Bacterial systems biology

The bacterium E. coli has around 300 transcriptional factors, but the functions of many of them, and the interactions between their respective regulatory networks, are unclear. Here, the authors study genetic interactions among all transcription factor genes in E. coli, revealing condition-dependent interactions and roles for uncharacterized transcription factors.

While phosphorylation is an essential post-translational modification in eukaryotes only recently the phosphoproteome of prokaryotes has been provided. Here, Schastnaya et al. mutate 52 phosphosites on 23 E. coli enzymes and apply metabolomics to provide evidence for the functional relevance of bacterial phosphorylation events.

Bock et al. characterise the adaptation of Pseudomonas aeruginosa to the antiseptic octenidine, using whole genome sequencing, gene expression studies and metabolomics. They attribute this increased tolerance to synergistic changes in efflux and plasma membrane composition via mutations in SmvR, the regulator of MFS efflux pump SmvA, and in phospholipid pathway proteins PssA and PgsA.

Rodionova et al. find that the putative transporter gene, ydhC and its regulator ydhB are involved in purine transportation and that the expression of the ydhC gene is activated by the YdhB in E. coli. The authors suggest renaming the regulator PunR and the transporter PunC, respectively.

Several Fusobacterium species, such as Fusobacterium nucleatum, have been associated with cancer. Here, using differential RNA-sequencing, the authors provide high-resolution global RNA maps for five clinically relevant fusobacterial strains, elucidating basic aspects of fusobacterial gene expression and identifying multiple non-coding RNAs, including an oxygen-induced small RNA, FoxI, which represses the major outer membrane porin FomA.