Our cells adjust to ever-changing conditions while preserving internal states necessary for survival, but exactly how they achieve both adaptability and stability remains unclear. For the first time, researchers including those from the University of Tokyo used a light-based technique called Raman spectroscopy to create snapshots of the entire protein landscape inside an E. coli cell in a nondestructive manner. Analysis of the data allowed the team to predict the ways in which protein abundances change in certain conditions, which could previously only be done by extracting the target proteins. This led them to observe how abundances of different proteins change depending on how they relate to basic function or situational adaptability.

All living things are made of cells, and the molecular machinery within them is imperative to survival. Different biomolecules, including RNA, proteins and more, have specialized roles and perform a range of functions. Proteins support living states by acquiring and metabolizing nutrients from external environments, synthesizing new material molecules for growth and division, and transmitting information to respond to the environment. Given their importance, researchers strive to characterize how protein abundances change under different conditions, and how the abundances are coordinated within cells.

“To explore the abundance of proteins in cells, the technique known as ‘proteomics’ is often used to create a dataset called a proteome profile. However, the standard approach requires extracting proteins to quantify them, which is destructive and takes many laborious steps. But, we have found a better way,” said Professor Yuichi Wakamoto from the Department of Basic Science at the University of Tokyo. “We demonstrated that cellular proteome profiles can be nondestructively inferred by simply exposing cells to light and analyzing their so-called Raman spectra, a type of scattered light from cells that conveys their molecular profiles.”

After they discovered this, Wakamoto, with Project Researcher Ken-ichiro F. Kamei and their team, wanted to understand why it is possible to predict a cell’s protein makeup from Raman light measurements or spectra. They found that abundance ratios of many proteins are globally coordinated across a range of conditions. A pattern emerged with a large core of proteins whose abundance ratios stay consistent and support basic cellular functions. Smaller groups of proteins tend to vary more depending on environmental changes, and this is what helps a cell adapt. This hierarchical structure explains how cells can remain stable while still responding flexibly to new conditions, and this study proves that Raman spectroscopy can be a powerful tool for exploring the complex world of cellular machinery.

“The biggest challenge for us was connecting and unifying the two distant fields of study, optics, in this case Raman spectroscopy, and omics, or the proteome, which have developed independently. Many measurements, data analyses and mathematical analyses were necessary to convince ourselves that the correspondence between cellular Raman spectra and omics profiles is real and has a firm foundation,” said Kamei. “It’s possible that by applying our method, we may be able to predict the early changes in cellular states associated with diseases and the molecular underpinnings that drive such changes. It's also important to dig deeper into how this pattern of protein ratios, which we call stoichiometry conservation, emerges. It is apparent in cell types beyond E. coli, including human cells, so it’s intriguing and likely important.”