Chemistry Graduate Program

Faculty Advisor: Joshua Coon


Anna’s research focuses on the large-scale quantification of phosphorylation, a post-translational modification that can alter the behavior of the protein it decorates in almost every conceivable way, in three main biological systems: yeast under salt stress, nematode germline, and the C-terminal domain (CTD) of RNA Pol II.

Yeast Salt Stress (collaboration with Gasch lab). The variability of environmental conditions demands that organisms develop mechanisms to sense and respond to changes in their surroundings. In the budding yeast Saccharomyces cerevisiae, the HOG (high osmolarity glycerol) MAP kinase cascade activates the key kinase Hog1 to regulate specific transcription factors in response to osmotic stress. Using highly sensitive and rapid quantitative mass spectrometry and replicate analyses, we detected and quantified changes in over 2000 sites of protein phosphorylation in wild-type and a Hog1 deletion strain as they acclimate after osmotic shock. Coupled with protein and transcript measurements, these data provide direct insight into the coordinated physiological responses employed by yeast in defending against environmental stress.

C. elegans Germline (collaboration with Kimble lab). The germline of the nematode Caenorhabditis elegans serves as a unique model for the study of stem cell self-renewal and differentiation, cell transition from mitosis to meiosis, and sexual specification. By encoding a member of the highly conserved LIN-12/Notch family of receptors, glp-1 mediates the mitosis/meiosis decision in the germline. We used wild-type and a glp-1 mutant strains shifted from a permissive temperature of 15 °C to a restrictive one of 25 °C at time points at which the decision to enter meiosis was known to be either reversible or permanent to qualitatively and quantitatively characterize over 4500 phosphoisoforms. Cell cycle and signaling regulators were notably enriched among the affected peptides in these experiments. Our results further suggest that GLP-1/Notch regulates the phosphoproteome independently of changes in protein abundance. Moreover, within our data set, multiple kinases themselves change their phosphorylation state.

CTD Phosphoisoforms (collaboration with Ansari lab). Dynamic post-translational modifications of the CTD specify a molecular recognition code akin to the histone code that is deciphered by proteins during transcription. While in vitro transcription can proceed without this domain, deletion of the CTD in mouse, Drosophila or yeast is lethal. Despite the progress made to track Ser2, Ser5, and Ser7 phosphorylation throughout the initiation-elongation-termination transcription cycle, the universality of these sequential patterns of phosphorylation across different CTD heptapeptides remains unknown. Furthermore, cross-talk between different modifications is a phenomenon often recognized for its importance, though to date poorly understood. Tandem mass spectrometry (MS/MS) by electron-transfer dissociation (ETD) is uniquely equipped to carry out this characterization of post-translationally modified CTD. Initial experiments have optimized conditions for the production, phosphorylation, and sequencing of triplet CTD constructs (CTD3). Using ETD performed in a specialized reaction cell, we improved the CTD3 sequence coverage by nearly 200% as compared to a conventional fragmentation method.

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