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Intracellular molecular network analysis using optical manipulation of enzymes

Genki Kawamura, Postdoctoral Researcher, Department of Chemistry
Takemasa Ozawa, Professor, Department of Chemistry


Cells are composed of many biomolecules, which work closely together to maintain biological functions.
For example, the nutrients we take in through our diet are utilized as a source of energy or a constituent material of the body through metabolic reactions involving many enzymes.
How can we identify the function of a single enzyme among these enzymes that work in concert?
We have developed a "light manipulation technique" to manipulate the activity of a specific enzyme at will, and by performing transomics analysis using a vast amount of biomolecular measurement data, we have clarified the intracellular role of a specific enzyme.

We maintain biological functions by taking in nutrients, mainly glucose (glucose), from the outside and converting them into energy, nucleic acids, proteins, and other biological components in the cells. This series of work consists of a wide variety of metabolic pathways. Even the same starting material can be converted into a different material if the metabolic pathway is different. For this reason, cells are equipped with a signaling system to select and guide the necessary metabolic pathway. One of the important proteins for this signaling is the protein phosphatase Akt2.

Activated Akt2 activates intracellular signals and induces various gene expressions. As a result, the amounts and activities of enzymes involved in metabolism are altered, resulting in large changes in the amounts of metabolites. It has been elucidated that Akt2 activation is required for the regulation of metabolic pathways. However, since the metabolites produced also regulate other enzyme activities (allosteric effect), the metabolic pathways are intricately intertwined, and the full metabolic network regulated by Akt2 is not yet understood.

Therefore, we have developed a method to produce light-sensitive Akt2 and to activate Akt2 in cells in a light-irradiation-dependent manner. This method enables spatio-temporal control of Akt2 activity by regulating the intensity of irradiated light. In order to identify the metabolic pathways regulated by Akt2, a large-scale analysis of biomolecules such as enzymes and their metabolites involved in the metabolic pathways (trans-omics analysis) *) was conducted. This analysis is characterized by identifying molecules that show changes in response to Akt2 activation based on the measurement results of biomolecule abundance changes, and by drawing a network of causal relationships among the molecules that show changes by referring to a database. The networked approach enables the identification of altered metabolic pathways, and reveals the existence of metabolic pathways in which Akt2 alone is sufficient, and metabolic pathways that require Akt2 but do not work sufficiently with Akt2 alone.

Although many enzymes are known to play key roles in intracellular signaling, the causal relationship between specific enzymes and the phenomena they induce is not clear for many enzymes. If the above analysis techniques are applied to other specific enzymes, it will be possible to elucidate the intracellular intermolecular networks regulated by those enzymes. Further research is also expected to be conducted to predict the effects of enzyme-targeted therapeutics.

We introduced artificial light-sensitive Akt2 into cultured cells and measured and analyzed the biomolecular changes that occur when Akt2 activation is induced on a large scale. By networking the relationships among biomolecules, the role of Akt2 can be identified.


This study was published in G. Kawamura et al., Sci. Signal. 16 , eabn0782 (2023).

(Note) An analytical method for estimating interactions between biomolecules by integrating multiple omics layers longitudinally (trans-omics) using large data sets (omics layers) of biomolecules with similar physical properties that have been comprehensively investigated.


(Press release, February 22, 2023)

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