Biochemical, analytical high-throughput methods used to map proteome of plants

By Emily Henderson, B.Sc.Mar 13 2020

Plants play a crucial role in the survival of life on earth. They offer oxygen for breathing and food for all organisms, as well as regulating the planet’s climate.

Proteins are vital in controlling all aspects of life, including plants.

By mapping more than 18,000 proteins, TUM scientists have created an extensive molecular reference for the popular model plant Arabidopsis thaliana, which is freely accessible via the online database “ProteomicsDB.” Image Credit: Lehrstuhl für Proteomik und Bioanalytik.

Led by the Technical University of Munich (TUM), a group of researchers has mapped nearly 18,000 of all the proteins occurring in the model plant Arabidopsis thaliana.

In any organism, each cell contains the entire genetic information or the blueprint of a living being, encoded in the sequence of what is called the nucleotide building blocks of DNA.

It is still not clear how a plant produces tissues as diverse as a leaf, transforming light into chemical energy to produce oxygen or a root that takes in nutrients from the soil.

The solution to this question is in the protein pattern of cells of the respective tissue. Proteins are the major molecular players of cells. They serve as biocatalysts, form the structure of a cell, transmit signals within and between cells, and have many more functions.

To form the protein pattern, it is not only important which proteins are present in a tissue, but, more importantly, in what quantities.”

Bernhard Kuster, Professor of Proteomics and Bioanalytics, Technical University of Munich

For instance, proteins involved in the photosynthesis machinery are mainly found in leaves, as well as in seeds, but 1000 times lower than in leaves.

Laboratory plants as a model for basic research

The team led by Dr. Julia Mergner and Prof. Bernhard Kuster investigated the model plant Arabidopsis thaliana, also called thale cress, using biochemical and analytical high-throughput methods to determine its molecular composition in detail.

For nearly four decades, this insignificant weed with small white flowers has been the “laboratory mouse” for studies on plant biology. It is small, easy to grow, and mostly undemanding. These properties have enabled its frequent use in the fields of molecular biology and genetics.

Since knowledge gathered from fundamental studies can usually be applied to crop plants, Arabidopsis is great for investigating plant breeding.

A major portion of the data was produced by a method called liquid chromatography-tandem mass spectrometry, in which thousands of proteins can be analyzed in parallel in a single experiment, while bioinformatics methods were used for the analysis of enormous amounts of data.

Arabidopsis—atlas for the global scientific community

For the first time, we have comprehensively mapped the proteome, that is, all proteins from the tissues of the model plant Arabidopsis. This allows new insights into the complex biology of plants.”

Bernhard Kuster, Professor of Proteomics and Bioanalytics, Technical University of Munich

The outcomes of the study were summarized in a virtual atlas that offers initial answers to the questions listed below:

• How many of the roughly 27,000 genes exist in plants as proteins (>18,000)?
• Where are the genes located within the organism (e.g. leaf, flower, or stem)?
• In what quantities, approximately, do the genes occur?

The entire data was made freely available in an online database—ProteomicsDB—which already includes a protein catalog for the human proteome, which was decoded by the same team at TUM in 2014.

Research results as the basis for future analysis of crop plants

One can predict that there exist similarities between Arabidopsis and the molecular maps of other plants. According to Prof. Kuster, “The Atlas should, therefore, also inspire research on other plant.”

As a next step, the researchers will focus on the analysis of crops. Specifically, they will examine the changes in the proteome when plants are attacked by pests, or ways in which plants can adapt to climate change.