DNA Microarrays in Analysis of Quorum Sensing: Strengths and Limitations

Quorum sensing in prokaryotic biology refers to the ability of a bacterium to sense information from other cells in the population when they reach a critical concentration (i.e., a quorum).In the context of this commentary the information sensed by some gram-negative bacteria is extracellular lowmolecular-weight compounds called acyl homoserine lactones (AHL), whose levels in the medium are related to the population density of the producing species.AHL-mediated quorum sensing was first discovered in marine vibrios over 30 years ago, but Pseudomonas aeruginosa has arguably been the most thoroughly scrutinized species in this regard.Over 100 publications since 1994 were found in the PubMed database under the query "quorum sensing Pseudomonas aeruginosa."Over one-half of these publications emanated from the laboratories of E. P. Greenberg and B. H. Iglewski, the corresponding authors of two separate reports (14,20) in this issue describing the use of DNA-based microarray assays to evaluate the transcription of P. aeruginosa genes that are directly or indirectly regulated by AHL-mediated quorum sensing.During the last decade a cadre of P. aeruginosa genes and phenotypes were reported to be affected by AHL-mediated quorum sensing, including genes and phenotypes that contribute to biofilm development (5,15,16), virulence in diverse hosts, including slime molds, plants, insects, invertebrate animals, and mammals (3,4,9,12,13,23,24), and resistance to antimicrobial agents (1,6,18).The bulk of these genes and phenotypes were identified by using genetic approaches, but sometimes different researchers reached contradictory conclusions about whether specific P. aeruginosa genes or phenotypes were responsive to quorum sensing (8,19,21).It is not unusual in experimental science to encounter apparently conflicting outcomes even when the same hypotheses are addressed by using nearly identical experimental methods.Fortunately, thoughtful analyses of apparently differing experimental data can provide novel insights into biological processes and provide fodder for further inquiry and conflict resolution.On the other hand, different experimental outcomes could be inconsequential or tangential to the main issue.They can be the residue of trivial technical matters or limitations of the methods employed, or they can be the result of a subtle or immaterial phenotypic characteristic that allows different interpretations of similar data.