Research shows how a sugar-sensitive protein acts as a ‘machine’ to switch plant growth (and oil production) on and off

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This image shows a plant protein known as KIN10 (yellow) that acts as a sensor and switch to turn oil production off or on depending on whether it interacts with another protein (green). Credit: Brookhaven National Laboratory

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This image shows a plant protein known as KIN10 (yellow) that acts as a sensor and switch to turn oil production off or on depending on whether it interacts with another protein (green). Credit: Brookhaven National Laboratory

Proteins are molecular machines, with flexible parts and moving parts. By understanding how these parts move, scientists can unravel a protein’s function in living things – and possibly change its effects. Biochemists at the U.S. Department of Energy’s (DOE) Brookhaven National Laboratory and colleagues at DOE’s Pacific Northwest National Laboratory (PNNL) have published a new example of how such a molecular machine works.

Their article in the magazine Scientific progress describes how the moving parts of a given plant protein determine whether plants can grow and make energy-intensive products like oil – or instead take a series of steps to conserve precious resources. The study focuses specifically on how the molecular machinery is regulated by a molecule that rises and falls with the level of sugar: plants’ main energy source.

“This paper reveals the detailed mechanism that tells plant cells, ‘we have a lot of sugar,’ and then how that signaling affects the biochemical pathways that trigger processes such as plant growth and oil production,” said biochemist Jantana Blanford of Brookhaven Lab, who led the study . author.

The study builds on previous work by the Brookhaven team that uncovered molecular links between sugar levels and oil production in plants. A possible goal of this research is to identify specific proteins (and parts of proteins) that scientists can engineer to create plants that produce more oil for use as biofuels or other oil-based products.

“Precisely identifying the interactions between these molecules and proteins, as this new study does, brings us closer to identifying how we can engineer these proteins to increase vegetable oil production,” said John Shanklin, chair of the department Brookhaven Lab Biology and research team leader. .

Unraveling molecular interactions

The team used a combination of laboratory experiments and computational modeling to explore how the molecule that serves as a sugar proxy binds to a “sensor kinase” known as KIN10.

KIN10 is the protein that contains the moving parts that determine which biochemical pathways are on or off. The scientists already knew that KIN10 acts as both a sugar sensor and a switch: When sugar levels are low, KIN10 interacts with another protein to initiate a cascade of reactions that ultimately shut down oil production and release energy-rich molecules like oil and other substances breaking down. starch to make energy that powers the cell.

But when sugar levels are high, KIN10’s shutdown function is disabled, meaning plants can grow and make lots of oil and other products with the abundant energy.

But how does the sugar proxy that binds to KIN10 flip the switch?


This diagram shows the two pathways that KIN10 and a neighboring protein, GRIK1, follow in low and high sugar conditions. A low sugar content allows the addition of a phosphate (P) to KIN10, which initiates a phosphorylation cascade leading to the breakdown of enzymes involved in oil synthesis. This includes degradation of WRI1, the master switch for oil synthesis. However, when sugar is abundant, a sugar proxy molecule (T6P) binds to the KIN10 loop to block the interaction with GRIK1. This keeps the oil synthesis route open. Credit: Brookhaven National Laboratory

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This diagram shows the two pathways that KIN10 and a neighboring protein, GRIK1, follow in low and high sugar conditions. A low sugar content allows the addition of a phosphate (P) to KIN10, which initiates a phosphorylation cascade leading to the breakdown of enzymes involved in oil synthesis. This includes degradation of WRI1, the master switch for oil synthesis. However, when sugar is abundant, a sugar proxy molecule (T6P) binds to the KIN10 loop to block the interaction with GRIK1. This keeps the oil synthesis route open. Credit: Brookhaven National Laboratory

To find out, Blanford started with the adage “opposites attract.” She identified three positively charged parts of KIN10 that could potentially be attracted to abundant negative charges on the sugar proxy molecule. A laboratory-based elimination process in which variations of KIN10 were created with modifications to these sites identified the one true binding site.

Next, the Brookhaven team turned to computational colleagues at PNNL.

Marcel Baer and Simone Raugei from PNNL investigated at the atomic level how the sugar proxy and KIN10 fit together.

“Using multiscale modeling, we found that the protein can exist in multiple conformations, but only one of them can effectively bind the sugar proxy,” Baer said.

The PNNL simulations identified important amino acids in the protein that control the binding of the sugar. These computational insights were subsequently confirmed experimentally.

The combined amount of experimental and computational information helped the scientists understand how the interaction with the sugar proxy directly affects the downstream action of KIN10.

Flip the switch

“Additional analyzes showed that the entire KIN10 molecule is rigid, except for one long flexible loop,” Shanklin said. The models also showed that the loop’s flexibility allows KIN10 to interact with an activator protein, triggering the cascade of reactions that ultimately shut down oil production and plant growth.

When sugar levels are low and there is little sugar proxy molecule present, the cycle remains flexible and the shutdown mechanism can kick in to reduce plant growth and oil production. That makes sense to preserve precious resources, Shanklin said.


This animation shows how a flexible loop (orange) on a plant protein known as KIN10 (yellow) allows it to interact with another protein (green) – but only when sugar levels are low. The interaction of the two proteins triggers a cascade of reactions that break down other proteins involved in oil synthesis so that the plant can conserve its resources. When sugar levels are high, meaning the plant has abundant resources, a sugar proxy molecule blocks the swinging motion of the loop. This prevents protein interaction, leaving the oil production route open. Credit: Brookhaven National Laboratory

But when sugar levels are high, the sugar proxy binds tightly to KIN10.

“The calculations show how this small molecule blocks the loop from spinning and prevents it from triggering the shutdown cascade,” Blanford said.

Again, this makes sense because there are abundant sugars available for plants to make oil.

Now that scientists have this detailed information, how can they use it?

“We could potentially use our new knowledge to design KIN10 with modified binding strength for the sugar proxy to change the set point at which plants make things like oil and break things down,” Shanklin said.

More information:
Jantana Blanford et al, Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1, Scientific progress (2024). DOI: 10.1126/sciadv.adn0895. www.science.org/doi/10.1126/sciadv.adn0895

Magazine information:
Scientific progress

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