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From model organism to a model family

For many decades, the thale cress (Arabidopsis thaliana) has served as an excellent model for biologists. However, in the future it may also be joined by cruciferous plants (Brassicaceae) serving as a model. A few years ago, the plant physiologist Dr. Gerhard Leubner and his team at the University of Freiburg discovered that garden cress (Lepidium sativum) was an excellent model for their research on germinating seeds. This small plant with its acrid taste seems to be better suited to many experiments than other plants. In addition, modern approaches in biology are increasingly focusing on the comparison of different species. Is it possible that researchers will be working with model clans in future?

The photo shows a tip of a radicle protruding from a seed – first, the seed coat (brown) bursts, and is then followed by the endosperm (white) which is located just beneath. © www.seedbiology.de

Dr. Gerhard Leubner and his Department of Plant Physiology team at the Institute of Biology II at the University of Freiburg occasionally work with what could be referred to as somewhat "tired" plants. In order for plants to restrict their germination to times when optimal environmental conditions exist, many plant species have established a strategy known as dormancy. This "sleep-like" state is a kind of a physiological blockage that prevents the plants from germinating - a phenomenon characterized by complex molecular mechanisms. When it is that the radicle finally grows, it does so in a big way. The embryo is protected by two coats - the outer seed coat and the endosperm, which are layers that provide protection and food. The seedling has to break through these two coats in order to emerge. What are the underlying mechanical processes? What happens at the physiological level? "Many of these questions can be answered by carrying out experiments on the most important plant model organism of recent years," said Leubner referring to Arabidopsis thaliana or thale cress. "But it cannot be used to answer all the questions that arise - far from it."

Suitable for tweezers and scalpel

Garden cress - Lepidium sativum © Source: Rainer Zenz

Biologists have been using Arabidopsis thaliana as a model organism in genetic studies since the 1940s. With its five pairs of chromosomes, its relatively small genome and up to ten thousand seeds per plant, Arabidopsis has become a practical and popular study object. Foreign genes can easily be introduced into the Arabidopsis genome using Agrobacterium tumefaciens. In 2000, the entire genome of the plant was sequenced, which in turn has catapulted the inconspicuous plant many steps forward in terms of molecular biology research. However, Arabidopsis also has some disadvantages, especially in the area of seed research. "The seeds are very small and it is difficult to isolate individual tissues," said Leubner adding, "this does not enable an organ-specific separation in experiments using molecular biology methods." In contrast, garden cress is an excellent plant for such experiments. Lepidium sativum seeds are very similar to those of Arabidopsis, only a lot bigger. The embryo, endosperm and the radicle can be easily separated using tweezers and scalpels. The plant has since become established as a new model organism in the laboratory of Leubner and his team.

The photo shows two brown seeds against a black background. The Arabibidopsis thaliana seed on the left is a lot smaller than the Lepidium sativum seed on the right
Garden cress seeds (right) are much larger than Arabidopsis seeds (left) and can easily be dissected. © www.seedbiology.de

The following example shows the advantages of using two model organisms from the same family. Using gene chips, Leubner and his team have examined the entire transcriptome of cress seeds during germination. The transcriptome refers to all RNAs that serve as templates for proteins and that are generated at a specific point in time when the genes are transcribed. The researchers were able to identify the cress genes that are active during germination and that play an important role in this process, and the team is now in the process of clarifying the functions of these genes in subsequent experiments. The size of the cress seeds has also enabled the researchers to differentiate the transcriptomes of the individual tissues from each other. In addition, since garden cress is closely related to Arabidopsis, they have been able to compare the RNA sequences with known Arabidopsis sequences in order to identify homologies. “Since the function of many Arabidopsis genes is already known, this enables us to make founded assumptions on the function of the respective cress genes,” explained Leubner. “And we are also in a better position to investigate unknown genes using molecular genetic methods that have been developed for Arabidopsis research.” By using this comparative approach, the Freiburg researchers found that the volatile hormone ethylene is an important regulator of germination.

The photo shows a rectangular bar, divided into small small squares containing many small blue spots.<br />
Result of a transcriptome analysis: The chip contains Arabidopsis RNA probes. The blue/yellow spots show that the cress RNAs, stained with fluorescence, have bound to these probes. This enables the identification of RNAs that are present in cress. The strength of luminescence provides the researchers with information about the quantity of RNAs produced. © Work Group Gerhard Leubner

Individual or universal?

Logo of the most popular global Internet site on seed biology. The ‘Seed Biology Place' is maintained by Gerhard Leubner. © Work Group Gerhard Leubner

The two green relatives, therefore, complement each other well in experiments: the strengths of the one compensate the weaknesses of the other and vice versa. Leubner and his team are investigating the physiological processes that initiate and regulate the germination process, including the process that leads to the radicle breaking through the inner coat (i.e. endosperm). This is made possible since the endosperm starts to weaken during the germination process, initiated by the enzymes that degrade the cell wall of the enveloping tissue. The scientists use molecular biology and genetics methods in order to identify the genes that are involved in this process, in both Arabidopsis and Lepidium. The latter can also be easily genetically modified using Agrobacterium tumefaciens. The researchers use a biomechanical apparatus to find out what happens after the endosperm weakens. Puncture-force measurements enable them to determine the force required by the radicle to protrude through the endosperm. Garden cress is excellently suited to this type of experiment due to the size of its seeds.

Using a second model organism from the Brassicaceae family has another advantage: Many researchers who have found a specific gene in Arabidopsis that has a decisive function are bound to ask themselves whether this particular gene is only important in Arabidopsis or whether it has been conserved during evolution, and is therefore also important in a wider group of plants. If such biological knowledge is to be used for the optimisation of agriculturally relevant crops, then this knowledge needs to be as generalised as possible. A relevant assessment can only be made by comparing different species, as is being done by Leubner’s team and many other groups of researchers worldwide. “I think we are seeing a new development,” said Leubner. “In future the mustard family (Brassicaceae) will provide us with several model organisms, and our work will then most likely focus on model families or clans rather than individual model organisms. And sooner or later it is inevitable that other plant families will be used,” said Leubner. Leubner and his colleagues are hoping that the genome sequence of garden cress will soon be deciphered, as this will make their experiments even easier.

Further information:

PD Dr. Gerhard Leubner
Institute of Biologiy II, Botany/Plant Physiology
Schänzlestr. 1
University of Freiburg
Tel: +49 (761) 203 2936
Fax : +49 (761) 203 2612
E-mail: gerhard.leubner(at)biologie.uni-freiburg.de

Website address: https://www.biooekonomie-bw.de/en/articles/news/from-model-organism-to-a-model-family