The biofilm lifestyle is the pervasive method for bacteria to resist environmental stress. Biofilm protection results in a decreased ability for human hosts to clear infections and an increased rate of antibiotic resistance among bacteria. In Escherichia coli, biofilm formation depends curli and cellulose, which form a protective extracellular matrix around the cells. Cells within a colony biofilm can be divided into at least two physically distinct subpopulations, including a population that produces the extracellular matrix and a population that does not produce matrix. Extracellular matrix production during biofilm formation is under complex regulation that is still poorly understood. My work has identified new pathways and regulators that alter extracellular matrix production and subpopulation development in E. coli. We identified over 300 genes including those involved in LPS biosynthesis, gluconeogenesis, purine metabolism, cellular respiration, and other fundamental cellular processes which, when disrupted, result in changed curli production. To better understand subpopulation development, whole transcriptome and proteome data was collected from both the matrix and non-matrix cells. Gene products involved in anaerobic respiration were dramatically increased in the cells comprising the non-matrix subpopulation as compared to the matrix subpopulation. Deletion of nrfA, which is a gene involved in anaerobic respiration, resulted in a loss of the non-matrix cells producing subpopulation. Finally, I identified small RNAs and c-di-GMP produced by DgcN that regulate the expression of csgD, the master biofilm transcription factor. CsgD levels and matrix production were altered by redox changes sensed by the periplasmic repressor of DgcN, YfiR. Cysteine auxotrophic UPEC isolates were hyper-oxidized and produced more curli under normal and non-permissive biofilm growth temperatures. Deletion of YfiR or supplementation with a reducing agent restored WT curli production in cysteine auxotrophic strains. Taken together this work defines the complex regulatory network controlling biofilm matrix production.PHDMolecular, Cellular, and Developmental BiologyUniversity of Michigan, Horace H. Rackham School of Graduate Studieshttp://deepblue.lib.umich.edu/bitstream/2027.42/162875/1/janetep_1.pd
