Loss of function alleles of PtEPSP-TF and its regulatory targets in rice

Xie, Meng; Chen, Jin-Gui; Gunter, Lee E.; Jawdy, Sara S.; Muchero, Wellington; Tuskan, Gerald; Zhang, Jin

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Title: Loss of function alleles of PtEPSP-TF and its regulatory targets in rice

Abstract

The present disclosure provides genetically modified plants, plant cells and plant tissues that show reduced lignin content as compared to a control plant which was not genetically modified. In addition, the disclosure provides methods of regulating lignin content in a plant. The disclosure also provides methods of producing bioproducts using the genetically modified plants of the instant disclosure.

Inventors:: Xie, Meng; Chen, Jin-Gui; Gunter, Lee E.; Jawdy, Sara S.; Muchero, Wellington; Tuskan, Gerald; Zhang, Jin

Issue Date:: 2022-10-18

Research Org.:: Oak Ridge National Laboratory (ORNL), Oak Ridge, TN (United States)

Sponsoring Org.:: USDOE

OSTI Identifier:: 1986696

Patent Number(s):: 11473086

Application Number:: 16/445,888

Assignee:: UT-Battelle LLC (Oak Ridge, TN)

DOE Contract Number:: AC05-00OR22725

Resource Type:: Patent

Resource Relation:: Patent File Date: 06/19/2019

Country of Publication:: United States

Language:: English

Citation Formats


                    Xie, Meng, Chen, Jin-Gui, Gunter, Lee E., Jawdy, Sara S., Muchero, Wellington, Tuskan, Gerald, and Zhang, Jin. Loss of function alleles of PtEPSP-TF and its regulatory targets in rice.  United States: N. p., 2022. 
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                    Xie, Meng, Chen, Jin-Gui, Gunter, Lee E., Jawdy, Sara S., Muchero, Wellington, Tuskan, Gerald, & Zhang, Jin. Loss of function alleles of PtEPSP-TF and its regulatory targets in rice.  United States.

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                    Xie, Meng, Chen, Jin-Gui, Gunter, Lee E., Jawdy, Sara S., Muchero, Wellington, Tuskan, Gerald, and Zhang, Jin. Tue .  
        "Loss of function alleles of PtEPSP-TF and its regulatory targets in rice".  United States.  https://www.osti.gov/servlets/purl/1986696.

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@article{osti_1986696,

  title        = {Loss of function alleles of PtEPSP-TF and its regulatory targets in rice},

  author       = {Xie, Meng and Chen, Jin-Gui and Gunter, Lee E. and Jawdy, Sara S. and Muchero, Wellington and Tuskan, Gerald and Zhang, Jin},

  abstractNote = {The present disclosure provides genetically modified plants, plant cells and plant tissues that show reduced lignin content as compared to a control plant which was not genetically modified. In addition, the disclosure provides methods of regulating lignin content in a plant. The disclosure also provides methods of producing bioproducts using the genetically modified plants of the instant disclosure.},

  doi          = {},

  journal      = {},
number       = ,

  volume       = ,

  place        = {United States},

  year         = {2022},

  month        = {10}

}

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Provided herein are methods for delivering a molecule in situ to a cell and for treating a cancer via the in situ delivery. The methods comprise contacting or administering to the cell, as two separate components, a morpholino oligonucleotide comprising a targeting moiety followed by a single wall nanotube construct comprising second morpholino oligonucleotides complementary to the first morpholino oligonucleotides and one or both of a therapeutic or diagnostic payload molecule linked to the single wall nanotube construct. Upon self-assembly of a single wall nanotube complex via hybridization of the first morpholino and second complementary morpholino oligonucleotides at the cell,more » « less
Full Text Available
Targeted self-assembly of functionalized carbon nanotubes on tumors

Patent Scheinberg, David A.; McDevitt, Michael R.; Villa, Carlos H.; ...

Provided herein is the two component self-assembly single wall nanotube system and the single wall nanotube construct that is the second component. The two component self-assembly single wall nanotube system has a morpholino oligonucleotide with a targeting moiety followed by a single wall nanotube construct with second morpholino oligonucleotides complementary to the first morpholino oligonucleotides and one or both of a therapeutic or diagnostic payload molecule linked to the single wall nanotube construct.
Full Text Available
Label-free functional nucleic acid sensors for detecting target agents

Patent Lu, Yi; Xiang, Yu

A general methodology to design label-free fluorescent functional nucleic acid sensors using a vacant site approach and an abasic site approach is described. In one example, a method for designing label-free fluorescent functional nucleic acid sensors (e.g., those that include a DNAzyme, aptamer or aptazyme) that have a tunable dynamic range through the introduction of an abasic site (e.g., dSpacer) or a vacant site into the functional nucleic acids. Also provided is a general method for designing label-free fluorescent aptamer sensors based on the regulation of malachite green (MG) fluorescence. A general method for designing label-free fluorescent catalytic and molecularmore » « less
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Title: Loss of function alleles of PtEPSP-TF and its regulatory targets in rice

