Excellence in Research:Understanding environmental adaptation by elucidating the changes in molecular mechanisms associated with genetic selection in two-component response systems

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Bacteria, just as all living organisms, often find themselves in harsh environments ranging from extreme temperatures, to toxic waste, or even exposure to antibiotics. In order to survive, they must react quickly. Their response for survival comes in two ways: they either can acclimate through changes in gene expression, or they can adapt by specifically changing their DNA. Two-component response systems (TCRS) are one of the best studied genetic elements bacteria use for environmental acclimation. Previous work has shown that under extreme conditions, TCRS genes acquire mutations that allow the bacteria to survive, but the exact effect these mutations have on the growth and reproduction of bacteria are unknown. This research aims to understand the role that TCRS play in adaptation to high levels of silver (a well-studied stressor), by studying mutations acquired during experimental evolution, and how those mutations will affect the overall fitness of the bacteria. The research will benefit four broader impact areas: (1) The larger scientific community, as synthetic engineering of TCRS have been proposed for many applications ranging from bioremediation to antimicrobial drug design. (2) By improving underrepresented minority retention in STEM fields by mentoring undergraduates and a PhD student at an HBCU to integrate approaches in microbiology, molecular biology, evolution, genomics, and computational biology to make them more competitive for professional school and/or STEM careers. (3) By engaging and exposing local communities to the world of microbiology and evolution by volunteering in local K-5 afterschool programs; and (4) by using the data to write teaching case studies to be used by educators around the world.Two-component response systems (TCRS) are among the best studied genetic elements for environmental acclimation in bacteria, although very little is known about their role in adaptation. The overall goal of this research is to show that evolutionary adaptation commonly occurs through the acquisition of mutations in TCRS genes after prolonged acclimation. This then allows selection for differential reproduction leading to the survival of the adapted bacteria, although likely with negative consequences on their fitness and function. TCRS consist of two proteins, a histidine kinase (HK) that senses changes in the external environment and is activated via autophosphorylation. The phosphate is then transferred to a response regulator (RR) which activates transcription of relevant response genes. In this study, the investigators will assess TCRS mutations acquired through the adaptation of Escherichia coli to silver via experimental evolution. In silver adapted strains, three independent studies identified mutations in two TCRS proteins: CusS, a HK which regulates copper/silver homeostasis; and OmpR, a RR which regulates outer membrane porin expression. The motivation for this study is to show the cellular costs associated with the acquisition of such mutations by (1) associating mutations in specific domains of TCRS to a particular phenotype; (2) assessing the fitness cost and reversion rates associated with biologically relevant mutations in TCRS; and (3) identifying changes in global cellular physiology affected by mutations in a single TCRS. The innovation lies in the assessment of mutations that have been selected by the organism through experimental evolution and are therefore biologically relevant. The project will lead to further understanding of the role TCRS play in adaptation and the fitness cost associated with these genetic adaptations which may then be used to predict the outcome of competition and fitness by linking these phenotypes to genomic determinants.This award reflects NSF's statutory mission and has been deemed worthy of support through evaluation using the Foundation's intellectual merit and broader impacts review criteria.