Exploration of Eukaryotic Cells and Organelle NMR Signatures

Abstract

Whole-cell protein profiling, spatial localization, and quantification of activities such as gene transcription and even protein translation are possible with modern biochemical and biophysical techniques. Yet, addressing questions of overall compositional changes within an intact cell – capturing the relative amounts of protein and ribosomal RNA levels and lipid content simultaneously - pose a challenge to many analytical methods and would require numerous extractions and purifications with caveats due to isolation yields and detection methods. A holistic view of cellular composition could aid in the study of cellular function and misfunction. Here, solid state NMR is used to identify 13C NMR signatures for cellular organelles in HeLa cells, without the use of any isotopic labeling. These signatures were characterized both in isolated organelles and in the context of whole HeLa cells. The results reveal that a cell can be deconstructed into its cellular machinery on a spectroscopic level. We additionally performed 13C NMR on intact cells from additional mammalian cell lines, demonstrating biological variability and similarities between them. Many diseases are known to effect specific organelles, such as mitochondrial diseases. An ability to measure parameters of composition and to provide quantitative comparisons among samples, without ambiguities possible from cellular digests and extractions, is an attractive approach to guide analysis of biochemical changes in a cell or tissue. Fundamentally, it is also intriguing to catalog and examine the different ratios of biomolecule types in cells with single-sample spectroscopic snapshots. We believe that this exploration will serve as a discovery tool to reveal changes in cellular pools to help dissect the modes of action of molecules that influence cellular processes and to understand changes in mis-functioning cells.