Another Brick in the Wall: Transcriptional networks controlling secondary cell walls

Plant cell wall research has undergone a renaissance in the last few years, as the biotech industry has woken up to the potential of manipulating cell walls to enhance the amount of sugar released from plant-based biofuels. One research focus is secondary cell walls, which are composed of cellulose, hemicelluloses and lignin and provide the mechanical strength in xylem vessels. While lignin provides the waterproofing needed for water transport in vessels, it restricts the ability for sugars in the wall to be extracted in biofuel production. Understanding how secondary wall production is controlled may therefore have great significance in biotechnology.

A new paper in Nature (Taylor-Teeples et al., 2015) explores the control of wall production through a network based approach, looking for genes and proteins that interact to regulate polymer production. The researchers firstly used the literature and previously published datasets to identify 50 genes encoding either cell wall associated components or regulators of cell wall development. They then conducted a Yeast One-Hybrid (Y1H) screen of 467 root-xylem specific transcription factors, looking for combinations of promoters and transcription factors which could initiate gene expression.  Over 600 protein-DNA interactions were identified, which allowed the researchers to construct a network of regulatory control. Many of the protein-DNA interactions represented one transcription factor initiating the expression of another transcription factor, revealing the cell wall control network is rich in ‘master regulators’ and ‘feed forward’ loops, as shown in the figure below.

The cell wall regulatory network contains a hierarchy of transcription factors, which are organised into multiple feed-forward loops. Image reproduced from Nature.
The cell wall regulatory network contains a hierarchy of transcription factors, which are organised into multiple feed-forward loops to control both other transcription factors and genes directly involved in cell wall synthesis.  Image reproduced from Nature.

To test the model, the study focused on the known cell wall regulatory transcription factors VND6 and VND7. The network analysis predicted that these transcription factors would themselves be controlled by E2Fc, a transcription factor not previously associated with cell wall production, which sits near the ‘top’ of the regulatory cascade. Plants containing an RNAi construct against E2Fc had increased expression of VND6 and 7, indicating E2Fc is a repressor of cell wall synthesis. E2Fc-RNAi lines also had increased levels of both lignin and cellulose. E2Fc bound to the promoters of 23 genes in the network, indicating it is a major regulator of cell wall development.

The authors also used their model to investigate the impact of abiotic stress on xylem development. Many components of the network had previously been shown to be expressed differently in response to either iron-deprivation or salt stress. Another transcription factor REVOLUTA (REV) had a large number of upstream regulators under iron-deprivation, so the authors hypothesised that REV was a significant control element of cell wall synthesis in response to iron. Expression of many cell wall synthesis genes was altered in a rev-5 mutant, supporting the predictions of the model.

While much of the model needs further detailed analysis to confirm all of its predictions, it is clear that this network based approach can be very powerful in understanding complex control networks. The fact that the network model contains so many feed-forward loops suggests the cell wall development pathway is very robust, and may exhibit a strong switch-like behaviour, where cell wall synthesis is strongly activated by multiple proteins in one cell, and actively repressed by multiple proteins in another. Understanding these interactions in more detail may allow the manipulation of cell wall development, ultimately to improved lignocellulosic biofuels.

Reference: An Arabidopsis gene regulatory network for secondary cell wall synthesis. Taylor-Teeples et al. (2015) Nature 517:572-5. DOI:10.1038/nature14099

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