The Diva of Plant Research: "Arabidopsis thaliana"
A biological study starts with the identification of an unknown phenomenon, a research question to be addressed. In this manner, researchers need to simplify the molecular mechanisms they intend to work on by the utilization of non-human organisms that can serve as models. These are named "model organisms" and serve as a foundation for clinical trials to be performed (Hunter, 2008). In plant sciences, model organisms provide researchers with a clear path to understand the basics of key biological processes in a simpler aspect. There are numerous plant species to be discovered in nature, and using model organisms can help researchers overcome the lack of knowledge and research material (Abdurakhmonov, 2022). One of the commonly known model organisms in plant sciences that researchers have been taking advantage of is Arabidopsis thaliana. Research on A. thaliana has been utilized to integrate different fields of science such as molecular genetics as well as to understand the biological mechanisms of other plant and non-plant species. This article highlights the importance of A. thaliana research in plant sciences by explaining the evolutionary nature of the plant as well as exemplifying the biological research that has been performed throughout the years.
Diving into the History of Arabidopsis thaliana Research
Friedrich Laibach, a German botanist, was the first person to emphasize the idea of conducting A. thaliana research. During his doctoral studies, among the plant species he collected to analyze, he successfully identified the number of chromosomes of A. thaliana (Koornneef & Meinke, 2010). Later in his research, Laibach highlighted the advantages of performing research with A. thaliana and supported his claims with a developmental and physiological analysis of the plant. Nevertheless, Laibach’s research caused some skepticism due to a lack of information and experimental accuracy in the field of botany that were yet to be discovered. In the following years, one scientist who developed an interest in Laibach’s research, György P. Rédei, performed a mutagenesis screen for the Landberg A. thaliana seeds he originally obtained from Laibach (Somssich, 2018). After a few years of research, he identified a different line of A. thaliana, ‘Columbia’ that is commonly used in today’s botanical research.
The first conference on A. thaliana was held in 1965 in Gottingen, Germany. Since then, more than 50,000 academic papers have been published, which showed how the plant could be used as a model organism in different fields of science such as genetics, agronomy, cytology, and biochemistry. Using the Colombia line as the wild-type version of the plant species (as it is a homozygous line resistant to mutations), the full sequence of A. thaliana was published in 2000 (Somssich, 2018). It was the first plant genome to become available in plant research and has contributed immensely to other fields of science such as comparative genomics, pharmacology, and biochemistry.
Why Arabidopsis thaliana?
The advantage of using A. thaliana as a model organism relies on the fact that it has a relatively small genome size composed of approximately 135 mega-bases (1 mega-base equals to 1 million bases) that are completely sequenced. The plant has only five chromosomes, thus, it is relatively less complicated to be analyzed genetically when compared to other species. Thanks to the fact that it is small in size and self-fertile, it is easy to maintain, plus, it has a short generation time. In other words, the generation of a high number of seeds within a short period of time (48 days from germination) is possible (Krämer, 2015), thus, the average time required to conclude the research can be fairly short. Another advantage includes the availability of a broad library of mutants that can be used in order to perform functionality research on unknown genes. There are two major stock centers for A. thaliana (ABRC and NASC) from which scientists can order seeds and choose between different lines of the plant, which adds accessibility to the list of advantages.
In vivo studies of A. thaliana reveal that the plant can grow indoors when sufficient light and water conditions are maintained. The plant has all the visible features required to perform phenotypic analysis: flowers, stem, apical meristems, etc. Some of the gene families present in A. thaliana were revealed to be present in other plant species too, indicating that A. thaliana studies play a major role in comparative genomics and translational research (Woodward & Bartel, 2018).
Reverse and Forward Genetics in Arabidopsis thaliana Research
In order to determine the function of unknown genes, scientists tend to follow mutant analysis performed via two different strategies: reverse and forward genetics. In forward genetics, the experimental procedure starts with the identification of a biological process. After a highly redundant population of mutant plants is generated, they are screened for a change in phenotype. Later on, the gene that is thought to be causing the phenotype change is cloned and mapped for further studies. Reverse genetics, on the other hand, focuses on the gene first. After the generation of the mutant population, sequence-based mutant screens are performed. Lastly, the phenotype change is observed (Alonso & Ecker, 2006) in order to see the effects of the mutant gene on the physiological development of the plant.
Crop Research Examples Using Arabidopsis thaliana as a Model Organism
Using model organisms as tools, scientists have found multiple strategies to facilitate crop research. Similarly, A. thaliana remains to be one of the essential organisms to shed light on crop development. There are several case studies focusing on the use of Arabidopsis genome to generate drought or disease-resistant genotypes of different crop plants, as well as increasing the nutritional yield:
Studies of Solanum pimpinellifolium (tomato) with A. thaliana AtMYB12 - a transcription factor that regulates flavonoid metabolism - shows increased production of phenolic compounds in tomato (Zhang et al., 2015). In this way, it is possible to engineer tomato species that contain different concentrations of polyphenolic phytonutrients and provide a clearer understanding of their dietary properties.
