The Model System Arabidopsis thaliana

The large majority of molecular insights into stress responses and acclimation, as well as into most other aspects of plant biology, have come through studies performed in the past three decades with the model system A. thaliana (vernacular names: thale cress or mouse-ear cress) (Fig. 2.23). Thus, throughout the first part of this book, A. thaliana is the most frequently mentioned species name. The main reason for this prominence is the status of A. thaliana as a model system for molecular and genetic studies. The remarkable progress achieved in elucidating mechanisms underlying a plant’s phenomenal ability to develop and survive in fluctuating environments has been possible only by focusing the attention and resources of a large global scientific community on one plant, for which sophisticated experimental tools have been developed.

Fig. 2.23. The model species Arabidopsis thaliana. (Photo courtesy of Bo Melander, Aarhus University, Aarhus, Denmark)

As initially proposed by Friedrich Laibach in 1943, A. thaliana was widely adopted as a model system in the 1980s (Provart et al. 2016). Important features guiding this choice were its short life cycle, ease of cultivation, high fecundity (abundance of offspring), self-compatibility and small genome. Rather fortuitously, it was later found that transformation—that is, the introduction of foreign genes—is particularly easy in A. thaliana. Together, these features greatly facilitate genetic analyses.

A short life cycle and high fecundity enable access to several generations and many different genotypes. Self-compatibility results in widely homozygous genomes, which are much easier to analyse, because in most loci only one allele is present. Ease of cultivation makes it possible to screen thousands of individuals from mutagenised populations for particular phenotypes. Finally, the year 2000 brought the breakthrough of the first completely sequenced plant genome (Arabidopsis Genome Initiative 2000).

The perception of light; hormone signalling pathways; pathogen resistance; transcriptional regulation mediating stress acclimation; transport of sugars, nitrate and micronutrients; cell cycle control; the biological clock; lignin biosynthesis— these and countless other fundamental aspects of plant biology have been molecularly dissected in A. thaliana. Genes involved in these processes were cloned, which then enabled studies on the encoded proteins and the interaction between components of a pathway. The principal approach was the isolation of mutants showing a phenotype of interest—for example, lack of response to a hormone or light stimulus. Such mutants were then analysed physiologically to obtain a more detailed understanding of the process in question.

Finally, through tedious, painstaking work, the causal mutation was located in the genome. After the sequencing of the A. thaliana genome, the so-called map-based cloning of genes became much easier. Numerous genetic screens have been performed with mutagenised transgenic plants. A good example is the identification of genes involved in cold, salt and drought acclimation. A strongly stress-responsive promoter was fused to the reporter gene luciferase and transformed into A. thaliana. Following mutagenesis, mutants were selected that showed a perturbed stress response such as a response even in the absence of stress, a stronger or weaker response than wild-type plants or a response to one stress factor but not another (Ishitani et al. 1997).

The isolation and characterisation of mutants, referred to as forward genetics, was—essentially after the completion of the genome sequence—complemented by reverse genetics. A mutant line for a particular gene is isolated and then physiologically characterised to infer the function of the gene. The prerequisites for this approach are knowledge about the existence of the genes, provided by the genome sequence, and the availability of mutant collections for ideally every gene in an organism. For A. thaliana such a resource was developed over many years by generating several hundred thousand transgenic lines with a random insertion of transfer DNA (T-DNA) from Agrobacterium tumefaciens, the bacterium widely used for plant transformation.

The site of insertion was determined in these several hundred thousand transgenic lines, the information deposited in a database (Alonso et al. 2003) and the seeds stored at a stock centre, where researchers can obtain them for a small fee. Owing largely to these approaches, information on the functions of the majority of the approximately 28,000 genes in A. thaliana is now available. At the same time it is important to note that this is by no means equivalent to a comprehensive understanding of plant biology. Most of the interactions between the hundreds of thousands of molecules within a plant have not been described and analysed yet.

Specifically, with respect to stress physiology, most acclimative and adaptive mechanisms are understood only qualitatively, not quantitatively. For example, many of the components of signal transduction cascades are known but the exact dose-response relationships are not understood. Similarly, the integration of multiple environmental cues has only in the past few years become a focus of intensive research activities. How does a plant integrate potentially conflicting stimuli into an appropriate response? This and other questions mark a frontier in molecular stress physiology.

A. thaliana has not just been instrumental in identification of hormone receptors, ion channels, transcription factors and many other key players in basic plant biological processes such as growth regulation, nutrition or stress acclimation. A. thaliana is a pioneer species native to Europe, Asia and north-western Africa, and has been introduced into North America. It thrives in diverse habitats throughout the northern hemisphere. Also, unlike crops, which are often studied for stress physiology, species that are naturally occurring in a wide range of habitats, such as A. thaliana, have not gone through genetic bottlenecks due to selection by humans.

They therefore encompass much greater genetic diversity. Thus, A. thaliana is also an ideal model system for studying the molecular basis of local adaptation (Mitchell-Olds and Schmitt 2006; Assmann 2013). What are the mechanisms underlying differences in cold tolerance between Scandinavian and northern African accessions of A. thaliana (Chap. 4, Sect. 4.2)? What were the molecular events selected during the colonisation of such diverse habitats? These and other questions can now be asked, and sometimes answered, with a resolution down to single bases of the DNA.

Still, one might ask why studies on one plant species can be so enlightening with respect to the stress acclimation and adaptation of most other plants species, even though those species may have colonised habitats with sometimes vastly different conditions. The answer lies in the principal conservation of mechanisms. Every higher plant regulates the aperture of its stomata in response to the internal and external water status. Understanding of the processes involved in opening and closing of stomata, and of signals and signal transduction chains employed to integrate diverse information into a physiological response, can then be used to study differences between plants. Likewise, modulation of growth depends on the same basic mechanisms of control over cell cycle activity and cell expansion. Furthermore, most plants possess basal tolerance of most environmental stress factors.

Differences in the degree of tolerance are due to variations in the fundamental mechanisms. The examples of halophytes and metallophytes, discussed in Chap. 7, can illustrate this. A. thaliana has a considerable ability to tolerate elevated salt or metal concentrations. This becomes apparent as hypersensitivity when genes involved in this tolerance are non-functional. Plant species adapted to extreme conditions that are not tolerable for A. thaliana often employ the same mechanisms involved in basal tolerance but with some variation.

Nonetheless, there are phenomena relevant to molecular stress physiology that cannot be studied in A. thaliana. Perhaps the most obvious ones are the major plant symbioses of mycorrhizae and nitrogen fixation. Most Brassicaceae, including A. thaliana, do not engage in these symbioses. Thus, other model systems have been established—namely, the legumes Lotus japonicus and Medicago truncatula.