Scientists from Novosibirsk State University and the Institute of Ecology and Genetics SB RAS, Together with German Colleagues Build a 3D Model of a Plant Root for Stem Cell Research

Researchers at the Computer Transcriptomics and Evolutionary Bioinformatics Laboratory at the NSU Natural Science Department, together with scientists fr om the Institute of Cytology and Genetics SB RAS and the University of Freiburg (Germany) constructed a 3D model of root cell nuclei to study how stem cells are located in the tissue.

The root itself is very interesting to research because it provides the plant with the necessary water for growth of trace elements fr om the soil and holds the plant in the ground. The tip of the root is the "parent" of the whole organ and it contains the stem cells that divide and lengthen allowing the root to grow.

Victoria Lavreha, Junior Researcher at the NSU Computer Transcriptomics and Evolutionary Bioinformatics Laboratory, acting Head of System Biology of Plant Morphogenesis Sector at the Institute of Genetics and Genetics SB RAS talked about their research:

— We worked with the Arabidopsis thaliana as our model object examining the root tip area that was up to 1 mm in length. We used laser confocal microscopy that allowed us to look inside the root without cutting it. This required special preparation of the plants with fluorescent dye-proteins embedded in the cellular nuclei of the root system before the test. A laser beam with a specific wavelength excites these fluorescent proteins, the microscope "sees" the cell nuclei and scans the root with horizontal layers - up to 150 layers per hundred microns. Processing the resulting data set was done with a program developed by our colleagues from the University of Freiburg that reconstructed the transverse and longitudinal sections. The program uses the technology of nuclei recognition with their application to the cylindrical coordinate system and restores the three-dimensional arrangement of the cell nuclei. As a result, we got a model of the root that can be "twisted" from all sides and we can even look inside to see the spatial relationships between the cells inside the organ.

If we consider the transverse section of the root tip, there are several types of cells arranged in cylindrical layers one after another, from the outer part to the center. They are the epidermis, cortex, endodermis, pericyclic and vascular tissue in the middle. In the vascular tissue there are subtypes of cells, phloem and xylem, and their «objective» is to conduct organic and inorganic substances. Using the 3D model, researchers showed how this structure is formed from undifferentiated cells at the tip of the root.

Lavreha continued her description:

— At the root of the plant model are two columns of phloem and xylem cells penetrating along the entire length of the root. They differ from each other functionally and histologically and are arranged according to the laws of diarchic symmetry. This means that through the center of the body you can draw two mutually perpendicular planes and relative to each of them, the root is symmetrical i.e. the cells of the same type are repeated. There are root systems, wh ere these bundles of cells are three, four or more. How does division happen? Phloem is born from protophloem cells: first they differentiate (choose their destination), the nuclei disappear and cells begin to resemble vessels. Protoxylem cells are perpendicular to protophloem, and although they divide longer, they also specialize quite early. It turns out that at the tip of the root there are peculiar poles near wh ere the division takes place. For example, lateral roots are formed from the cells of the pericyclic (a layer of tissue around the vascular) at the protoxylem poles.

Based on observations, scientists were able to find out that even in vascular tissue stem cells, protofluid and protoxylem poles, there is a special microclimate that affects the rate of fission on nearby stem cells. In the pericycle protoxylem poles, the cells end up dividing earlier and pass into the «waiting mode», a state that is maintained until these cells begin to form lateral roots. The presence of protoxylem and protofluid poles is also characteristic of the endodermis, the layer following the pericyclic. For example, an increase in the endodermis layer rows occurs due to division only at the protoxylem poles. The authors believe that the choice of these cells for fission is associated with the concentration of phytohormones that propagate from the xylem in the transverse plane of the root.

Understanding the details of the appearance of new cells in the tip of the root is especially important for those cases when the normal processes of division in it are violated. The behavior of stem cells within the whole organ is still poorly understood. For animals this is complicated by the ability of cells to move. The 3D model of the plant root tip is the first example of a description of a complete stem cell niche, demonstrating how complexity and symmetry are born from one cell.