Revealing global stoichiometry conservation architecture in cells by Raman and gene expression correspondences

Ken-ichiro F Kamei, postdoc from Wakamoto Laboratory, Graduate School of Arts and Sciences, The University of Tokyo

Biological cells globally change their gene expression and metabolic states depending on their biological contexts and external conditions. Despite the complexity of molecular compositions in cells, the changes in molecular abundance are often correlated. However, what kinds of biological principles produce such low dimensionality of global molecular profiles of cells remains to be characterized.
Vibrational spectroscopy might help investigate such global constraints. It potentially provides the information on comprehensive molecular composition of target cells. Although biological interpretation of global spectral patterns remained unclear, recently we have shown that cellular Raman spectra could be computationally linked to multiple types of omics layers such as quantitative proteomes. Furthermore, the quantitative correspondence allows us to predict global changes in omics from Raman spectra. Importantly, the Raman-spectroscopic omics estimation was performed by using dimension-reduced Raman spectra.
In this study, examining the correspondence between proteomes and cellular Raman spectra of Escherichia coli, we characterize core and peripheral stoichiometrically-conserved groups in the proteomes. With methods in graph theory, we reveal a low-dimensional proteome structure based on global stoichiometry conservation relations of genes. Interestingly, this structure is reflected in major changes in cellular Raman spectra. Furthermore, the centrality of the characterized stoichiometry conservation architecture correlates with the essentiality and evolutionary conservation of genes. These results provide an omics-level interpretation of cellular Raman spectra and uncover an architectural principle of global omics profiles.