Arabidopsis
In Germany in 1905, Friedrich Laibach, a 20-year-old student of botany, picked a small grass on the banks of the Lan River near his hometown of Limburg and preserved it in a solution of acetic acid. Returning to his lab at the University of Bonn, Laibach stained the plant's cells and looked under a microscope and found that there were only 5 chromosomes in the cell, an exciting discovery, as the scientific community knew at the time that the minimum number of chromosomes was 5 when the number of odd numbers of chromosomes was known. The plant is Arabidopsis thaliana, and although the site where Laibach collected it was covered by highways in the 1930s and is now untraceable, this species has since become one of the most important tools in biological research.
Today, Arabidopsis thaliana has long been a model organism for basic functional research and will be used in a wider range of fields in the future. Arabidopsis thaliana has the characteristics of a small number of chromosomes, small plants, short life cycles, and many knots, in addition to being the first plant with a complete sequence of genomes, which took seven years and cost $70 million to complete the Arabidopsis Genome Initiative (AGI) by researchers from Europe, Japan and the United States [1], at this time as Carl in 1753 It has been 240 years since Linnaeus named it Arabis thaliana in honor of the German botanist Johannes Thal, who first described the plant, and only 50 years after Elliot Meyerowitz first discovered its potential as a model organism in 1943 [2].
Arabidopsis thaliana (source: Arabidopsis thaliana - Alchetron, The Free Social Encyclopedia)
Arabidopsis
Joanne Chory and Joseph Ecker of the Salk Institute made important contributions to the launch of the Arabidopsis Genome Project in the United States, "In the early '90s, whole genome sequencing was in full swing for all model organisms such as yeast, fruit flies, worms and rats," Ecker said, "So people who were studying Arabidopsis thaliana at the time asked, are we going to put other species ahead of Arabidopsis thaliana?" If better research tools are developed in other model organisms, will anyone be willing to continue their research work on plants? Chory's 1989 research paper, which reported on det1, an Arabidopsis mutant that can grow in the dark, was unique in applying genetic techniques to explore plant physiology questions, revealing complex pathways by which plants sense light [3]. This study, which had a significant impact on the field of botany, was quite difficult to carry out at the time due to the lack of a complete sequence and the limitations of gene recognition and cloning tools.
With the elucidation of the Arabidopsis genome, Chory was able to locate the DET1 gene on chromosome 4, which led to the determination of the genome sequence and specific location in 1994 [4]. In part, the work involves looking for fragments in a DNA fragment library that overlap with recent markers, through a repetitive search process called "chromosome walking" to eventually find the gene of interest. AGI makes it easier for researchers to locate genes in the Arabidopsis genome, for example, by searching for the DNA sequence of the gene, or by examining whether known sequences in other plants are present in the Arabidopsis genome. What's more, the identification of unknown genes by genetic transformation methods has become possible, researchers have developed T-DNA insertion methods, locate and sequence corresponding regions for gene identification, and researchers have successfully identified about 28,000 genes using hundreds of thousands of inserted lines. The "Salk lines" constructed by Ecker et al. are the best-known Arabidopsis T-DNA insertion mutant library [5], which has been accessed more than 11 million times to date and is available to Arabidopsis researchers worldwide.
Joanne Chory
Joseph Ecker
Arabidopsis
Due to the fact that sequencing techniques at the time were more suitable for short and variable sequences, AGI did not complete the assembly of the entire genome of Arabidopsis thaliana, and centromere was the unsequenced and assembled region that was left behind, and Todd Michael of the Salk Institute participated in the sequencing and assembly of this part containing more long and repetitive fragments [6]. As an expert in genome sequencing, assembly, and analysis, Michael has expanded from arabidopsis research to other species, first reporting the near-complete genome of the drought-tolerant grass oropiteium thomaeum in 2015, revealing the intact centromere structure [7], and more recently completing the sequencing of the genome of the aquatic plant Duckweed (Wolffia), an aquatic organism with a unique photosynthetic approach. It is the fastest growing plant in the world known [8].
In addition, Michael has also participated in the sequencing and pan-genome research of sorghum , as one of the world's top five cereals, sorghum has good drought resistance and can grow well on barren land, so it has important agricultural value under global warming. Although the genome of sorghum was sequenced a decade ago, the researchers hope to breed new disease-resistant, drought-tolerant and high-yield species by sequencing more cultured and wild-related strains. Michael's commitment to sequencing structurally and functionally unique plants is designed to reveal how genomic differences enable plants to better respond to and utilize their environment, and this knowledge is critical to the Harrising Plants Initiative (HPI), through which the Salk Institute aims to develop the ability of crops and wetland plants to capture and store atmospheric CO2 to explore ways to mitigate climate warming.
Wolfgang Busch and Chory of the Salk Institute are co-leaders of the HPI project, where he works to explore genes and mechanisms associated with the characteristics of different plant lines through genome-wide association analysis (GWAS). In one study, Busch used a combination of genetics, genomics, computational biology, and molecular cell biology to determine how specific traits for roots are encoded in plants' genetic blueprints. After years of research, Busch has identified a large number of genes, including a gene that regulates deeper roots in plants [9], and crops with this gene can store more CO2 with more and deep roots, and Busch is currently conducting experiments in greenhouses and multiple experimental fields to advance the application of this result.