Abstract

Citation Formats

A rice cab gene promoter contains separate cis-acting elements that regulate expression in dicot and monocot plants. journal, August 1992

Ribozymes patent, October 1993

Method for transforming indica rice patent, December 2001

Glucose-Induced Inactivation/Degradation-Resistant Transporter Gene and Use Thereof patent-application, May 2011

Modified gene-silencing RNA and uses thereof patent-application, September 2003

Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants journal, January 2004

TALEN-mediated genome engineering to generate targeted mice journal, January 2015

Tissue-specific light-regulated expression directed by the promoter of a C4 gene, maize pyruvate,orthophosphate dikinase, in a C3 plant, rice. journal, October 1993

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2 journal, December 2014

RNA ribozyme polymerases, dephosphorylases, restriction endoribonucleases and methods patent, January 1991

Method for preparing fertile transgenic corn plants patent, July 1996

Rice straw as a feedstock for biofuels: Availability, recalcitrance, and chemical properties journal, October 2017

Morpholino Antisense Oligomers: Design, Preparation, and Properties journal, June 1997

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting journal, April 2011

Expansion and Diversification of the Populus R2R3-MYB Family of Transcription Factors journal, December 2008

Vascular-specific expression of the bean GRP 1.8 gene is negatively regulated. journal, October 1991

Method and apparatus for introducing biological substances into living cells patent, April 1993

Simple gene silencing using the trans-acting siRNA pathway journal, March 2015

Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses journal, April 2018

An octopine synthase enhancer element directs tissue-specific expression and binds ASF-1, a factor from tobacco nuclear extracts. journal, October 1989

Transcriptional repression by MYB 3R proteins regulates plant organ growth journal, June 2015

RNA-Seq analysis in MeV journal, October 2011

Genetic engineering of novel plant phenotypes patent, July 1991

MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis journal, January 2009

Identification of Transcription Factors Involved in Rice Secondary Cell Wall Formation journal, October 2013

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks journal, November 2003

The Commelina yellow mottle virus promoter is a strong promoter in vascular and reproductive tissues. journal, February 1992

Methods for obtaining modified phenotypes in plant cells patent, July 2002

Methods and means for obtaining modified phenotypes patent-application, October 2004

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations journal, August 2014

Promoters from Genes for Plastid Proteins Possess Regions with Different Sensitivities toward Red and Blue Light journal, March 1994

New Construct Approaches for Efficient Gene Silencing in Plants journal, June 2006

Composition and Methods for Regulated Expression of a Guide RNA/CAS Endonuclease Complex patent-application, January 2018

Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis journal, May 2014

RNA-Guided Human Genome Engineering via Cas9 journal, January 2013

Survey of Genes Involved in Rice Secondary Cell Wall Formation Through a Co-Expression Network journal, October 2013

MYB46 and MYB83 Bind to the SMRE Sites and Directly Activate a Suite of Transcription Factors and Secondary Wall Biosynthetic Genes journal, December 2011

Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations journal, January 2012

The Phenylpropanoid Pathway in Arabidopsis journal, January 2011

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions journal, January 2013

Gene silencing patent-application, September 2003

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update journal, May 2017

The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription journal, January 2003

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP‐TF and determination of its transcriptional effect journal, January 2020

Regulation of Lignin Biosynthesis and Its Role in Growth-Defense Tradeoffs journal, September 2018

A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus journal, June 2018

Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.) and other monocot species: Gateway-compatible vectors for monocot transformation journal, September 2011

RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease journal, January 2004

Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode journal, July 2017

Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants. journal, October 1989

Fertile transgenic corn plants patent, January 2000

Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis journal, June 2007

Switchgrass (Panicum virgatum L.) polyubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation journal, July 2011

Isolation of Transcriptionally Regulated Root-Specific Genes from Tobacco journal, July 1990

Development and Applications of CRISPR-Cas9 for Genome Engineering journal, June 2014

Methods and means for producing barley yellow dwarf virus resistant cereal plants patent, August 2004

Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog journal, January 2012

RNA-guided editing of bacterial genomes using CRISPR-Cas systems journal, January 2013

The genetic control of lignin deposition during plant growth and development: Tansley review journal, July 2004

Method for altering the nutritional content of plant seed patent, December 2001

The Arabidopsis Transcription Factor MYB12 Is a Flavonol-Specific Regulator of Phenylpropanoid Biosynthesis journal, May 2005

Methods to assay for post-transcriptional suppression of gene expression patent, September 2002

SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus journal, January 2011

Gene silencing patent, June 2004

Transcriptional Activation of Secondary Wall Biosynthesis by Rice and Maize NAC and MYB Transcription Factors journal, September 2011

