Research

“Metabolism and physiology of the DHAP shunt in pathogenic species”

Ongoing

Extraintestinal pathogenic Escherichia coli (ExPEC) are globally prevalent pathogens responsible for causing infections outside the intestinal tract, most commonly urinary tract infections. Caitlin's research focuses on understanding how ExPEC acquire nutrients in the nutrient-limited environment of urine to support growth and subsequent infection. To address this, her work is organized around three primary aims: (1) defining the regulation of previously unrecognized carbon metabolism pathways that enable utilization of modified sugars under glucose-limiting conditions; (2) determining if and when ExPEC strains use these compounds during growth in urine; and (3) identifying additional human pathogens that possess protein homologs of these metabolic pathways and validating their ability to use modified sugars for growth.

Regulatory control of DHAP shunt gene expression

Investigated transcriptional mechanisms governing expression of the DHAP shunt pathway in extraintestinal pathogenic E. coli (ExPEC). Designed and executed molecular biology and biochemistry workflows to identify regulatory elements and protein-DNA interactions.

Techniques: genomic deletions, cloning, protein expression and purification, electrophoretic mobility shift assays (EMSA), transcription start site mapping by primer extension, computational genomics, SDS-PAGE/PAGE, fluorescence-based assays, bacterial growth analysis (BSL-1).

Metabolism of ExPEC strains under physiological conditions

Evaluated whether ribose byproducts of S-adenosyl-L-methionine metabolism are utilized as carbon sources during bacteriuria. With combined metabolomics, gene expression, bacterial growth analysis approaches, the bacterial metabolic flexibility under infection-relevant conditions are being characterized.

Techniques: bacterial culture and growth analysis (BSL-2), genomic deletions, cloning, HPLC, LC-MS, carbohydrate derivatization, transcriptomics, Illumina sequencing, qRT- PCR.

Activity comparison of homologous DHAP shunt proteins

Compared enzymatic activity of DHAP shunt homologs from pathogenic strains to assess functional conservation across species. Generated recombinant proteins and performed kinetic and biophysical analyses.

Techniques: cloning, expression vector transformation, protein expression and purification, BCA assays, enzyme kinetics (UV-Vis, coupled assays), thermal shift assays, SDS-PAGE.

Significance

Collectively, these approaches contribute to the foundational understanding of pathogenic metabolism and may directly enable the identification of new, targeted therapies for urinary tract infections that disproportionately affect specific populations.