Works (22)
Updated: August 8th, 2023 21:20
2023 journal article
Overexpression of a gibberellin 20-oxidase gene in poplar xylem led to an increase in the size of nanocellulose fibrils and improved paper properties
CARBOHYDRATE POLYMERS, 314.
author keywords: Nanocellulose microfibril; Poplar; Gibberellin; Pulp
MeSH headings : Gibberellins; Xylem / genetics; Xylem / metabolism; Mixed Function Oxygenases / metabolism; Wood / metabolism; Cellulose / chemistry; Arabidopsis / genetics; Arabidopsis / metabolism; Populus / genetics; Populus / metabolism
Source: Web Of Science
Added: May 30, 2023
2021 journal article
BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAl5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar
FRONTIERS IN PLANT SCIENCE, 12.
author keywords: lignin; BEL1-like homeodomain protein; transcription factor; yeast one hybrid
TL;DR:
It is proposed that BLH6a is a negative regulator of CAld5H2, which acts through combinatorial regulation of multiple TFs for sinapyl alcohol (S monolignol) biosynthesis in poplar.
(via Semantic Scholar)
www.frontiersin.org (publisher PDF)
Source: Web Of Science
Added: July 19, 2021
2021 article
BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAld5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar (vol 12,& nbsp;695223, 2021)
Wang, Q., Dai, X., Pang, H., Cheng, Y., Huang, X., Li, H., … Li, Q. (2021, September 9). BEL1-like Homeodomain Protein BLH6a Is a Negative Regulator of CAld5H2 in Sinapyl Alcohol Monolignol Biosynthesis in Poplar (vol 12,& nbsp;695223, 2021). FRONTIERS IN PLANT SCIENCE, Vol. 12.
author keywords: lignin; BEL1-like homeodomain protein; transcription factor; yeast one hybrid
TL;DR:
This research presents a novel probabilistic procedure that allows for direct measurement of the response of the immune system to earthquake-triggered landsliding.
(via Semantic Scholar)
Source: Web Of Science
Added: November 29, 2021
2019 journal article
CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa
NEW PHYTOLOGIST, 222(1), 244–260.
author keywords: co-immunoprecipitation; enzyme activity; monolignol biosynthetic pathway; nuclear magnetic resonance (NMR); Populus trichocarpa; stem-differentiating xylem protein
MeSH headings : Aldehyde Oxidoreductases / genetics; Aldehyde Oxidoreductases / metabolism; Down-Regulation / genetics; Gene Expression Regulation, Plant; Lignin / metabolism; Magnetic Resonance Spectroscopy; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Populus / genetics; Populus / metabolism; RNA Interference; Recombinant Proteins / metabolism; Xylem / metabolism
TL;DR:
Evidence is provided for the formation of PtrCAD1/PtrCCR2 protein complexes in monolignol biosynthesis in planta, and biomolecular fluorescence complementation and pull-down/co-immunoprecipitation experiments supported a hypothesis of P Tr trichocarpa heterodimer formation.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: December 17, 2018
2015 article
Populus trichocarpa
AGROBACTERIUM PROTOCOLS, VOLUME 2, THIRD EDITION, Vol. 1224, pp. 357–363.
author keywords: Agrobacterium tumefaciens; Genetic transformation; Populus trichocarpa; Transgenic trees
MeSH headings : Agrobacterium tumefaciens / genetics; Agrobacterium tumefaciens / growth & development; Coculture Techniques; Genetic Engineering / methods; Plant Roots / growth & development; Plant Shoots / growth & development; Populus / genetics; Populus / growth & development; Populus / physiology; Regeneration; Transformation, Genetic
TL;DR:
A modified step-by-step protocol for Agrobacterium-mediated transformation of stem explants is described here and the health of the tissue explants and the time of cocultivation are among the critical steps in the protocol for successful transformation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
A robust chromatin immunoprecipitation protocol for studying transcription factor-DNA interactions and histone modifications in wood-forming tissue
NATURE PROTOCOLS, 9(9), 2180–2193.
MeSH headings : Base Sequence; Chromatin Immunoprecipitation / methods; DNA / metabolism; DNA Fragmentation; Histones / metabolism; Immunoprecipitation; Molecular Sequence Data; Populus / cytology; Populus / metabolism; Sequence Analysis, DNA; Transcription Factors / metabolism; Wood / cytology; Xylem / genetics; Xylem / metabolism
TL;DR:
This protocol is the only working ChIP system for wood-forming tissue and uses stem-differentiating xylem to identify genome-wide specific TF-DNA interactions during wood formation and histone modifications associated with regulation of wood formation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2014 journal article
A simple improved-throughput xylem protoplast system for studying wood formation
NATURE PROTOCOLS, 9(9), 2194–2205.
MeSH headings : Cell Wall / metabolism; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Green Fluorescent Proteins; Populus / cytology; Populus / growth & development; Protoplasts / metabolism; Transfection / methods; Wood / cytology; Wood / growth & development; Xylem / chemistry
TL;DR:
A protocol for the isolation and transfection of protoplasts from wood-forming tissue, the stem-differentiating xylem (SDX), in the model woody plant Populus trichocarpa is presented.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2014 journal article
Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling
The Plant Cell, 26(3), 876–893.
