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Sugar-Sensing Proteins: A Potential Breakthrough for Sustainable Biofuel

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Saturday, June 15, 2024

Recent research by the Brookhaven National Laboratory explores how plant proteins respond to sugar levels. The study reveals that the sugar proxy molecule’s binding to the KIN10 protein influences plant growth and oil production. This insight could lead to genetic modifications in plants to enhance oil output for biofuels. Credit: SciTechDailyA new study shows how sugar levels influence plant growth and oil production through the protein KIN10, offering the potential for advancements in biofuel production.Proteins function as molecular machines, equipped with flexible components and moving parts. Gaining insight into these movements is crucial for scientists as it helps them understand the role a protein plays in organisms, and it may also guide them in modifying its effects. A team of biochemists from the U.S. Department of Energy’s Brookhaven National Laboratory and the Pacific Northwest National Laboratory have provided new insights into the mechanisms of these molecular machines within plants.In their recent study, published in Science Advances, the researchers focus on how the movements of a specific sugar-sensing protein determine whether plants grow and produce energy-intensive products, such as oil, or if they engage in conservatory measures. This image shows a plant protein known as KIN10 (yellow) that acts as a sensor and a switch to turn oil production off or on depending on whether it interacts with another protein (green). Credit: Brookhaven National LaboratoryMolecular Mechanisms UnveiledJantana Blanford, a Brookhaven Lab biochemist and the study’s lead author, explains, “This paper reveals the detailed mechanism by which plant cells are informed of high sugar availability, influencing biochemical pathways that facilitate plant growth and oil production.”The research expands upon earlier work from Brookhaven’s team that uncovered molecular links between sugar levels and oil production in plants. One potential goal of this research is to identify specific proteins and their components that scientists can engineer to make plants produce more energy-intensive products, such as oil.“Identifying exactly how these molecules and proteins interact, as this new study does, brings us closer to identifying how we might engineer these proteins to increase plant oil production,” said John Shanklin, lead author and chair of Brookhaven Lab’s Biology Department.VIDEOThis 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 the plant can conserve its resources. When sugar levels are high, meaning the plant has abundant resources, a sugar-proxy molecule blocks the loop’s swinging motion. That prevents the protein interaction, which keeps the oil-production pathway open. Credit: Brookhaven National LaboratoryNew Research on Protein InteractionsThe team used a combination of laboratory experiments and computational modeling to zero in on 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 set off a cascade of reactions that ultimately shut down oil production and break down energy-rich molecules like oil and starch to make energy that powers the cell. But when sugar levels are high, KIN10’s shut-down function is shut off — meaning plants can grow and make lots of oil and other products with abundant energy.This diagram shows the two pathways KIN10 and an adjacent protein, GRIK1, follow in the low- and high-sugar conditions. Low sugar allows the addition of a phosphate (P) to KIN10, which triggers a phosphorylation cascade that leads to the breakdown of enzymes involved in oil synthesis. This includes degradation of WRI1, the master-switch for oil synthesis. When sugar is abundant, however, a sugar-proxy molecule (T6P) binds to the KIN10 loop to block its interaction with GRIK1. That keeps the oil synthesis pathway open. Credit: Brookhaven National LaboratoryTo identify how the sugar proxy binding to KIN10 flips the switch, Blanford started with the adage “opposites attract.” She identified three positively charged parts of KIN10 that might be attracted to abundant negative charges on the sugar proxy molecule. A laboratory-based process of elimination that involved making variations of KIN10 with modifications to these sites identified the one true binding site.Then the Brookhaven team turned to computational colleagues at PNNL. Marcel Baer and Simone Raugei at PNNL examined at the atomic level how the sugar proxy and KIN10 fit together. “By using multiscale modeling we observed 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 key amino acids within the protein that control the binding of the sugar. These computational insights were then confirmed experimentally.The combined body of experimental and computational information helped the scientists understand how interaction with the sugar proxy directly affects the downstream action of KIN10.Brookhaven Lab members of the research team: Jantana Blanford, Zhiyang Zhai, Hui Li, Qun Liu, and John Shanklin (not shown: Gongrui Guo). Credit: Brookhaven National LaboratoryThe Role of Flexibility in Protein Function“Additional analyses 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 is what allows KIN10 to interact with an activator protein to trigger the cascade of reactions that ultimately shut down oil production and plant growth.Pacific Northwest National Laboratory co-authors Marcel Baer and Simone Raugei. Credit: Pacific Northwest National LaboratoryWhen sugar levels are low, and little sugar proxy molecule is present, the loop remains flexible, and the shutdown mechanism can operate to reduce plant growth and oil production. That makes sense to conserve precious resources, Shanklin said. However, when sugar levels are high, the sugar proxy binds tightly to KIN10.“The calculations show how this small molecule blocks the loop from swinging around and prevents it from triggering the shutdown cascade,” Blanford said.“We could potentially use our new knowledge to design KIN10 with altered binding strength for the sugar proxy to change the set point at which plants make things like oil and break things down,” Shanklin said. This knowledge could lead to more efficient production of biofuels and other oil-based products.Reference: “Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1” by Jantana Blanford, Zhiyang Zhai, Marcel D. Baer, Gongrui Guo, Hui Liu, Qun Liu, Simone Raugei and John Shanklin, 17 May 2024, Science Advances.DOI: 10.1126/sciadv.adn0895This work was supported by the DOE Office of Science (BES). Computer time was provided by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory and the Molecular Sciences Computing Facility (MSCF) in the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory. NERSC and MSCF are DOE Office of Science user facilities.

