MOLECULAR ADAPTATIONS IN ANTIMICROBIAL RESISTANCE AND STRESS RESPONSE ACROSS BIOLOGICAL SYSTEMS

Living organisms respond to stress through a variety of molecular adaptations. These adaptations are critical for survival in hostile environments, including the presence of antibiotics and other stressors. The overall objective of this dissertation is to investigate the mechanisms underlying antimicrobial resistance and stress responses across different biological systems using a combination of proteomics, phenotypic analysis, and metabolomics.The majority of this work focuses on bacterial systems, resistance and -omics technologies to monitor such molecular adaptations to stress. Chapter 2 establishes foundational experimental procedures and analytical strategies for resistance evolution studies and quantitative proteomics.In Chapter 3, the phenotypic consequences of antibiotic resistance were assessed in Escherichia coli, uncovering how resistance reshapes bacterial behavior and phenotype. In Chapter 4, further investigation of proteomic changes in E. coli resistant to the novel AMP CC-AMP1 identified specific proteins and pathways contributing to resistance. In Chapter 5, metabolomic techniques were employed to identify potential biocontrol agents from Pseudomonas protegens to combat Bacterial Panicle Blight in rice, demonstrating the potential of microbial metabolites in agricultural applications. Diverging to a multicellular system, Chapter 6 investigates the role of reversible cysteine oxidation in tardigrade osmobiosis. By labeling free cysteine thiols with a fluorescent probe, separating proteins through two-dimensional electrophoresis, and measuring fluorescence intensity, we observed a decrease in fluorescence signal as tardigrades transitioned into the osmobiotic state, indicating increased cysteine oxidation. Subsequent LC-MS analysis of protein spots with reduced fluorescence provided insights into the adaptive mechanisms that enable extremophiles to survive in hostile environments.Together, these findings provide an improved understanding of the molecular mechanisms that underlie antimicrobial resistance, stress response, and survival, with implications for the development of novel antimicrobial therapies and biocontrol strategies.