Quorum Sensing (QS)-regulated target predictions of Hafnia alvei H4 based on the joint application of genome and STRING database

In this study, we sequenced and characterized the genome of H. alvei to grasp the genetic basis of its physiological activities, including QS, metabolism, virulence and antibiotic resistance, and then mapped these functional gene clusters obtained from KEGG pathways to the STRING database to predict the QS-regulated targets in these pathways. H. alvei was found to possess 63 QS-related genes, most of which were closely related to amino acid metabolism, especially methionine pathway, but were not directly related to carbon and energy metabolism. Furthermore, the adhesion gene clusters were closely relevant to the QS gene clusters as well as to the infection gene clusters, while only one node (KdsD) was predicted between the QS gene clusters and infection gene clusters, suggesting that QS might influence the infection by regulating adhesion. QS might confer cross-resistance to microorganisms not only by regulating the formation of biofilms but also by affecting the efflux of antibiotics. In addition, the interspecies and intraspecies patterns of absence/presence for QS and its target genes were determined to shed light on the conservation of the QS regulatory mechanism among the phylogenetically related species. Taken together, the proposed methodology could expand the spectrum of possible applications of genome-based analysis to decipher the basic metabolic relationship of a microorganism, especially when studying new isolates.