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Title: Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect

Abstract

In plants, the phenylpropanoid pathway is responsible for the synthesis of a diverse array of secondary metabolites that include lignin monomers, flavonoids, and coumarins, many of which are essential for plant structure, biomass recalcitrance, stress defense, and nutritional quality. Our previous studies have demonstrated that Populus trichocarpa PtrEPSP-TF, an isoform of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, has transcriptional activity and regulates phenylpropanoid biosynthesis in Populus. In this study, we report the identification of single nucleotide polymorphism (SNP) of PtrEPSP-TF that defines its functionality. Populus natural variants carrying this SNP were shown to have reduced lignin content. Here, we demonstrated that the SNP-induced substitution of 142nd amino acid (PtrEPSP-TF D142E) dramatically impairs the DNA-binding and transcriptional activity of PtrEPSP-TF. When introduced to a monocot species rice ( Oryza sativa) in which an EPSP synthase isoform with the DNA-binding helix-turn-helix (HTH) motif is absent, the PtrEPSP-TF, but not PtrEPSP-TF D142E, activated genes in the phenylpropanoid pathway. More importantly, heterologous expression of PtrEPSP-TF uncovered five new transcriptional regulators of phenylpropanoid biosynthesis in rice. Collectively, this study identifies the key amino acid required for PtrEPSP-TF functionality and provides a strategy to uncover new transcriptional regulators in phenylpropanoid biosynthesis.

Authors:
 [1];  [2];  [3];  [4];  [4];  [2];  [2];  [5];  [2];  [3];  [3];  [6];  [4];  [7];  [2];  [2];  [2]; ORCiD logo [8]
  1. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); Univ. of Tennessee, Knoxville, TN (United States)
  2. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
  3. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States)
  4. Univ. of Georgia, Athens, GA (United States)
  5. Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States); National Renewable Energy Lab. (NREL), Golden, CO (United States)
  6. USDOE Joint Genome Institute (JGI), Walnut Creek, CA (United States); HudsonAlpha Inst. for Biotechnology, Huntsville, AL (United States)
  7. Univ. of Tennessee, Knoxville, TN (United States)
  8. National Renewable Energy Lab. (NREL), Golden, CO (United States); Oak Ridge National Lab. (ORNL), Oak Ridge, TN (United States)
Publication Date:
Research Org.:
National Renewable Energy Lab. (NREL), Golden, CO (United States)
Sponsoring Org.:
USDOE Office of Science (SC), Biological and Environmental Research (BER) (SC-23); USDOE Office of Science (SC), Basic Energy Sciences (BES) (SC-22). Scientific User Facilities Division
OSTI Identifier:
1593683
Report Number(s):
NREL/JA-2700-75861
Journal ID: ISSN 2475-4455; PLD3
Grant/Contract Number:  
AC36-08GO28308; AC05‐00OR22725; AC02‐05CH11231
Resource Type:
Accepted Manuscript
Journal Name:
Plant Direct
Additional Journal Information:
Journal Volume: 4; Journal Issue: 1; Journal ID: ISSN 2475-4455
Publisher:
Wiley and American Society of Plant Biologists and Society for Experimental Biology
Country of Publication:
United States
Language:
English
Subject:
09 BIOMASS FUELS; 59 BASIC BIOLOGICAL SCIENCES; DNA binding; EPSP synthase; phenylpropanoid; rice; transcriptional regulation

Citation Formats

Xie, Meng, Zhang, Jin, Singan, Vasanth R., McGranahan, Melissa J., LaFayette, Peter R., Jawdy, Sara S., Engle, Nancy, Doeppke, Crissa L., Tschaplinski, Timothy J., Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Parrott, Wayne A., Chen, Feng, Tuskan, Gerald A., Chen, Jin-Gui, Muchero, Wellington, and Davis, Mark. Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect. United States: N. p., 2020. Web. doi:10.1002/pld3.178.
Xie, Meng, Zhang, Jin, Singan, Vasanth R., McGranahan, Melissa J., LaFayette, Peter R., Jawdy, Sara S., Engle, Nancy, Doeppke, Crissa L., Tschaplinski, Timothy J., Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Parrott, Wayne A., Chen, Feng, Tuskan, Gerald A., Chen, Jin-Gui, Muchero, Wellington, & Davis, Mark. Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect. United States. doi:10.1002/pld3.178.
Xie, Meng, Zhang, Jin, Singan, Vasanth R., McGranahan, Melissa J., LaFayette, Peter R., Jawdy, Sara S., Engle, Nancy, Doeppke, Crissa L., Tschaplinski, Timothy J., Lindquist, Erika, Barry, Kerrie, Schmutz, Jeremy, Parrott, Wayne A., Chen, Feng, Tuskan, Gerald A., Chen, Jin-Gui, Muchero, Wellington, and Davis, Mark. Fri . "Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect". United States. doi:10.1002/pld3.178. https://www.osti.gov/servlets/purl/1593683.
@article{osti_1593683,
title = {Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP-TF and determination of its transcriptional effect},
author = {Xie, Meng and Zhang, Jin and Singan, Vasanth R. and McGranahan, Melissa J. and LaFayette, Peter R. and Jawdy, Sara S. and Engle, Nancy and Doeppke, Crissa L. and Tschaplinski, Timothy J. and Lindquist, Erika and Barry, Kerrie and Schmutz, Jeremy and Parrott, Wayne A. and Chen, Feng and Tuskan, Gerald A. and Chen, Jin-Gui and Muchero, Wellington and Davis, Mark},
abstractNote = {In plants, the phenylpropanoid pathway is responsible for the synthesis of a diverse array of secondary metabolites that include lignin monomers, flavonoids, and coumarins, many of which are essential for plant structure, biomass recalcitrance, stress defense, and nutritional quality. Our previous studies have demonstrated that Populus trichocarpa PtrEPSP-TF, an isoform of 5-enolpyruvylshikimate 3-phosphate (EPSP) synthase, has transcriptional activity and regulates phenylpropanoid biosynthesis in Populus. In this study, we report the identification of single nucleotide polymorphism (SNP) of PtrEPSP-TF that defines its functionality. Populus natural variants carrying this SNP were shown to have reduced lignin content. Here, we demonstrated that the SNP-induced substitution of 142nd amino acid (PtrEPSP-TFD142E) dramatically impairs the DNA-binding and transcriptional activity of PtrEPSP-TF. When introduced to a monocot species rice (Oryza sativa) in which an EPSP synthase isoform with the DNA-binding helix-turn-helix (HTH) motif is absent, the PtrEPSP-TF, but not PtrEPSP-TFD142E, activated genes in the phenylpropanoid pathway. More importantly, heterologous expression of PtrEPSP-TF uncovered five new transcriptional regulators of phenylpropanoid biosynthesis in rice. Collectively, this study identifies the key amino acid required for PtrEPSP-TF functionality and provides a strategy to uncover new transcriptional regulators in phenylpropanoid biosynthesis.},
doi = {10.1002/pld3.178},
journal = {Plant Direct},
number = 1,
volume = 4,
place = {United States},
year = {2020},
month = {1}
}

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