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Japanese researchers provide the first large-scale identification of protein control sites from the model plant Arabidopsis

06.10.2008
A team of Japanese biologists, including Ken Shirasu from the RIKEN Plant Science Center in Yokohama, has provided a snap-shot of the proteins regulated by phosphate, collectively known as the ‘phospho-proteome’, in living plant cells. This is the first time such a large-scale comprehensive analysis has been performed in plants.

In plants, protein modification by the introduction of a phosphate group, a process known as phosphorylation, regulates cell signaling in response to a wide range of external and internal stimuli such as pathogen attack or hormone release (Fig. 1). Nearly all cellular processes are controlled by switching proteins on and off using phosphate, a molecule containing phosphorous and oxygen atoms. Phosphate modulates protein functions by bonding to an amino acid residue, such as serine, threonine or, less commonly, tyrosine.

The whole-cell approach

In previous studies of phosphorylation in plants, only parts of the cell such as the plasma membrane were assessed. Uniquely, the team, led by Shirasu and Yasushi Ishihama from Keio University, Tsuruoka, used unfractionated, whole cells to provide an overall view of phosphorylation in all the cellular components of the model plant Arabidopsis thaliana (Fig. 2). The team employed six procedures to isolate phosphorylated peptides—ensuring a wide variety of peptides were captured—and analyzed them using mass spectrometry, a technique that identifies the chemical composition of molecules.

Their approach identified 2,172 unique phosphorylation sites on 1,346 proteins from Arabidopsis cells. Over 85% of the identified phosphoproteins were novel, establishing this data-set—published recently in Molecular Systems Biology1—as the largest available to date. “This work is just the beginning of a long journey to understand the ‘complete map’ of phosphorylation sites in plants,” says Shirasu.

Firstly, the researchers surveyed the characteristics of phosphoproteins and phosphorylation sites in Arabidopsis. Then they analyzed the abundance, distribution, molecular and biological functions and cellular localization of identified phosphoproteins and compared these traits with those of all proteins encoded by the Arabidopsis genome. The distributions of the molecular functions of the phosphoproteins were aligned to those of all genome-encoded proteins, suggesting that most cellular processes in Arabidopsis are likely to be regulated at least in part by various phosphorylation events. They also showed that all sub-cellular compartments of the plant cells investigated contained phosphorylated proteins, but that nuclear proteins were the most popular targets for phosphate groups with approximately 40% of phosphorylation events taking place in the cells’ headquarters.

An unexpected similarity between plants and humans

Shirasu, Ishihama and colleagues found phosphorylation to be focused mainly on serine and threonine; 85.0 and 10.7% of all phosphate introductions took place on these amino acid residues. Surprise came when 94 of the 2,172 identified sites of phosphorylation were found to occur on tyrosine residues. This level of phosphotyrosine was much higher than expected, explains Shirasu, indicating that the extent of tyrosine phosphorylation has been largely underestimated in plants. At 4.3%, the level of phosphorylation events that occur on tyrosine is similar to that found in humans, where the range is between 1.8 and 6%.

Intriguingly, humans employ over 90 enzymes, collectively known as tyrosine kinases, that work specifically to phosphorylate tyrosine residues, but these enzymes do not exist in Arabidopsis. The researchers investigated the mechanism that might be used by plants to attain this high level of tyrosine phosphorylation by comparing patterns of amino acids around tyrosine phosphorylation sites in Arabidopsis and humans. They found most of the plant-based motifs to be novel and distinct from those in humans, indicating that tyrosine phosphorylation in Arabidopsis is carried out by a novel class of kinases that are specific to plants. Candidates for the role could include multi-specific serine/threonine/tyrosine protein kinases or enzymes called tyrosine-specific protein kinase-like kinases (TKLs), which are especially abundant in plants.

The function of TKLs remains unclear, but their plentitude in plants suggests that they are significant in catalyzing molecular reactions. It will be of particular interest to investigate whether plant TKLs possesses tyrosine phosphorylation activity, according to Shirasu.

Elucidating the roles of key players

Tyrosine phosphorylation plays a central role in a variety of signal transduction pathways regulating animal cell growth and differentiation, but its relevance in plants is still largely unknown. Shirasu, Ishihama and colleagues found that many tyrosine phosphorylated proteins are involved in cellular signaling and are likely to be crucial players in the regulation of cellular processes.

Trends in the protein-based position of phosphorylation sites can provide clues to their functions. The research team investigated whether the phosphorylation sites identified in this study are located in important areas known as conserved domains. These domains are conserved through evolutionary time and contain essential features that perform vital protein functions. Phosphorylation sites involving serine and threonine were found to be located mainly outside conserved domains, but, strikingly, nearly half of the phosphorylated tyrosine residues were located on conserved domains. These data indicate that tyrosine phosphorylation may have more impact on key regulatory processes compared to serine and threonine phosphorylation.

To further enrich the map of phosphorylated proteins, the researchers will need to extract proteins from different cell types over various developmental stages and under different environmental cues such as light, temperature, humidity and pathogen exposure. A future goal of the team is to determine the role of phosphorylation in plant immunity by isolating proteins that are phosphorylated when plants encounter pathogens. According to Shirasu, “we show here that the technology is ready and the next stage is to ‘just do it’.”

Reference
1. Sugiyama, N., Nakagami, H., Mochida, K., Daudi, A., Tomita, M., Shirasu, K. & Ishihama, Y. Large-scale phosphorylation mapping reveals the extent of tyrosine phosphorylation in Arabidopsis. Molecular Systems Biology 4, 193 (2008).

The corresponding author for this highlight is based at the RIKEN Plant Immunity Research Group

Ken Shirasu

Ken Shirasu graduated from the Department of Agricultural Chemistry at the University of Tokyo in 1988. He moved to the USA and earned his PhD in genetics at the University of California, Davis, in 1993. He then obtained a Salk/Noble postdoctoral fellowship to study plant immunity at the Salk Institute in the USA. In 1996 Shirasu moved to the Sainsbury Laboratory in the UK as a researcher, where he later became a group leader in 2000. In 2006 he returned to Japan and became a group director at RIKEN Plant Science Center. He has also been a visiting professor in the Department of Biological Sciences in the University of Tokyo since 2008. His research focuses on molecular elucidation of the mechanism for plant immunity.

Saeko Okada | ResearchSEA
Further information:
http://www.rikenresearch.riken.jp/research/525/
http://www.researchsea.com

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