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UmuDAb and DdrR coregulate error-prone polymerases in the multi-drug resistant opportunistic pathogen, Acinetobacter baumannii, by repressing polymerase expression until after DNA damage. New evidence indicates that these proteins may also regulate other genes that are repressed following DNA damage. We performed an in silico analysis of RNA-Seq data from wild-type, ddrR, and umuDAb mutant strains to examine the expression levels of genes repressed after DNA damage. We used two different algorithms to analyze Cuffnorm- and HTSeq normalized gene counts. This analysis revealed nineteen (CuffDiff) or twenty-nine (DESeq2) genes repressed in wild-type cells that were derepressed after DNA damage in either one or both of the mutant strains. The proteins encoded by these genes include an induced acetoin metabolism operon, a putative YfbU family member (often required for MazF-mediated cell death after DNA damage), RlpA (a septal ring lytic transglycosylase), and a putative cold-shock protein. We carried out RT-qPCR verification of the RNA-Seq data and found that these genes are dysregulated after DNA damage, indicating DdrR and UmuDAb’s regulatory functions. Upon completion of RT-qPCR, we will construct strains containing mutations in these genes to test if DdrR and UmuDAb co-regulate these repressed genes. This will aid us in our understanding of how their downregulation may be involved in the pathogen’s response to DNA damage-induced stress.
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Flannigan, Mollee; Li, Xiaohong; Rouchka, Eric; Cook, Deborah; and Hare, Janeele, "Genes repressed after DNA damage in Acinetobacter baumannii are co-regulated by UmuDAb and DdrR" (2022). 2022 Celebration of Student Scholarship - Poster Presentations. 6.
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