Editorial: An Emerging View of Plant Cell Walls as an Apoplastic Intelligent System

Nishitani, Kazuhiko; Demura, Taku

doi:10.1093/pcp/pcv001

Cited by 21 publications

(12 citation statements)

References 34 publications

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“…In addition, MYB58 and MYB63, which are transcriptional activators of lignin biosynthesis in the SND1-mediated transcriptional regulatory network ( 47 ), were identified by TGMI algorithm. TGMI also identified LBD15 ( 48 ), XND1 ( 49 ), bZIP6 ( 50 ) and GATA12 ( 51 ), which are involved in regulating various aspects of secondary cell wall synthesis.…”

Section: Resultsmentioning

confidence: 99%

TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction

Gunasekara

Zhang

Deng

et al. 2018

Nucleic Acids Research

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Despite their important roles, the regulators for most metabolic pathways and biological processes remain elusive. Presently, the methods for identifying metabolic pathway and biological process regulators are intensively sought after. We developed a novel algorithm called triple-gene mutual interaction (TGMI) for identifying these regulators using high-throughput gene expression data. It first calculated the regulatory interactions among triple gene blocks (two pathway genes and one transcription factor (TF)), using conditional mutual information, and then identifies significantly interacted triple genes using a newly identified novel mutual interaction measure (MIM), which was substantiated to reflect strengths of regulatory interactions within each triple gene block. The TGMI calculated the MIM for each triple gene block and then examined its statistical significance using bootstrap. Finally, the frequencies of all TFs present in all significantly interacted triple gene blocks were calculated and ranked. We showed that the TFs with higher frequencies were usually genuine pathway regulators upon evaluating multiple pathways in plants, animals and yeast. Comparison of TGMI with several other algorithms demonstrated its higher accuracy. Therefore, TGMI will be a valuable tool that can help biologists to identify regulators of metabolic pathways and biological processes from the exploded high-throughput gene expression data in public repositories.

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Section: Resultsmentioning

confidence: 99%

TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction

Gunasekara

Zhang

Deng

et al. 2018

Nucleic Acids Research

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“…The cell wall properties are controlled on many levels, such as by the transcriptional regulation of genes, membrane trafficking and molecular interaction between different components of the cell wall. The wall is organised with three layers: middle lamella, primary cell wall and secondary cell wall (Figure 1) [43]. During cell division (cytokinesis), one cell is divided into two by the formation of the cell plate.…”

Section: Cell Wallmentioning

confidence: 99%

Plant Fibre: Molecular Structure and Biomechanical Properties, of a Complex Living Material, Influencing Its Deconstruction towards a Biobased Composite

et al. 2016

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Plant cell walls form an organic complex composite material that fulfils various functions. The hierarchical structure of this material is generated from the integration of its elementary components. This review provides an overview of wood as a composite material followed by its deconstruction into fibres that can then be incorporated into biobased composites. Firstly, the fibres are defined, and their various origins are discussed. Then, the organisation of cell walls and their components are described. The emphasis is on the molecular interactions of the cellulose microfibrils, lignin and hemicelluloses in planta. Hemicelluloses of diverse species and cell walls are described. Details of their organisation in the primary cell wall are provided, as understanding of the role of hemicellulose has recently evolved and is likely to affect our perception and future study of their secondary cell wall homologs. The importance of the presence of water on wood mechanical properties is also discussed. These sections provide the basis for understanding the molecular arrangements and interactions of the components and how they influence changes in fibre properties once isolated. A range of pulping processes can be used to individualise wood fibres, but these can cause damage to the fibres. Therefore, issues relating to fibre production are discussed along with the dispersion of wood fibres during extrusion. The final section explores various ways to improve fibres obtained from wood.

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“…How CAD is able to directly influence XTH/XET gene expression remains unclear. Therefore, by lowering accessibility to the xyloglucan and cellulose network [2,[76][77][78], the accessibility of the matrix to cellulases and other CWDEs would be substantially diminished.…”

Section: Pectin Organisation Varied Between the Sr1 And The Transgenimentioning

confidence: 99%

Overexpression of VviPGIP1 and NtCAD14 in Tobacco Screened Using Glycan Microarrays Reveals Cell Wall Reorganisation in the Absence of Fungal Infection

et al. 2020

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The expression of Vitis vinifera polygalacturonase inhibiting protein 1 (VviPGIP1) in Nicotiana tabacum has been linked to modifications at the cell wall level. Previous investigations have shown an upregulation of the lignin biosynthesis pathway and reorganisation of arabinoxyloglucan composition. This suggests cell wall tightening occurs, which may be linked to defence priming responses. The present study used a screening approach to test four VviPGIP1 and four NtCAD14 overexpressing transgenic lines for cell wall alterations. Overexpressing the tobacco-derived cinnamyl alcohol dehydrogenase (NtCAD14) gene is known to increase lignin biosynthesis and deposition. These lines, particularly PGIP1 expressing plants, have been shown to lead to a decrease in susceptibility towards grey rot fungus Botrytis cinerea. In this study the aim was to investigate the cell wall modulations that occurred prior to infection, which should highlight potential priming phenomena and phenotypes. Leaf lignin composition and relative concentration of constituent monolignols were evaluated using pyrolysis gas chromatography. Significant concentrations of lignin were deposited in the stems but not the leaves of NtCAD14 overexpressing plants. Furthermore, no significant changes in monolignol composition were found between transgenic and wild type plants. The polysaccharide modifications were quantified using gas chromatography (GC–MS) of constituent monosaccharides. The major leaf polysaccharide and cell wall protein components were evaluated using comprehensive microarray polymer profiling (CoMPP). The most significant changes appeared at the polysaccharide and protein level. The pectin fraction of the transgenic lines had subtle variations in patterning for methylesterification epitopes for both VviPGIP1 and NtCAD14 transgenic lines versus wild type. Pectin esterification levels have been linked to pathogen defence in the past. The most marked changes occurred in glycoprotein abundance for both the VviPGIP1 and NtCAD14 lines. Epitopes for arabinogalactan proteins (AGPs) and extensins were notably altered in transgenic NtCAD14 tobacco.

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Editorial: An Emerging View of Plant Cell Walls as an Apoplastic Intelligent System

Cited by 21 publications

References 34 publications

TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction

TGMI: an efficient algorithm for identifying pathway regulators through evaluation of triple-gene mutual interaction

Plant Fibre: Molecular Structure and Biomechanical Properties, of a Complex Living Material, Influencing Its Deconstruction towards a Biobased Composite

Overexpression of VviPGIP1 and NtCAD14 in Tobacco Screened Using Glycan Microarrays Reveals Cell Wall Reorganisation in the Absence of Fungal Infection

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