The Shabek Laboratory focuses on researching plant signaling pathways and molecular responses to light
UC Davis researcher and professor Nitzan Shabek and his laboratory were examining cryptochrome-2, a blue-light receptor, from the plant Arabidopsis thaliana when they determined part of its crystal structure, according to a study published in the journal Nature Communication Biology. The part of the molecule that they identified undergoes a structure change when it reacts with light particles, meaning that it transforms from a structure with one unit to four attached units, also known as a tetramer.
Shabek—an assistant professor at the College of Biological Sciences in the Department of Plant Biology—completed his postdoctoral at the University of Washington in Seattle. He originally focused his studies in cellular and molecular biology before gaining an interest in structural biology, which led to his current studies in plant molecular pathways.
He founded the Shabek Laboratory in the summer of 2018, where he and his team focus on researching plant signaling pathways and studying plants at the molecular level when they react to light.
“We are investigating at a molecular level, but also an organismal level how plants can sense their environment,” Shabek said.
In a recent paper by the Shabek Laboratory, researchers mutated plant genes to learn more about how plants sense blue light. They found that when the genes were mutated, the plant did not respond to blue light.
To determine the structure of the gene that underwent a change from one to four units, a protein was purified and crystallized so that a particle accelerator from the Advanced Light Source X-ray facility at the Lawrence Berkeley National Laboratory could shoot an X-ray beam through the crystals. The results would make it possible to form a calculation that gives the coordinates of where every atom is in space and ultimately the structure.
Samuel Deck, a junior specialist and lab manager at Shabek’s Laboratory, assisted with part of the project, including identifying when a plant is in a photoactive state.
“We took the crystals and were able to look at them with a spectrophotometer, and by the characteristics we could identify the oxidation or reduction states of the [flavin adenine dinucleotide (FAD)] which is a key component molecule in the protein,” Deck said.
Researchers decided to use an insect cell expression system to make enough proteins for crystallography, instead of the more common bacterial expression system. Though the Shabek Laboratory tried using a bacterial expression system, E.Coli did not produce an active state protein and it was not well behaved, so the insect cell expression system was used instead.
“It was definitely a difficult and expensive process,” Shabek said.
Shabek’s main protein structure was compared to many other protein structures. He was surprised that small changes were visible during the comparison, which otherwise would have been overlooked by viewing the main protein structure alone. These changes determined whether a protein was non-active or photoactive.
“It’s amazing to see what is causing a response in plants,” Deck said. “You could see the small details and that’s what really surprised me.”
Deck stressed that it is important to educate the public on these types of processes and how they are applied in science. One of the goals of the laboratory is to provide the fundamentals for understanding the pathways of plants to any individual who is curious.
When looking at the molecular level, it is possible to see the implications of how the whole organism works, according to Shabek. Organisms such as plants are able to sense their environment and react immediately. For example, it is simple to acknowledge at the phenotypic level that trees lose their leaves in fall. It is the molecular mechanism that causes this to happen that needs to be investigated.
A crucial aspect of exploring the question of how plants sense light is to study how they sense different spectrums of light. The variation in how they react in the dark versus in the light, as well as what sensors detect specific colors of light, need to be taken into consideration.
The Shabek Laboratory is currently interested in looking at the cryptochrome mode of action and gaining a structure level understanding of its interactions with other proteins. The lab also plans to work with hormone signaling pathways in plants and to explore how different organs in the plant communicate with other organs and the environment.
The process of proteins getting destroyed in a regulatory manner in the cell is being examined by the laboratory as well. When a protein is done performing its function, it will need to be removed or it will continue with the same function, which can implicate disease. The lab is interested in how the plant system recognizes the protein and destroys it.
Written by: Francheska Torres — science@theaggie.org
