Zhu S, Pan L, Vu LD, Xu X, Orosa-Puente B, Zhu T, Neyt P, van de Cotte B, Jacobs TB, Gendron JM, Spoel SH, Gevaert K, De Smet I.
New Phytol. 2024 Jan;241(2):687-702.
Functional annotation of proteins for signaling network inference in non-model species.
#ArtGenetics
Our fruits, vegetables, and cereal crops stem from a wild ancestor and have undergone major changes through millennia of domestication and selection. There are various ways to reveal plant diversity over time, and one of these is through the combination of art history and genetics (also known as #ArtGenetics).
We apply a gel-free phosphoproteomics pipeline to different biological systems: wheat and soybean organs, Arabidopsis cell suspension cultures, and Arabidopsis seedlings. We combine these systems with loss- and gain-of-function approaches (such as tightly controlled systems using a constitutively active form under a native, inducible promoter), engineered kinases, and specific stimuli to perform an untargeted mass spectrometric analysis of the phosphoproteome.
While the knowledge on post-translational regulation through transient phosphorylation in plants is growing because of its crucial importance in plant molecular networks, it remains an underexplored and challenging area.
In Arabidopsis and major crop species, phosphorylation is controlled by a large number of protein kinases and phosphatase complexes. However, for the majority of cytoplasmic kinases, membrane-associated receptor kinases and phosphatases unravelling physiological and developmental roles and identifying substrates remain a challenge.
Almost every organism is exposed to variation in temperature, on a daily and on a seasonal basis. This is especially true for plants that, as sessile organisms, need to continuously alter their growth, development, and physiology in response to temperature variation. To sense and respond to temperature changes, several molecular sensors and downstream signalling and response networks have evolved.
New tools, including a deep learning model, predict the functionality of proteins, even in non-model organisms
In 1822, Gregor Mendel - the founding father of genetics – was born. In 1866, he published “Experiments on plant hybrids”, a 40-pager in which he describes the transmission of characteristics in pea to their progeny. Little did he know that it would become the foundation of modern genetics. In the early 1900s, after his death in 1884, his findings were rediscovered and Mendel’s Laws of Inheritance grew into the basis of modern biology. To celebrate his 200th birthday we look back and ahead together with VIB scientists Ive De Smet, Joren De Ryck, and Matilde Sanches from the VIB-UGent Center for Plant Systems Biology, and Seppe De Winter from the VIB-KU Leuven Center for Brain & Disease Research.
