Diverse VIB team investigates the possibilities of plant proteins

11 February 2017
Although both plants and animals are made up of cells, plants are generally unable to relocate, and thus can’t migrate around freely like animals can. These constraints lead them to grow through cell division in three directions – forward, sideways or upwards – with proteins playing a role in giving cells the “identities” that eventually lead to wood and other plant tissues. A multidisciplinary group of scientists from the VIB-UGent Center for Plant Systems Biology and the VIB-UGent Center for Medical Biotechnology recently collaborated on fundamental research that explores how the processes of plant root growth and patterning are affected by proteins – specifically, those that interact with a protein called ACR4.

Investigating the allure of roots
“At first sight, roots aren’t exciting at all,” jokes Tom Beeckman, ‘root guru’ at the VIB Department of Plant Systems Biology. “Roots only become interesting when you take a good look at their biology. Without roots, plant growth and productivity wouldn’t be possible.” Plant roots generally follow an ‘open growth strategy’,
growing and branching over the entire life of the plant to provide the plant’s aboveground parts with water and nutrients. They have the ability to use a layer of stem cells to create completely different tissues on the fly by responding to soil conditions. “Intrigued by this mysterious stem cell layer, we stumbled across the ACR4 protein kinase, which plays a role in root development,” Tom explains. “Protein kinases can change a protein’s 3D structure, and the cell uses a process called phosphorylation to fine-tune how proteins adapt to different
stimuli,” elaborates Kris Gevaert. “Protein interactions play an important role in cell processes within plants and animals, which is why the study of protein networks results in some interesting biological findings.”

The crucial role of proteomics
When proteins interact with other proteins, they form highly dynamic complexes that perform different
functions, depending on their interaction partners at any given moment. Phosphorylation plays an important role in how proteins respond to their environments. To investigate phosphorylation, scientists must zoom in down to the molecular level. “We use mass spectrometry-based proteomics to analyze phosphopeptides and thus determine the natures of – and actually measure – phosphorylation events. There’s no other technology that gives us such an in-depth look,” says Kris.

“Geert De Jaeger’s ‘Tandem Affinity Purification’ platform, or TAP, was also important to the study. The tool allows us to map protein-protein interactions in all of their details,” notes Ive De Smet. TAP comes with
the advantage of being able to detect protein interactions in situ as they occur. “TAP, in combination with mass spectrometry-based proteomics, helped us to gain completely novel insights into plant root development.”

ACR4: the most interesting protein
Ive has been studying the ACR4 protein for a decade, ever since he was a PhD student in Tom Beeckman’s lab. “This protein keeps getting more and more interesting,” he says. “The ACR4 equivalent in corn controls the
development of leaves and seeds, but we don’t know very much at all about its other components.”

Ive is convinced that the VIB Plant Systems Biology labs are the ideal environments for performing this kind of top level cross-domain research. “I’ve lived abroad and have been exposed to many different kinds of research environments, so I can say this with conviction,” he asserts.

Multifaceted approach, surprising findings
The key to the success of this project was the multidisciplinary, multi-technique approach that the diverse teams used to study ACR4. Plenty of new information was revealed, including the identity of one of ACR4’s interaction partners, protein PP2A-3. The team was also surprised to discover an unexpected biochemical feedback loop between ACR4 and PP2A, in which ACR4 phosphorylates PP2A and PP2A dephosphorylates ACR4.

Publication
Yue et al., Proc. Natl. Acad. Sci. U.S.A. 2016

From left to right: Kun Yue, Tom Beeckman, Ive De Smet, Geert De Jaeger, Daniël Van Damme and Kris Gevaert