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Title: Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum )

Abstract

Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (Panicum virgatum), which has been selected as a biofuel crop in the United States. In this study, we present a combination of computational and experimental approaches to develop gene regulatory networks for lignin formation in switchgrass. To screen transcription factors (TFs) involved in lignin biosynthesis, we developed a modified method to perform co-expression network analysis using 14 lignin biosynthesis genes as bait (target) genes. The switchgrass lignin co-expression network was further extended by adding 14 TFs identified in this study, and seven TFs identified in previous studies, as bait genes. Six TFs (PvMYB58/63, PvMYB42/85, PvMYB4, PvWRKY12, PvSND2 and PvSWN2) were targeted to generate overexpressing and/or down-regulated transgenic switchgrass lines. The alteration of lignin content, cell wall composition and/or plant growth in the transgenic plants supported the role of the TFs in controlling secondary wall formation. RNA-seq analysis of four of the transgenic switchgrass lines revealed downstream target genes of the secondary wall-related TFs and crosstalk with other biological pathways. In vitro transactivation assays further confirmed the regulation of specificmore » lignin pathway genes by four of the TFs. Our meta-analysis provides a hierarchical network of TFs and their potential target genes for future manipulation of secondary cell wall formation for lignin modification in switchgrass.« less

Authors:
 [1];  [2];  [1];  [3];  [4];  [5];  [6];  [6];  [7];  [8];  [9];  [10]; ORCiD logo [10]
  1. BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA, BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA
  2. Center for Applied Mathematics Tianjin University Tianjin China
  3. Department of Agronomy, Horticulture, and Plant Science and Department of Mathematics and Statistics South Dakota State University Brookings SD USA
  4. Noble Research Institute Ardmore OK USA
  5. BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA, Noble Research Institute Ardmore OK USA
  6. BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA, Complex Carbohydrate Research Center and Department of Biochemistry and Molecular Biology University of Georgia Athens GA USA
  7. Department of Plant Sciences University of Tennessee Knoxville TN USA
  8. Department of Food Science University of Tennessee Knoxville TN USA
  9. BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA
  10. BioDiscovery Institute and Department of Biological Sciences University of North Texas Denton TX USA, BioEnergy Science Center (BESC) Oak Ridge National Laboratory Oak Ridge TN USA, Center for Bioenergy Innovation (CBI) Oak Ridge National Laboratory Oak Ridge TN USA
Publication Date:
Research Org.:
Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER). Biological Systems Science Division
OSTI Identifier:
1471144
Alternate Identifier(s):
OSTI ID: 1472152; OSTI ID: 1625926
Grant/Contract Number:  
AC05-00OR22725
Resource Type:
Journal Article: Published Article
Journal Name:
Plant Biotechnology Journal
Additional Journal Information:
Journal Name: Plant Biotechnology Journal Journal Volume: 17 Journal Issue: 3; Journal ID: ISSN 1467-7644
Publisher:
Wiley-Blackwell
Country of Publication:
United Kingdom
Language:
English
Subject:
59 BASIC BIOLOGICAL SCIENCES; 09 BIOMASS FUELS; Biotechnology & Applied Microbiology; Plant Sciences; Bi-clustering algorithm; bioenergy crop; co-expression analysis; transcription factors; transgenic switchgrass; secondary cell wall biosynthesis

Citation Formats

Rao, Xiaolan, Chen, Xin, Shen, Hui, Ma, Qin, Li, Guifen, Tang, Yuhong, Pena, Maria, York, William, Frazier, Taylor P., Lenaghan, Scott, Xiao, Xirong, Chen, Fang, and Dixon, Richard A.. Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum ). United Kingdom: N. p., 2018. Web. doi:10.1111/pbi.13000.
Rao, Xiaolan, Chen, Xin, Shen, Hui, Ma, Qin, Li, Guifen, Tang, Yuhong, Pena, Maria, York, William, Frazier, Taylor P., Lenaghan, Scott, Xiao, Xirong, Chen, Fang, & Dixon, Richard A.. Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum ). United Kingdom. https://doi.org/10.1111/pbi.13000
Rao, Xiaolan, Chen, Xin, Shen, Hui, Ma, Qin, Li, Guifen, Tang, Yuhong, Pena, Maria, York, William, Frazier, Taylor P., Lenaghan, Scott, Xiao, Xirong, Chen, Fang, and Dixon, Richard A.. Mon . "Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum )". United Kingdom. https://doi.org/10.1111/pbi.13000.
@article{osti_1471144,
title = {Gene regulatory networks for lignin biosynthesis in switchgrass (Panicum virgatum )},
author = {Rao, Xiaolan and Chen, Xin and Shen, Hui and Ma, Qin and Li, Guifen and Tang, Yuhong and Pena, Maria and York, William and Frazier, Taylor P. and Lenaghan, Scott and Xiao, Xirong and Chen, Fang and Dixon, Richard A.},
abstractNote = {Cell wall recalcitrance is the major challenge to improving saccharification efficiency in converting lignocellulose into biofuels. However, information regarding the transcriptional regulation of secondary cell wall biogenesis remains poor in switchgrass (Panicum virgatum), which has been selected as a biofuel crop in the United States. In this study, we present a combination of computational and experimental approaches to develop gene regulatory networks for lignin formation in switchgrass. To screen transcription factors (TFs) involved in lignin biosynthesis, we developed a modified method to perform co-expression network analysis using 14 lignin biosynthesis genes as bait (target) genes. The switchgrass lignin co-expression network was further extended by adding 14 TFs identified in this study, and seven TFs identified in previous studies, as bait genes. Six TFs (PvMYB58/63, PvMYB42/85, PvMYB4, PvWRKY12, PvSND2 and PvSWN2) were targeted to generate overexpressing and/or down-regulated transgenic switchgrass lines. The alteration of lignin content, cell wall composition and/or plant growth in the transgenic plants supported the role of the TFs in controlling secondary wall formation. RNA-seq analysis of four of the transgenic switchgrass lines revealed downstream target genes of the secondary wall-related TFs and crosstalk with other biological pathways. In vitro transactivation assays further confirmed the regulation of specific lignin pathway genes by four of the TFs. Our meta-analysis provides a hierarchical network of TFs and their potential target genes for future manipulation of secondary cell wall formation for lignin modification in switchgrass.},
doi = {10.1111/pbi.13000},
url = {https://www.osti.gov/biblio/1471144}, journal = {Plant Biotechnology Journal},
issn = {1467-7644},
number = 3,
volume = 17,
place = {United Kingdom},
year = {2018},
month = {9}
}

Journal Article:
Free Publicly Available Full Text
Publisher's Version of Record at https://doi.org/10.1111/pbi.13000

Citation Metrics:
Cited by: 11 works
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