The bioluminescent marine bacterium Vibrio fischeri lives symbiotically in the light organ of the bobtail squid, Euprymna scolopes. V. fischeri is a member of the family Vibrionaceae, which includes the causative agents of cholera and other diseases, as well as nonpathogenic and beneficial species. The luminescence produced by V. fischeri and some other members of the Vibrionaceae family—as well as other genera of bacteria—is controlled by a phenomenon known as quorum sensing. Once called density sensing, quorum sensing is the ability of bacteria to sense the density of their populations via the concentration of an autoinducer molecule, and to in turn regulate gene expression based on that density. It occurs in many bacterial species, and controls processes other than luminescence, such as the production of toxins and the utilization of nutrients. Bacterial quorum sensing provides researchers a means to study how information from the outside world is detected and transmitted to the interior of cells, how gene expression is altered in relation to population density, how cells communicate, and how this communication affects the behavior of individual cells and the populations they comprise. The principles of these processes are applicable not only to single-celled bacteria in their various communities, but to the individual cells of higher organisms in the context of their tissues and organs.
Quorum sensing also appears to underlie the communication among bacteria in the colony-like structures known as biofilms, and may be responsible for production of a protective matrix or secretion of virulence factors when colonies reach a certain population density. Biofilms have been implicated in detrimental situations—contributing to the pathology of diseases such as cystic fibrosis, colonizing medical implants and catheters, and contaminating water cooling towers and food and its packaging—but also serve in beneficial processes, such as the bioremediation of sewage and pollutants.
The complete genome sequence of V. fischeri (strain ES114) was published in 2005 (Ruby et al. 2005. PNAS 102:3004–3009), which enabled the comparison of similarities and differences in gene sequences and arrangement between it and pathogenic species, such as V. cholerae. Such accumulating sequence datasets are contributing to the use of comparative genomics and other techniques, such as computer-based modeling, to study of quorum sensing and cell signaling in bacterial systems. Understanding and manipulating cell signaling in bacteria will have implications beyond deciphering bacteria-host interactions and biofilm formation. It could lead to the development of new antibiotics or non-antibiotic–based anti-infective agents, as well as produce methods to block the toxicity of pathogenic organisms at certain cell densities.Scanning electron micrograph (SEM) of a grouping of Vibrio vulnificus bacteria (13,184× magnification).
“Since my group is theoretical, the ‘technology’ we are developing mostly consists of computer programs and modeling applications,” says Rahul V. Kulkarni, assistant professor in the Department of Physics at the Virginia Polytechnic Institute and State University (Blacksburg, VA). Bacterial virulence is often regulated by quorum sensing. Among several ongoing projects, Kulkarni's group has computationally predicted novel small RNAs that play a role in the regulation of virulence via quorum sensing and other pathways. (The methods employed are reviewed in Kulkarni et al. 2005. Methods 43:131.) Their predictions have been experimentally validated by collaborators and other groups worldwide in multiple bacterial species—in particular, the Vibrio genus. Because it is likely that the inhibition of quorum sensing pathways could convert virulent bacteria to avirulent, Kulkarni speculates that this might provide a way of treating bacterial infections without antibiotics.
Kulkarni first became interested in computational models as a post-doc, when he realized that these models might be helpful in determining quorum sensing pathway components that were difficult to discover using conventional molecular biology techniques. Computational approaches have been used to predict what he describes as ‘missing elements’ in the Vibrio quorum-sensing pathway, elements which his modeling predicted to be multiple small RNAs (sRNAs). Kulkarni was a collaborator with Bonnie Bassler, a professor in the Department of Molecular Biology at Princeton University (Princeton, NJ). Her group identified a protein, Hfq, as an additional component of the Vibrio quorum-sensing circuits. Hfq mediates interactions between sRNAs and specific messenger RNA (mRNA) targets, destabilizing mRNA that encode for the quorum-sensing master regulators. Using the experimental evidence, Kulkarni made computational predictions for the corresponding sRNAs in the Vibrio quorum-sensing pathways. A bioinformatics approach indicated that simultaneous deletion of all four candidate sRNAs identified in V. cholerae was required to disrupt quorum sensing (Lenz et al. 2004. Cell 118:1–2).