Expression of A. thaliana Qua-Quine Starch gene in the leaves and seeds of soybean, corn, and rice reveals an increase in the protein content of the crops (Li et al., 2015). This information can be used to generate protein-rich dietary substitutes from existing crop plants.
Isolation of A. thaliana NAC gene STRESS-RESPONSE NAC1 (SNAC1) and over-expression on rice shows improved resistance to drought and salt stress (Hu et al., 2006).
Arabidopsis thaliana and Human Health
Besides having multiple benefits for plant science, A. thaliana research also contributes to human health tremendously. Part of these contributions are related to agriculture, alterations in the nutritional value of crops have an effect on the human diet and, thus, human health. After the release of the whole genome sequence of A. thaliana in 2000, it became clear to researchers that some of the disease genes observed in humans actually have orthologs in A. thaliana (70%) and the similarities are highly comparable to other model organisms such as Drosophila melanogaster (67%) or Saccharomyces cerevisiae (41%) (Jones et al., 2008). Some examples of contributions of A. thaliana research on developing a more vivid understanding of human health include:
Light response studies in A. thaliana facilitated the understanding of mammalian tumor repressor p53 gene expression as well as T cell homeostasis and metabolism of lipids (Jones et al., 2008).
The origin of DNA methylation studies emerged from A. thaliana research. Since the plant has orthologs of the two main DNA methyltransferases (Dnmt1&3), it serves as an optimal tool for understanding the role of DNA methylation on human health (Jones et al., 2008).
Studies show that A. thaliana shares orthologs of genes associated with Alzheimer’s and Parkinson’s disease which have contributed to the understanding of the molecular mechanisms underlying these neurological disorders (Xu& Møller, 2011).
The understanding of A. thaliana cryptochromes involves deciphering the mechanisms of developmental processes like the circadian clock in humans (Jones et al., 2008).
Research suggests that A. thaliana can be used as a successful model organism in cancer research too. Clavijo-Buriticá et al. (2023) propose an alternative approach in order to discover the evolutionary relationship between Homo sapiens and A. thaliana: the cancer-hallmarks. In their study, they listed five hallmarks (i.e. mechanisms and processes) observed in both species. They concluded that A. thaliana can be used as a model organism in order to understand the basic biological principles that might guide carcinogenic onset and progression better.
Limitations of Arabidopsis thaliana Research
Although A. thaliana is considered to be one of the key model species in plant sciences, there are some criticisms including the narrowness of the specialty area. Researchers argue that other high-yield crops can be utilized instead, in order to perform more beneficial studies in agriculture (Provart et al., 2016). However, the broad range of data generated from A. thaliana research is open access and can be used for parallel plant studies, such as crops that tend to grow slower. Since the genome is fully sequenced, identification of genes derived from other crops would be easier by focusing on their homologs in A. thaliana.
Another limitation is due to the fact that there is no fruit production in A. thaliana. Since most of the food stocks around the world are obtained from plants that produce fruits, Arabidopsis research can remain insufficient to draw a conclusion about fruit-producing plants. Similarly, since A. thaliana is a dicot plant (the seed having a pair of embryonic leaves), it may be challenging to comment on monocots. Still and all, it is essential to keep in mind that A. thaliana research serves as an understructure for both botanical and medicinal innovations.
Future Implications of Arabidopsis thaliana Research
Up-to-date research on A. thaliana usually includes specific approaches that are related to single or multiple gene networks. In spite of this, plant science is starting to focus on a bigger picture that includes global approaches. Scientists are starting to use A. thaliana research in order to obtain further knowledge about evolutionary processes by linking the changes in the genome to phenotypic variation. This should not only contribute to the understanding of plant development but also of how evolution contributes to the differential development of species (Lavagi et al, 2012). Another approach is to generate computational models from pre-existing data in order to generate a road map for multiple fields of science such as metabolomics and proteomics. By this, it is possible to have a deeper knowledge of phenotypic plasticity not only in A. thaliana but also in other plant species (Provart et al., 2016).
It has been shown that A. thaliana research on the generation of deeper root systems can even contribute to overcoming climate problems, for example, by reducing atmospheric carbon dioxide levels (Ogura et al., 2019). In this way, crops that can more easily adapt to climate change can be generated to increase the yield of food production. This would not only contribute to fight climate change but also famine, which can both be considered as major problems that can threaten human populations in the future.
Conclusion
Model organisms in scientific research are essential tools for reducing the complexity of the scientific phenomenon. In plant sciences, the most commonly used model organism is A. thaliana, a self-fertile dicot that can generate a large number of seeds within a short period of time. Since it is a plant that can be easily handled and put into research to obtain results within weeks, it is considered to be a useful tool to intensify the pace of the research. Throughout centuries, numerous scientific researches have been performed on A. thaliana, allowing scientists to unravel the function of various genes that potentially have a role in human health. Like every scientific approach, using A. thaliana as a model organism also has its downsides such as showing characteristics that are very similar to only a group of plants that are closely related. This reduces the reproducibility of the findings due to the lack of information on plant species that have different biological origins. Nevertheless, it is always safe to remember that there is a high amount of data available that can lead researchers to breed new findings.
