Arabidopsis thaliana as an Experimental Organism

Abstract

In the recent years Arabidopsis thaliana has undoubtedly emerged as the model experimental organism for essentially all aspects of plant biology, due to its short generation time, its small genome size and the availability of its complete deoxyribonucleic acid sequence. In addition, Arabidopsis has proven to be an ideal organism for studying plant development at the molecular, cellular, organismal and ecological level. By concentrating their efforts on a single model system, Arabidopsis scientists have made outstanding advances in almost any field of plant research. Further, discoveries made in Arabidopsis have been translated to other plant species such as economically important crops, as well as to animal systems, including complex human disease processes.

Key Concepts

  • Arabidopsis is a small flowering plant, which has emerged as the primary experimental organism for the study of all aspects of plant biology.

  • Arabidopsis genome has been fully sequenced in 2000 and contains approximately 27‚ÄČ000 genes.

  • Several molecular tools have been established to identify Arabidopsis transcription profiles, epigenetic landscape, protein and metabolite composition.

  • Gain of function and loss of function transgenic lines for specific Arabidopsis genes can be easily made or obtained from public collections.

  • Most of the information on Arabidopsis research is available from dedicated websites.

  • Discoveries made in Arabidopsis can be easily translated to other plant species, as well as to animal systems.

Keywords: Arabidopsis thaliana; plant development; reverese genetics; mutagenesis; transgenic; transcriptome analysis

Figure 1.

An approximately 4‐week‐old plant of the frequently used laboratory accession Landsberg erecta. Total plant height is at this stage 15 cm. The inset shows a single flower.

Figure 2.

Establishment of the Arabidopsis body plan in the embryo and the structure of a primary root. A, apical region; C, central region; B, basal region; HY, hypophyseal cell; SAM, shoot apical meristem; COT, cotyledon; H, hypocotyl; ER, embryonic root; RM, root meristem; RMI, root meristem initials.

Figure 3.

Gene functional analysis using reverse genetics tools. (a) Outline of the ‘reverse genetics’ strategy used for the functional analysis of genes of interest. (b) Examples of the application of reverse genetics tools to the functional study of small gene families regulating crucial developmental pathways in Arabidopsis. In Arabidopsis, two COP9 signalosome complex (CSN) subunits, CSN5 and CSN6, are both encoded by two highly conserved genes, named CSN5A and CSN5B, and CSN6A and CSN6B, respectively. The availability of T‐DNA insertion lines in each member of these small gene families has allowed the generation of the csn5a csn5b and csn6a cns6b double null mutants. In both cases, as shown in (b), complete loss of function of CSN5 or CSN6, results in severe developmental defects causing post‐embryonic arrest at the seedling stage ( reproduced from Gusmaroli et al., , http://www.plantcell.org. Copyright American Society of Plant Biologists).

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References

Alonso JM and Ecker JR (2006) Moving forward in reverse: genetic technologies to enable genome‐wide phenomic screens in Arabidopsis. Nature Reviews Genetics 7: 524–536.

Alonso JM, Stepanova AN, Leisse TJ et al. (2003) Genome‐wide insertional mutagenesis of Arabidopsis thaliana. Science 301: 653–657.

Arabidopsis Genome Initiative (2000) Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408: 796–815.

Baerenfaller K, Grossmann J, Grobei MA et al. (2008) Genome‐scale proteomics reveals Arabidopsis thaliana gene models and proteome dynamics. Science 320: 938–941.

Bartel DP (2004) MicroRNAs: genomics, biogenesis, mechanism, and function. Cell 116: 281–297.

Bino RJ, Hall RD, Fiehn O et al. (2004) Potential of metabolomics as a functional genomics tool. Trends in Plant Science 9: 418–425.

Birnbaum K, Shasha DE, Wang JY et al. (2003) A gene expression map of the Arabidopsis root. Science 302: 1956–1960.

Bowers JE, Chapman BA, Rong J and Paterson AH (2003) Unravelling angiosperm genome evolution by phylogenetic analysis of chromosomal duplication events. Nature 422: 433–438.

Brady SM and Provart NJ (2009) Web‐queryable large‐scale data sets for hypothesis generation in plant biology. Plant Cell 21: 1034–1051.

Busch W and Lohmann JU (2007) Profiling a plant: expression analysis in Arabidopsis. Current Opinion in Plant Biology 10: 136–141.

Clough SJ and Bent AF (1998) Floral dip: a simplified method for Agrobacterium‐mediated transformation of Arabidopsis thaliana. Plant Journal 16: 735–743.

Coen ES and Meyerowitz EM (1991) The war of the whorls: genetic interactions controlling flower development. Nature 353: 31–37.

Cokus SJ, Feng S, Zhang X et al. (2008) Shotgun bisulphite sequencing of the Arabidopsis genome reveals DNA methylation patterning. Nature 452: 215–219.

de Ruijter NCA, Verhees J, van Leeuwen W and van der Krol AR (2003) Evaluation and comparison of the GUS, LUC and GFP reporter system for gene expression studies in plants. Plant Biology 5: 103–115.