Researchers at the Salk Institute are equally concerned about the mechanisms by which epigenetics affect plant phenotypes, and Julie Law's research is not only an important part of the HPI program, but also has some relevance to the study of human health and disease, because the same epigenetic processes occur not only in plant cells, but also in human cells such as the heart, liver, and skin, but also in function due to differences in the genes they are involved in activation. A study published by Law exploring how arabidopsis CLSY families regulate DNA methylation during plant development found that in different plant tissues, different CLSY families first targeted DNA methylation sites, resulting in differences in DNA methylation patterns in different tissues [10]. Given the importance of DNA methylation in regulating gene expression, these findings could help advances in areas ranging from increasing crop yields to precision medicine in humans.
A study published in 2021 by Chory and Ecker revealed another epigenetic mechanism, suggesting that neighboring plants produce shading effects that cause plants to grow higher. Arabidopsis mutants that are missing the PIFs transcription factor were found to exhibit elongation and rapid growth stops in simulated shading experiments, and further studies have shown that the PIF7 protein is activated within 5 minutes of the start of shading and removes the apparent stop signal H2A.Z [11]. As the "gene brakes" of growth are loosened, plants under the shade are able to grow faster. Chory said, "This study shows how plants respond to subtle changes in the environment at the cellular level, and such reactions will increasingly occur as plants themselves adapt to global climate change."
Joseph Noel's research interests focus on exploring the adaptation of plants to various ecosystems in the Earth's environment, using biochemical means to analyze the structure and chemical properties of compounds produced by different plants. For example, Noel analyzed suberin, a carbon-rich molecule that protects things from environmental stresses such as drought, flooding, disease and high salt. The study aims to develop wetland plants for better carbon storage, water purification and land conservation, and to grow in a variety of challenging environments. "Wetlands are not really aware of the importance of wetlands in environmental change," Noel says, "and wetland plants absorb 100 times more carbon per acre than dryland plants, so an important part of the HPI program is the genome of wetland plants, informing the increasingly urgent wetland restoration efforts." ”
The Harnessing Plants Initiative aims to help mitigate climate change by harnessing the carbon storage mechanisms of plant roots and wetlands on Earth. Plant biologists at the Salk Institute are working on crop improvements to absorb excess CO2 in the atmosphere and store it in the soil, using the roots' powerful carbon storage capacity to sequester carbon. Since the publication of the first Arabidopsis genome in 2000, sequencing technology has been greatly developed, and the international cooperation project AGI has lasted for seven years and cost $70 million. Today, Ecker can sequence the Arabidopsis genome in less than 3 minutes from a printer-sized machine in the office at a cost of about $16. Researchers at the Salk Institute are working on their own efforts to provide solutions to the global environmental problems that climate change brings.
Original link: https://inside.salk.edu/spring-2022/the-weed-that-changed-the-world/
Reference
[1] The Arabidopsis Genome Initiative. Analysis of the genome sequence of the flowering plant Arabidopsis thaliana. Nature 408, 796–815 (2000).
[2] Meyerowitz, E. Prehistory and History of Arabidopsis Research. Plant Physiology 125, 15-19 (2001).
[3] Chory, J., et al. Arabidopsis thaliana mutant that develops as a light-grown plant in the absence of light. Cell 58, 991-999 (1989).
[4] Pepper, A., et al. DET1, a negative regulator of light-mediated development and gene expression in Arabidopsis, encodes a novel nuclear-localized protein. Cell 78, 109-116 (1994).
[5] O Malley, R.C., et al. A user s guide to the Arabidopsis T-DNA insertion mutant collections. Methods in Molecular Biology 1284, 323-342 (2015).
[6] Naish, M., et al. The genetic and epigenetic landscape of the centromeres. Science 374，eabi7489 (2021).
[7] VanBuren, R., et al. Single-molecule sequencing of the desiccation-tolerant grass Oropetium thomaeum. Nature 527, 508-511 (2015).
[8] Hoang, P.N.T., et al. Generating a high-confidence reference genome map of the Greater Duckweed by integration of cytogenomic, optical mapping, and Oxford Nanopore technologies. Plant Journal 96, 670-684 (2018).
[9] Ogura, T., et al. Root System Depth in Arabidopsis Is Shaped by EXOCYST70A3 via the Dynamic Modulation of Auxin Transport. Cell 178, 400-412 (2019).
[10] Zhou, M., et al. Locus-specific control of the de novo DNA methylation pathway in Arabidopsis by the CLASSY family. Nature Genetics 50, 865-873 (2018).
[11] Willige, B.C., et al. PHYTOCHROME-INTERACTING FACTORs trigger environmentally responsive chromatin dynamics in plants. Nature Genetics 53, 955-961 (2021).
Source: Mol Plant Plant Sciences
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