The Poplar MYB Master Switches Bind to the SMRE Site and Activate the Secondary Wall Biosynthetic Program during Wood Formation journal, July 2013

Transcription Factor Which Regulates Flavonoid, Phenylpropanoid, Tyrosine, and Tryptophan Pathways patent-application, December 2015

Genetic constructs for delaying or repressing the expression of a target gene patent, June 2003

A Battery of Transcription Factors Involved in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis journal, October 2008

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants journal, October 2015

Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis journal, November 2000

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus journal, January 2015

Effective ribozyme delivery in plant cells. journal, June 1995

AtMYB32 is required for normal pollen development in Arabidopsis thaliana journal, December 2004

The Shikimate Pathway and Aromatic Amino Acid Biosynthesis in Plants journal, June 2012

Genome engineering using the CRISPR-Cas9 system journal, October 2013

A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation journal, January 2012

A rice cab gene promoter contains separate cis-acting elements that regulate expression in dicot and monocot plants.
journal, August 1992

Ribozymes
patent, October 1993

Method for transforming indica rice
patent, December 2001

Glucose-Induced Inactivation/Degradation-Resistant Transporter Gene and Use Thereof
patent-application, May 2011

Modified gene-silencing RNA and uses thereof
patent-application, September 2003

Overexpression of the rice Osmyb4 gene increases chilling and freezing tolerance of Arabidopsis thaliana plants
journal, January 2004

TALEN-mediated genome engineering to generate targeted mice
journal, January 2015

Tissue-specific light-regulated expression directed by the promoter of a C4 gene, maize pyruvate,orthophosphate dikinase, in a C3 plant, rice.
journal, October 1993

Moderated estimation of fold change and dispersion for RNA-seq data with DESeq2
journal, December 2014

RNA ribozyme polymerases, dephosphorylases, restriction endoribonucleases and methods
patent, January 1991

Method for preparing fertile transgenic corn plants
patent, July 1996

Rice straw as a feedstock for biofuels: Availability, recalcitrance, and chemical properties
journal, October 2017

Morpholino Antisense Oligomers: Design, Preparation, and Properties
journal, June 1997

Efficient design and assembly of custom TALEN and other TAL effector-based constructs for DNA targeting
journal, April 2011

Expansion and Diversification of the Populus R2R3-MYB Family of Transcription Factors
journal, December 2008

Vascular-specific expression of the bean GRP 1.8 gene is negatively regulated.
journal, October 1991

Method and apparatus for introducing biological substances into living cells
patent, April 1993

Simple gene silencing using the trans-acting siRNA pathway
journal, March 2015

Current Models for Transcriptional Regulation of Secondary Cell Wall Biosynthesis in Grasses
journal, April 2018

An octopine synthase enhancer element directs tissue-specific expression and binds ASF-1, a factor from tobacco nuclear extracts.
journal, October 1989

Transcriptional repression by MYB 3R proteins regulates plant organ growth
journal, June 2015

RNA-Seq analysis in MeV
journal, October 2011

Genetic engineering of novel plant phenotypes
patent, July 1991

MYB58 and MYB63 Are Transcriptional Activators of the Lignin Biosynthetic Pathway during Secondary Cell Wall Formation in Arabidopsis
journal, January 2009

Identification of Transcription Factors Involved in Rice Secondary Cell Wall Formation
journal, October 2013

Cytoscape: A Software Environment for Integrated Models of Biomolecular Interaction Networks
journal, November 2003

The Commelina yellow mottle virus promoter is a strong promoter in vascular and reproductive tissues.
journal, February 1992

Methods for obtaining modified phenotypes in plant cells
patent, July 2002

Methods and means for obtaining modified phenotypes
patent-application, October 2004

Population genomics of Populus trichocarpa identifies signatures of selection and adaptive trait associations
journal, August 2014

Promoters from Genes for Plastid Proteins Possess Regions with Different Sensitivities toward Red and Blue Light
journal, March 1994

New Construct Approaches for Efficient Gene Silencing in Plants
journal, June 2006

Composition and Methods for Regulated Expression of a Guide RNA/CAS Endonuclease Complex
patent-application, January 2018

Identification of direct targets of transcription factor MYB46 provides insights into the transcriptional regulation of secondary wall biosynthesis
journal, May 2014

RNA-Guided Human Genome Engineering via Cas9
journal, January 2013

Survey of Genes Involved in Rice Secondary Cell Wall Formation Through a Co-Expression Network
journal, October 2013

MYB46 and MYB83 Bind to the SMRE Sites and Directly Activate a Suite of Transcription Factors and Secondary Wall Biosynthetic Genes
journal, December 2011

Combined inactivation of the Clostridium cellulolyticum lactate and malate dehydrogenase genes substantially increases ethanol yield from cellulose and switchgrass fermentations
journal, January 2012

