An integrative, multi-omics analysis of the Hfq regulon

The ability of bacteria to respond to environmental change is based on the exploration of sophisticated regulatory landscapes. While we can learn a great deal from reductive analyses of individual pathways, and global approaches to gene regulation, a deeper understanding of these complex signalling networks requires the simultaneous consideration of several regulatory layers at the genome-scale. To highlight the power of this approach we analysed the Hfq transcriptional/translational regulatory network in the plant-associated rhizobacterium Pseudomonas fluorescens. Extensive multi-omics analyses including proteomics quantification using isobaric isotope labelling (iTRAQ )were used to assess how hfq deletion affects gene transcription, translation and protein abundance. The subsequent integration of these datasets highlighted the discrete contributions by Hfq to gene regulation at different levels, confirmed previous predictions, and suggested novel regulatory principles for Hfq function. The integrative approach to regulatory analysis described here has significant potential, for both dissecting individual signalling pathways and understanding the strategies bacteria use to cope with external challenges.