Investigation of the marA, soxS, rob, and ramA regulons of Salmonella enterica serovar Typhimurium

Antimicrobials have revolutionised modern medicine, but in our hubris, we have turned a blind eye to the potential ramifications of overusing these wonder drugs. As a consequence, the incidences of antimicrobial resistance have increased considerably and pose a great threat to modern medicine. Synonymous with food poisoning, Salmonella species accounted for 213,000 deaths in 2017. Whilst typically associated with a self-limiting gastroenteritis, the incidences of Salmonella infections resistant to one or more antimicrobials is also quickly increasing. As a foodborne pathogen that is generally transmitted through the faecal-oral route, Salmonella must be able to adapt to a wide variety of environmental conditions in order to ensure survival and transmission. This can be achieved through the complex, multicellular, structures of biofilms. Biofilms in Salmonella have important roles and greatly increase tolerance to environmental stresses, including antimicrobials. Previous work has linked the inhibition of biofilm formation in Salmonella to the homologous transcription factors, MarA, SoxS, Rob, and RamA, which are responsible for the control of antimicrobial resistance in both Salmonella and E. coli. In this work, the genome-wide binding profiles of these transcription factors is determined using ChIP-seq. Subsequent Cappable-seq analysis, to identify TSSs, allows the elucidation of the direct and indirect cellular effects of these transcription factors. One notable observation was the binding of SoxS upstream of the master biofilm regulator csgD, part of the csgDEFG operon. SoxS, and MarA, are known to indirectly inhibit csgD expression, and therefore biofilm formation, in E. coli through the ycgZ-ymgABC pathway. However, this pathway is absent in Salmonella. This work identifies SoxS as a direct inhibitor of csgDEFG expression in Salmonella via binding to the upstream region of csgDEFG and repressing transcription. This observation is also observed in the presence of the master activator of csgD expression, MlrA; further highlighting the importance of SoxS in the inhibition of biofilm formation in Salmonella. The results presented in this work bridge the gap between understanding how E. coli and Salmonella utilise the global regulators of antimicrobial stress to repress biofilm formation. Furthering the notion that the repression of biofilms by these global stress response regulators provides a survival mechanism against antimicrobials. It is hypothesised that if planktonic bacteria are subjected to antimicrobial stress, biofilm formation is repressed by direct binding of SoxS to the csgDEFG intergenic region. This counterintuitive repression of an antimicrobial resistance mechanism by a regulator of antimicrobial resistance could benefit the bacteria, as formation of a biofilm at this time would be energetically costly and insufficient to aid survival. Therefore, repression of biofilm formation by SoxS could allow the bacteria escape the harmful environment

The multiple antibiotic resistance operon of enteric bacteria controls DNA repair and outer membrane integrity

Transcription factors MarR and MarA confer multidrug resistance in enteric bacteria by modulating efflux pump and porin expression. Here, Sharma et al. show that MarA also upregulates genes required for lipid trafficking and DNA repair, thus reducing antibiotic entry and quinolone-induced DNA damage

BBF RFC 106: A Standard Type IIS Syntax for Plants

Here we define a standard syntax for assembling standard parts for expression in plant cells, extensible to all other eukaryotes. Variations of the Type IIS mediated cloning method known as Golden Gate Cloning, most notably Golden Braid (GB2.0) and Golden Gate Modular Cloning (MoClo) are in common use, particularly for the assembly of plasmids for delivery to plant cells. Many characterised plant parts compatible with Type IIS mediated assembly are available outside of the Registry of Standard Parts, as well as plasmids with the features necessary for delivery of DNA to plants cells via the shuttle chassis, Agrobacterium tumefaciens. This RFC describes a consensus Type IIS syntax for plant parts to allow assembly into complete eukaryotic transcriptional units in plasmid vectors that contain the necessary features for transfection of plant chassis. We use Marchantia polymorpha, a primitive and easy-to-engineer liverwort and Nicotiana benthamiana a model plant as exemplar chassis