Bibliographical References
Alonso, J., Ecker, J. Moving forward in reverse: genetic technologies to enable genome-wide phenomic screens in Arabidopsis. (2006). Nat Rev Genet 7, 524–536 . https://doi.org/10.1038/nrg1893
Clavijo-Buriticá, D. C., Sosa, C. C., Heredia, R. C., Mosquera, A. J., Álvarez, A., Medina, J., & Quimbaya, M. (2023). Use of Arabidopsis thaliana as a model to understand specific carcinogenic events: Comparison of the molecular machinery associated with cancer-hallmarks in plants and humans. Heliyon, 9(4), e15367. https://doi.org/10.1016/j.heliyon.2023.e15367
Hu, H., Dai, M., Yao, J., Xiao, B., Li, X., Zhang, Q., & Xiong, L. (2006). Overexpressing a NAM, ATAF, and CUC (NAC) transcription factor enhances drought resistance and salt tolerance in rice. Proceedings of the National Academy of Sciences of the United States of America, 103(35), 12987–12992. https://doi.org/10.1073/pnas.0604882103
Hunter P. (2008). The paradox of model organisms. The use of model organisms in research will continue despite their shortcomings. EMBO reports, 9(8), 717–720. https://doi.org/10.1038/embor.2008.142
Jones AM, Chory J, Dangl JL, Estelle M, Jacobsen SE, Meyerowitz EM, Nordborg M, Weigel D.(2008) The impact of Arabidopsis on human health: diversifying our portfolio. Cell. June 13;133(6):939-43. doi: 10.1016/j.cell.2008.05.040. PMID: 18555767; PMCID: PMC3124625.
Koornneef, M., & Meinke, D. (2010). The development of Arabidopsis as a model plant. The Plant journal: for cell and molecular biology, 61(6), 909–921. https://doi.org/10.1111/j.1365-313X.2009.04086.x
Krämer, U. (2015). The Natural History of Model Organisms: Planting molecular functions in an ecological context with Arabidopsis thalianaeLife 4:e06100. https://doi.org/10.7554/eLife.06100
Lavagi I, Estelle M, Weckwerth W, Beynon J, Bastow RM. (2012) From bench to bountiful harvests: a road map for the next decade of Arabidopsis research. Plant Cell. 24(6):2240-7. doi: 10.1105/tpc.112.096982. Epub. PMID: 22751212; PMCID: PMC3406909.
Li, L., Zheng, W., Zhu, Y., Ye, H., Tang, B., Arendsee, Z. W., Jones, D., Li, R., Ortiz, D., Zhao, X., Du, C., Nettleton, D., Scott, M. P., Salas-Fernandez, M. G., Yin, Y., & Wurtele, E. S. (2015). QQS orphan gene regulates carbon and nitrogen partitioning across species via NF-YC interactions. Proceedings of the National Academy of Sciences of the United States of America, 112(47), 14734–14739. https://doi.org/10.1073/pnas.1514670112
Ogura T, Goeschl C, Filiault D, Mirea M, Slovak R, Wolhrab B, Satbhai SB, Busch W. (2019) Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport. Cell. ;178(2):400-412.e16. doi: 10.1016/j.cell.2019.06.021. PMID: 31299202.
Provart, N. J., Alonso, J., Assmann, S. M., Bergmann, D., Brady, S. M., Brkljacic, J., Browse, J., Chapple, C., Colot, V., Cutler, S., Dangl, J., Ehrhardt, D., Friesner, J. D., Frommer, W. B., Grotewold, E., Meyerowitz, E., Nemhauser, J., Nordborg, M., Pikaard, C., Shanklin, J., … McCourt, P. (2016). 50 years of Arabidopsis research: highlights and future directions. The New phytologist, 209(3), 921–944. https://doi.org/10.1111/nph.13687
Somssich, Marc. (2018). A short history of Arabidopsis thaliana (L.) Heynh. Columbia-0. 10.7287/peerj.preprints.26931v1.
Woodward, A. W., & Bartel, B. (2018). Biology in Bloom: A Primer on the Arabidopsis thaliana Model System. Genetics, 208(4), 1337–1349. https://doi.org/10.1534/genetics.118.300755
Xu XM, Møller SG. (2011). The value of Arabidopsis research in understanding human disease states. Curr Opin Biotechnol.300-7. doi: 10.1016/j.copbio.2010.11.007. PMID: 21144728.
Y. Abdurakhmonov, I. (2022). Introductory Chapter: Model Plants for Discovering the Key Biological Processes in Plant Research. IntechOpen. doi: 10.5772/intechopen.103759
Zhang, Y., Butelli, E., Alseekh, S., Tohge, T., Rallapalli, G., Luo, J., Kawar, P. G., Hill, L., Santino, A., Fernie, A. R., & Martin, C. (2015). Multi-level engineering facilitates the production of phenylpropanoid compounds in tomato. Nature communications, 6, 8635. https://doi.org/10.1038/ncomms9635
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