Eckert H, LaVallee B, Schweiger BJ et al. (2006) Co‐expression of the borage D6 desaturase and the Arabidopsis D15 desaturase results in high accumulation of stearidonic acid in the seeds of transgenic soybean. Planta 224: 1050–1057.

Gardiner J and Marc J (2011) Arabidopsis thaliana, a plant model organism for the neuronal microtubule cytoskeleton? Journal Experimental Botany 62: 89–97.

Gelvin SB (1998) The introduction and expression of transgenes in plants. Current Opinion in Biotechnology 9: 227–232.

Gelvin SB (2009) Agrobacterium in the Genomics Age. Plant Physiology 150: 1665–1676.

Gusmaroli G, Figueroa P, Serino G and Deng XW (2007) Role of the MPN subunits in COP9 signalosome assembly and stability and their regulatory interaction with Arabidopsis CUL3‐based E3 ligases. Plant Cell 19: 564–581.

Lister R, O'Malley RC, Tonti‐Filippini J et al. (2008) Highly integrated single‐base resolution maps of the epigenome in Arabidopsis. Cell 133: 523–536.

Lorence A and Verpoorte R (2004) Gene transfer and expression in plants. Methods in Molecular Biology 267: 329–350.

McGary KL, Park TJ, Woods JO et al. (2010) Systematic discovery of nonobvious human disease models through orthologous phenotypes. Proceedings of the National Academy of Sciences of the USA 107: 6544–6549.

McGinnis KM (2010) RNAi for functional genomics in plants. Briefings in Functional Genomics 9: 111–117.

Page DR and Grossniklaus U (2002) The art and design of genetic screens: Arabidopsis thaliana. Nature Reviews Genetics 3: 124–136.

Parinov S and Sundaresan V (2000) Functional genomics in Arabidopsis: large‐scale insertional mutagenesis complements the genome sequencing project. Current Opinions in Biotechnology 11: 157–161.

Qi B, Fraser T, Mugford S et al. (2004) Production of very long chain polyunsaturated omega‐3 and omega‐6 fatty acids in plants. Nature Biotechnology 22: 739–745.

Schwab R, Ossowski S, Riester M et al. (2006) Highly specific gene silencing by artificial microRNAs in Arabidopsis. Plant Cell 18: 1121–1133.

Sessions A, Burke E, Presting G et al. (2002) A high‐throughput Arabidopsis reverse genetics system. Plant Cell 14: 2985–2994.

Song YH, Ito S and Imaizumi T (2010) Similarities in the circadian clock and photoperiodism in plants. Current Opinion in Plant Biology 13: 594–603.

Stepanova AN and Ecker JR (2000) Ethylene signaling: from mutants to molecules. Current Opinion in Plant Biology 3: 353–360.

Surovtseva YV, Churikov D, Boltz KA et al. (2009) Conserved telomere maintenance component 1 interacts with STN1 and maintains chromosome ends in higher eukaryotes. Molecular Cell 36: 207–218.

Till BJ, Reynolds SH, Greene EA et al. (2003) Large‐scale discovery of induced point mutations with high‐throughput TILLING. Genome Research 13: 524–530.

Waterhouse PM and Helliwell CA (2003) Exploring plant genomes by RNA‐induced gene silencing. Nature Reviews Genetics 4: 29–38.

Wei N and Deng XW (1996) The role of the COP/DET/FUS genes in light control of Arabidopsis seedling development. Plant Physiology 112: 871–878.

Wei N, Serino G and Deng XW (2008) The COP9 signalosome: more than a protease. Trends in Biochemical Science 33: 592–600.

Weigel D and Nordborg M (2005) Natural variation in Arabidopsis. How do we find the causal genes? Plant Physiology 138: 567–568.

Yao K, Bacchetto RG, Lockhart KM et al. (2003) Expression of the Arabidopsis ADS1 gene in Brassica juncea results in a decreased level of total saturated fatty acids. Plant Biotechnology Journal 1: 221–229.

Further Reading

Koornneef M and Meinke D (2010) The development of Arabidopsis as a model plant. Plant Journal 61: 909–921.

Raikhel N (2010) 2020 vision for biology: the role of plants in addressing grand challenges in biology. Molecular Plant 1: 561–563.

Salinas J and Sanchez‐Serrano JJ (eds) (2006) Arabidopsis Protocols, 2nd edn. Totowa, NJ: Humana Press.

Weigel D and Glazebrook J (2002) Arabidopsis: A Laboratory Manual. Cold Spring Harbor, NY: Cold Spring Harbor Laboratory Press.

Zhang S, Raina S, Li H et al. (2003) Resources for targeted insertional and deletional mutagenesis in Arabidopsis. Plant Molecular Biology 53: 133–150.

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Serino, Giovanna, and Gusmaroli, Giuliana(Jul 2011) Arabidopsis thaliana as an Experimental Organism. In: eLS. John Wiley & Sons Ltd, Chichester. http://www.els.net [doi: 10.1002/9780470015902.a0002031.pub2]