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Title: Novel DNA binding and regulatory activities for s54 (RpoN) in Salmonella Typhimurium 14028s

Author
item BONO, ASHLEY - University Of Georgia
item HARTMAN, CHRISTINE - University Of Georgia
item SOLAIMANPOUR, SINA - University Of Georgia
item TONG, HAO - University Of Georgia
item PORWOLLIK, STEFFEN - University Of California
item MCCLELLAND, MICHAEL - University Of California
item Frye, Jonathan
item MRAZEK, JAN - University Of Georgia
item KARLS, ANNA - University Of Georgia

Submitted to: Journal of Bacteriology
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 3/27/2017
Publication Date: 4/3/2017
Citation: Bono, A., Hartman, C., Solaimanpour, S., Tong, H., Porwollik, S., McClelland, M., Frye, J.G., Mrazek, J., Karls, A. 2017. Novel DNA binding and regulatory activities for s54 (RpoN) in Salmonella Typhimurium 14028s. Journal of Bacteriology. doi:10.1128/JB.00816-16.

Interpretive Summary: The bacterium Salmonella enterica subspecies enterica serovar Typhimurium is often food borne and causes gastroenteritis and septicemia in humans. It is also a model system for the physiology of bacteria, and can be used to study how pathogens respond to rapidly changing conditions to survive in the environment, during transmission through animals, in food products, and during infection of a human host. One of the ways bacteria adjust to their environment is though changing expression of genes used to survive under stressful conditions. Sigma factors control the expression of specific genes by binding to DNA located in front of the gene called the promoter and initiating expression of the gene. sigma54 is unique because after binding to the promoter it cannot initiate gene expression until activated by systems that sense environmental conditions. Once one of these systems senses the right environmental signal, it then activates sigma54 leading to the expression of genes which enable the bacteria to adapt and survive in the new environment. In this study a mutated activator was used to activate all sigma54 dependent genes without any environmental signals. This allowed the identification of all of the genes that can be controlled by sigma54. The analysis identified 186 sigma54 binding sites, and the genes they control. Analysis of this data has suggested new roles for sigma54 in controlling gene expression. This is the first report of all genes regulated by sigma54, the "sigma54 regulon", and is one of the first complete regulons defined in the Salmonella model system. Knowing how the sigma54 regulon works helps us understand how pathogens respond rapidly to new environments like a human host, and will help us identify ways to disrupt this adaptation and prevent infections.

Technical Abstract: Salmonella enterica subspecies enterica serovar Typhimurium, the causative agent of gastrointestinal disease and septicemia in humans, has been extensively studied, providing a comprehensive model system in which to study how pathogens respond to the rapidly changing conditions during persistence in the environment, transmission through zoonotic reservoirs, and infection of the human host. The variable sigma subunit of the bacterial RNA polymerase (RNAP) holoenzyme, which is responsible for promoter specificity and open complex formation, plays a strategic role in the response to environmental changes. S. Typhimurium utilizes six s factors: the housekeeping sigma70, and five alternative sigma factors, sigmaE/24, sigmaH/32, sigmaS/38, sigma28, and sigmaN/54. The sigma54-RNAP differs from other sigma-RNAP holoenzymes in that it forms a stable closed complex with the promoter and requires ATP hydrolysis by an activated cognate bEBP (bacterial enhancer-binding protein) to transition to open complex and initiate transcription. This work defines the global sigma54-RNAP DNA binding sites and transcriptome for the s54 regulon of S. Typhimurium utilizing a constitutively-active, promiscuous bEBP that activates transcription from sigma54-dependent promoters that normally respond to 13 different bEBPs each of which is activated under a different growth condition. The position and context of many of the 186 identified sigma54-RNAP DNA binding sites suggest regulatory roles for sigma54-RNAP, e.g. in transcriptional interference and expression of sigmaRNAs, that connect the sigma54 regulon to regulons of other sigma factors to provide a dynamic response to rapidly changing environmental conditions.