab is to identify, characterize, and understand new genetic components of multicellular behavior in undomesticated B. subtilis. With this information, we hope to create a larger model that explains how swarming motility and biofilm formation interact and in which environments each is favored.