The Phenylpropanoid Pathway in Arabidopsis
journal, January 2011

TopHat2: accurate alignment of transcriptomes in the presence of insertions, deletions and gene fusions
journal, January 2013

Gene silencing
patent-application, September 2003

agriGO v2.0: a GO analysis toolkit for the agricultural community, 2017 update
journal, May 2017

The Roles of Auxin Response Factor Domains in Auxin-Responsive Transcription
journal, January 2003

Identification of functional single nucleotide polymorphism of Populus trichocarpa PtrEPSP‐TF and determination of its transcriptional effect
journal, January 2020

Regulation of Lignin Biosynthesis and Its Role in Growth-Defense Tradeoffs
journal, September 2018

A 5-Enolpyruvylshikimate 3-Phosphate Synthase Functions as a Transcriptional Repressor in Populus
journal, June 2018

Gateway-compatible vectors for high-throughput gene functional analysis in switchgrass (Panicum virgatum L.) and other monocot species: Gateway-compatible vectors for monocot transformation
journal, September 2011

RF2b, a rice bZIP transcription activator, interacts with RF2a and is involved in symptom development of rice tungro disease
journal, January 2004

Proteomics Coupled with Metabolite and Cell Wall Profiling Reveal Metabolic Processes of a Developing Rice Stem Internode
journal, July 2017

Site-specific mutations alter in vitro factor binding and change promoter expression pattern in transgenic plants.
journal, October 1989

Fertile transgenic corn plants
patent, January 2000

Arabidopsis mesophyll protoplasts: a versatile cell system for transient gene expression analysis
journal, June 2007

Switchgrass (Panicum virgatum L.) polyubiquitin gene (PvUbi1 and PvUbi2) promoters for use in plant transformation
journal, July 2011

Isolation of Transcriptionally Regulated Root-Specific Genes from Tobacco
journal, July 1990

Development and Applications of CRISPR-Cas9 for Genome Engineering
journal, June 2014

Methods and means for producing barley yellow dwarf virus resistant cereal plants
patent, August 2004

Down-regulation of the caffeic acid O-methyltransferase gene in switchgrass reveals a novel monolignol analog
journal, January 2012

RNA-guided editing of bacterial genomes using CRISPR-Cas systems
journal, January 2013

The genetic control of lignin deposition during plant growth and development: Tansley review
journal, July 2004

Method for altering the nutritional content of plant seed
patent, December 2001

The Arabidopsis Transcription Factor MYB12 Is a Flavonol-Specific Regulator of Phenylpropanoid Biosynthesis
journal, May 2005

Methods to assay for post-transcriptional suppression of gene expression
patent, September 2002

SND2, a NAC transcription factor gene, regulates genes involved in secondary cell wall development in Arabidopsis fibres and increases fibre cell area in Eucalyptus
journal, January 2011

Gene silencing
patent, June 2004

Transcriptional Activation of Secondary Wall Biosynthesis by Rice and Maize NAC and MYB Transcription Factors
journal, September 2011

The Poplar MYB Master Switches Bind to the SMRE Site and Activate the Secondary Wall Biosynthetic Program during Wood Formation
journal, July 2013

Transcription Factor Which Regulates Flavonoid, Phenylpropanoid, Tyrosine, and Tryptophan Pathways
patent-application, December 2015

Genetic constructs for delaying or repressing the expression of a target gene
patent, June 2003

A Battery of Transcription Factors Involved in the Regulation of Secondary Cell Wall Biosynthesis in Arabidopsis
journal, October 2008

PlantPAN 2.0: an update of plant promoter analysis navigator for reconstructing transcriptional regulatory networks in plants
journal, October 2015

Transcriptional repression by AtMYB4 controls production of UV-protecting sunscreens in Arabidopsis
journal, November 2000

High-resolution genetic mapping of allelic variants associated with cell wall chemistry in Populus
journal, January 2015

Effective ribozyme delivery in plant cells.
journal, June 1995

AtMYB32 is required for normal pollen development in Arabidopsis thaliana
journal, December 2004

The Shikimate Pathway and Aromatic Amino Acid Biosynthesis in Plants
journal, June 2012

Genome engineering using the CRISPR-Cas9 system
journal, October 2013

A subgroup of SGS3-like proteins act redundantly in RNA-directed DNA methylation
journal, January 2012

NAC Transcription Factor SPEEDY HYPONASTIC GROWTH Regulates Flooding-Induced Leaf Movement in Arabidopsis
journal, December 2013

NAC-MYB-based transcriptional regulation of secondary cell wall biosynthesis in land plants
journal, May 2015

A 268 bp upstream sequence mediates the circadian clock-regulated transcription of the wheat Cab-1 gene in transgenic plants
journal, December 1990