Design And Applications Of Fluorescent Protein Based Biosensors For Live Cell Imaging

Fluorescent proteins (FPs) are essential tools of biochemical research. Traditionally, FPs have been utilized as markers of gene expression, protein localization, and organelle structure. In recent years, however, FPs have gained in popularity as active biosensors of cellular activity, in which the fluorescence intensity or colour of a FP chromophore is modulated in response to a change in its environment. Current methods for converting FPs into active biosensors of live cell biochemistry remain few in number and are technically challenging. In addition, a growing demand has emerged for spectrally orthogonal biosensors for monitoring multiple biological parameters in a single live cell. A challenge in realizing this goal is that the broad spectral profiles of FPs have limited the number of biosensors that can be used together. In this thesis I describe the engineering of new FP-based biosensors and further validating them via live cell multiparameter imaging. The first class of FP-based biosensors addressed in this thesis is Förster resonance energy transfer (FRET) biosensors. I described our efforts to use optimized spectrally distinct FRET-based biosensors to image Ca2+ dynamics in two distinct subcellular compartments as well as Ca2+ and caspase-3 activity in the same subcellular compartment. Although the inherently ratiometric response of FRET biosensor permits quantitative measurements, the fact that two FPs are involved in each FRET pair present a challenge with respect to their application in multiparameter imaging. To overcome this issue, we engineered intensiometric biosensors based on the recently introduced dimerization-dependent fluorescent protein (ddFP) technology. I demonstrate that ddFP-based protease biosensors enable the reporting of protease activity either by the intensiometric loss of the initially bright fluorescence or with dramatic green-to-red and red-to-green colour switches and translocation from the cytoplasm to the nucleus. In addition to detection of caspase activities, we also achieved specific highlighting of the mitochondria-associated membrane (MAM) using ddFP technology. Attempts to detect polyADP-ribose and polyubiquitin using ddFP technology were ultimately unsuccessful. Overall, this work serves to expand the scope of current FRET and ddFP-based biosensor designs and applications.