A new study shows how sugar levels influence plant growth and oil production through the protein KIN10, offering the potential for advancements in biofuel production....

A new study shows how sugar levels influence plant growth and oil production through the protein KIN10, offering the potential for advancements in biofuel production.

Proteins function as molecular machines, equipped with flexible components and moving parts. Gaining insight into these movements is crucial for scientists as it helps them understand the role a protein plays in organisms, and it may also guide them in modifying its effects. A team of biochemists from the U.S. Department of Energy’s Brookhaven National Laboratory and the Pacific Northwest National Laboratory have provided new insights into the mechanisms of these molecular machines within plants.

In their recent study, published in Science Advances, the researchers focus on how the movements of a specific sugar-sensing protein determine whether plants grow and produce energy-intensive products, such as oil, or if they engage in conservatory measures.

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

Molecular Mechanisms Unveiled

Jantana Blanford, a Brookhaven Lab biochemist and the study’s lead author, explains, “This paper reveals the detailed mechanism by which plant cells are informed of high sugar availability, influencing biochemical pathways that facilitate plant growth and oil production.”

The research expands upon earlier work from Brookhaven’s team that uncovered molecular links between sugar levels and oil production in plants. One potential goal of this research is to identify specific proteins and their components that scientists can engineer to make plants produce more energy-intensive products, such as oil.

“Identifying exactly how these molecules and proteins interact, as this new study does, brings us closer to identifying how we might engineer these proteins to increase plant oil production,” said John Shanklin, lead author and chair of Brookhaven Lab’s Biology Department.

VIDEO
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 the plant can conserve its resources. When sugar levels are high, meaning the plant has abundant resources, a sugar-proxy molecule blocks the loop’s swinging motion. That prevents the protein interaction, which keeps the oil-production pathway open. Credit: Brookhaven National Laboratory

New Research on Protein Interactions

The team used a combination of laboratory experiments and computational modeling to zero in on 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 set off a cascade of reactions that ultimately shut down oil production and break down energy-rich molecules like oil and starch to make energy that powers the cell. But when sugar levels are high, KIN10’s shut-down function is shut off — meaning plants can grow and make lots of oil and other products with abundant energy.

This diagram shows the two pathways KIN10 and an adjacent protein, GRIK1, follow in the low- and high-sugar conditions. Low sugar allows the addition of a phosphate (P) to KIN10, which triggers a phosphorylation cascade that leads to the breakdown of enzymes involved in oil synthesis. This includes degradation of WRI1, the master-switch for oil synthesis. When sugar is abundant, however, a sugar-proxy molecule (T6P) binds to the KIN10 loop to block its interaction with GRIK1. That keeps the oil synthesis pathway open. Credit: Brookhaven National Laboratory

To identify how the sugar proxy binding to KIN10 flips the switch, Blanford started with the adage “opposites attract.” She identified three positively charged parts of KIN10 that might be attracted to abundant negative charges on the sugar proxy molecule. A laboratory-based process of elimination that involved making variations of KIN10 with modifications to these sites identified the one true binding site.

Then the Brookhaven team turned to computational colleagues at PNNL. Marcel Baer and Simone Raugei at PNNL examined at the atomic level how the sugar proxy and KIN10 fit together. “By using multiscale modeling we observed 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 key amino acids within the protein that control the binding of the sugar. These computational insights were then confirmed experimentally.

