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An inter-university research group has succeeded in constructing the gene expression network behind the vascular development process in plants.
They achieved this by doing bioinformatics analysis using the’VISUAL’ tissue culture stage, which generates vascular stem cells from cells. Within this network, they also found a new BES/BZR transcription factor, BEH3, which modulates vascular stem cells. Additionally, they illuminated a novel vascular cell maintenance system whereby BEH3 competes with other transcription factors from the same BES/BZR family to be able to stabilize vascular stem cell multiplication and differentiation.
The researchers expect to identify more regulatory factors for stem cells, which will contribute towards our understanding of the molecular basis behind continuous stem cell activity in plants.
These research results were published in the American plant sciences journal The Plant Cell on June 1, 2021.
Main points 1.The researchers extracted a total of 394 genes specific to vascular stem cells from extensive gene expression datasets. 2.They discovered that unlike the other BES/BZR transcription factors, BEH3 has virtually no operational domains and inhibits the activity of these other aspects. 3.The study team showed that this competitive relationship between BES/BZR transcription factors stabilizes the multiplication and differentiation of vascular stem cells, illuminating the regulatory system that maintains vascular stem cells’ continuous activity.
Research background Plants take shape by self-replicating their stem cells and differentiating these stem cells so that they have specialized functions for constructing portions of the plant, such as its organs and tissues. Unlike animals, plants continue to regenerate and grow by producing stem cells throughout their life. By way of example, trees like cryptomeria can have long lifespans (the Jomon Cedar Tree on Japan’s Yakushima Island is at least 2000 years old), and every year they encourage secondary growth which leads to another tree ring around their trunks.
This secondary growth is occurs inside a region of meristem tissue known as the cambium layer where vascular stem cells multiply and differentiate into xylem cells and phloem cells, enabling the trunk to grow wider. In other words, plant must continuously produce neural stem cells throughout their lives in order to keep growing, and it’s vital for them to keep the balance between stem cell multiplication and differentiation.
In recent years, studies using the model plant Arabidopsis thaliana have been done into the way the multiplication and differentiation of stem cells are regulated from the perspectives of genetics, life sciences and informatics research. However, the mechanism by which plants regulate and maintain the right balance of stem cells has yet to be understood.
Research methodology and findings In order to analyze the process by which vascular stem cells differentiate into xylem cells and phloem cells (Figure 1), Associate Professor Kondo et al.’s research team developed the tissue culture system’VISUAL’ to artificially create stem cells from leaf cells.
VISUAL has many benefits which make it suitable for research on vascular stem cells, as an instance, it is not difficult to genetically analyze plants that have a particular gene function eliminated (i.e. mutants) and it’s also possible to observe the temporal development of vascular stem cell differentiation. In this study, the researchers collected data on multiple mutants and carried out large-scale analyses of gene expression at various time points.
They conducted gene co-expression network analysis on similarities in the expression patterns to assess the relationship between different genes. From this analysis, they succeeded in identifying the identifying groups of genes in xylem cells, phloem cells and vascular stem cells (Figure 1). Using VISUAL, this study group previously revealed that the BES/BZR transcription factors BES1 and BZR1 play an important role in vascular stem cell differentiation. This time, they identified another BES/BZR transcription factor, BEH3, in the vascular stem cell gene group through network analysis, and also examined its vascular stem cell suppressing function.
Then, the researchers investigated vascular formation using mutants with BEH3’s role eliminated. They found that the mutants had substantial variations in vascular size in comparison with the wild type (non-mutant plant) and reasoned that BEH3 stabilizes vascular stem cells.
The study group had previously discovered that strengthening the function of BES1 (which promotes vascular cell differentiation) caused the number of vascular cells to decrease, however they found that when they strengthened the function of BEH3 reverse occurred and the amount of vascular stem cells increased.
Upon studying this further, the research group found that even though BEH3 could bind to the same DNA motif (BRRE motif) as another BES/BZR transcription factors, BEH3’s ability to regulate the expression of downstream genes was significantly weaker. These results demonstrated that BEH3 hinders the action of other BES/BZR transcription factors (Figure 2), and the investigators gleaned from this relationship that BEH3’s function in vascular stem cells compared to that of the factors in the same family, including BES1.
A mathematical model was used to verify and simulate this competitive relationship between BEH3 and another BES/BZR transcription factors, and the results indicated that the existence of BEH3 in vascular stem cells leads towards stabilizing vascular size (Figure 3).
There are believed to be a number of important gene candidates in this research group’s neural stem cell gene expression system which will contribute towards understanding of vascular development and functions. It’s estimated that the valuable information obtained through this research will accelerate vascular research. In addition, further illuminating the connections between BEH3 and other BES/BZR transcription factors and their various differences will deepen our understanding of the mechanism by which plants keep the balance between stem cell multiplication and differentiation.
Ultimately, this knowledge could contribute towards biomass production techniques, and other areas that need large-scale stable plant growth.
Furuya, T., et al. (2021) Gene co-expression network analysis identifies BEH3 as a stabilizer of secondary vascular development in Arabidopsis. The Plant Cell. doi.org/10.1093/plcell/koab151.