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

Brookhaven Lab members of the research team: Jantana Blanford, Zhiyang Zhai, Hui Li, Qun Liu, and John Shanklin (not shown: Gongrui Guo). Credit: Brookhaven National Laboratory

The Role of Flexibility in Protein Function

“Additional analyses 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 is what allows KIN10 to interact with an activator protein to trigger the cascade of reactions that ultimately shut down oil production and plant growth.

Pacific Northwest National Laboratory co-authors Marcel Baer and Simone Raugei. Credit: Pacific Northwest National Laboratory

When sugar levels are low, and little sugar proxy molecule is present, the loop remains flexible, and the shutdown mechanism can operate to reduce plant growth and oil production. That makes sense to conserve precious resources, Shanklin said. However, when sugar levels are high, the sugar proxy binds tightly to KIN10.

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

“We could potentially use our new knowledge to design KIN10 with altered binding strength for the sugar proxy to change the set point at which plants make things like oil and break things down,” Shanklin said. This knowledge could lead to more efficient production of biofuels and other oil-based products.

Reference: “Molecular mechanism of trehalose 6-phosphate inhibition of the plant metabolic sensor kinase SnRK1” by Jantana Blanford, Zhiyang Zhai, Marcel D. Baer, Gongrui Guo, Hui Liu, Qun Liu, Simone Raugei and John Shanklin, 17 May 2024, Science Advances.
DOI: 10.1126/sciadv.adn0895

This work was supported by the DOE Office of Science (BES). Computer time was provided by the National Energy Research Scientific Computing Center (NERSC) at Lawrence Berkeley National Laboratory and the Molecular Sciences Computing Facility (MSCF) in the Environmental Molecular Sciences Laboratory at Pacific Northwest National Laboratory. NERSC and MSCF are DOE Office of Science user facilities.

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(Reuters) -James D. Watson, the brilliant but controversial American biologist whose 1953 discovery of the structure of DNA, the molecule of...

(Reuters) -James D. Watson, the brilliant but controversial American biologist whose 1953 discovery of the structure of DNA, the molecule of heredity, ushered in the age of genetics and provided the foundation for the biotechnology revolution of the late 20th century, has died at the age of 97.His death was confirmed by Cold Spring Harbor Laboratory on Long Island, where he worked for many years. The New York Times reported that Watson died this week at a hospice on Long Island.In his later years, Watson's reputation was tarnished by comments on genetics and race that led him to be ostracized by the scientific establishment.Even as a younger man, he was known as much for his writing and for his enfant-terrible persona - including his willingness to use another scientist's data to advance his own career - as for his science.His 1968 memoir, "The Double Helix," was a racy, take-no-prisoners account of how he and British physicist Francis Crick were first to determine the three-dimensional shape of DNA. The achievement won the duo a share of the 1962 Nobel Prize in medicine and eventually would lead to genetic engineering, gene therapy and other DNA-based medicine and technology.Crick complained that the book "grossly invaded my privacy" and another colleague, Maurice Wilkins, objected to what he called a "distorted and unfavorable image of scientists" as ambitious schemers willing to deceive colleagues and competitors in order to make a discovery.In addition, Watson and Crick, who did their research at Cambridge University in England, were widely criticized for using raw data collected by X-ray crystallographer Rosalind Franklin to construct their model of DNA - as two intertwined staircases - without fully acknowledging her contribution. As Watson put it in "Double Helix," scientific research feels "the contradictory pulls of ambition and the sense of fair play."In 2007, Watson again caused widespread anger when he told the Times of London that he believed testing indicated the intelligence of Africans was "not really ... the same as ours."Accused of promoting long-discredited racist theories, he was shortly afterwards forced to retire from his post as chancellor of New York's Cold Spring Harbor Laboratory (CSHL). Although he later apologized, he made similar comments in a 2019 documentary, calling different racial attainment on IQ tests - attributed by most scientists to environmental factors - "genetic."James Dewey Watson was born in Chicago on April 6, 1928, and graduated from the University of Chicago in 1947 with a zoology degree. He received his doctorate from Indiana University, where he focused on genetics. 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Watson was only 25 years old then and while he never made another scientific discovery approaching the significance of the double helix, he remained a scientific force."He had to figure out what to do with his life after achieving what he did at such a young age," biologist Mark Ptashne, who met Watson in the 1960s and remained a friend, told Reuters in a 2012 interview. "He figured out how to do things that played to his strength."That strength was playing "the tough Irishman," as Ptashne put it, to become one of the leaders of the U.S. leap to the forefront of molecular biology. Watson joined the biology department at Harvard University in 1956."The existing biology department felt that molecular biology was just a flash in the pan," Harvard biochemist Guido Guidotti related. 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