Contributors: H. Chen n, J. Song n, J. Wang n , Y. Lin n, J. Ducoste n , C. Shuford n, J. Liu n, n
MeSH headings : Coenzyme A Ligases / genetics; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Immunoprecipitation; Lignin / biosynthesis; Mass Spectrometry; Models, Biological; Populus / metabolism; Propionates; RNA, Messenger / genetics; Substrate Specificity; Systems Biology
TL;DR:
This work shows that 4CL, an enzyme in monolignol biosynthesis, is found as a heterotetrameric complex of two isoforms in Populus trichocarpa, where the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterosymmetric protein complex.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018
2014 journal article
nnThe influence of lignin-carbohydrate complexes on the cellulase-mediated saccharification I: Transgenic black cottonwood (western balsam poplar, California poplar) P-trichocarpa including the xylan down-regulated and the lignin down-regulated lines
FUEL, 119, 207–213.
author keywords: Transgenic P. trichocarpa; Lignin-carbohydrate complexes (LCCs); Enzymatic saccharification; Fermentable sugars; H-1-C-13 HSQC NMR
TL;DR:
The correlation between the LCCs and enzymatic saccharification nearly conclusively demonstrated that the L CCs accounting for the recalcitrance of lignocellulosic biodegradation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(Web of Science)
12. Responsible Consumption and Production
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
High-level gene expression in differentiating xylem of tobacco driven by a 2.0 kb Poplar COMT2 promoter and a 4 x 35S enhancer
PLANT BIOTECHNOLOGY, 30(2), 191–198.
author keywords: PtrCOMT2 promoter; xylem-specific; 4 x 35S enhancer; woody plants; genetic engineering
TL;DR:
While expression of some of the enhancer-plus-promoter constructs increased expression, there was a loss of specificity in the PtrCOMT2 promoter.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(OpenAlex)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes
PLANT PHYSIOLOGY, 161(3), 1501–1516.
Contributors: H. Chen n, J. Song n, C. Williams n , C. Shuford n, J. Liu n, J. Wang n , n, R. Shi n
MeSH headings : Allosteric Regulation / drug effects; Binding Sites; Biosynthetic Pathways / drug effects; Blotting, Western; Caffeic Acids / pharmacology; Coenzyme A / metabolism; Coenzyme A Ligases / antagonists & inhibitors; Coenzyme A Ligases / metabolism; Computer Simulation; Coumaric Acids / chemistry; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Kinetics; Lignin / biosynthesis; Lignin / chemistry; Phenylpropionates / metabolism; Phosphoproteins / metabolism; Phosphorylation / drug effects; Plant Extracts; Populus / drug effects; Populus / enzymology; Propionates; Proteomics; Recombinant Fusion Proteins / metabolism; Sequence Homology, Amino Acid; Substrate Specificity / drug effects; Xylem / drug effects; Xylem / metabolism
TL;DR:
Evidence is presented of two monolignol 4CLs, Ptr4CL3 and P tr4CL5, in Populus trichocarpa that act to mitigate the inhibition by caffeic acid to maintain a proper ligation flux and coenzyme A flux with novel specificity.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2013 journal article
Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa
Proceedings of the National Academy of Sciences, 110(26), 10848–10853.
MeSH headings : Base Sequence; Down-Regulation / genetics; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Gene Regulatory Networks; Genes, Plant; Laccase / antagonists & inhibitors; Laccase / genetics; Lignin / antagonists & inhibitors; Lignin / chemistry; Lignin / metabolism; MicroRNAs / genetics; MicroRNAs / metabolism; Phylogeny; Plant Proteins / genetics; Populus / enzymology; Populus / genetics; RNA, Plant / genetics; RNA, Plant / metabolism
TL;DR:
A hierarchical genetic regulatory network (GRN) built by a bottom-up graphic Gaussian model algorithm provides additional support for a role of ptr-miR397a as a negative regulator of laccases for lignin biosynthesis in wood formation.
(via Semantic Scholar)
Sources: Web Of Science, Crossref, ORCID
Added: August 6, 2018
2013 journal article
Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa
Planta, 238(3), 487–497.
Contributors: R. Shi n, C. Shuford n, J. Wang n , Y. Sun n, Z. Yang n, H. Chen n, S. Tunlaya-Anukit n, n
MeSH headings : Gene Expression Regulation, Plant / physiology; Mass Spectrometry; Phenylalanine Ammonia-Lyase / metabolism; Populus / enzymology; Populus / metabolism
TL;DR:
A greater functional significance of subgroup A PtrPALs for stem wood formation is indicated, and the role of gene post-transcriptional regulation is highlighted.
(via Semantic Scholar)
Sources: NC State University Libraries, ORCID
Added: August 6, 2018
2013 journal article
SND1 Transcription Factor-Directed Quantitative Functional Hierarchical Genetic Regulatory Network in Wood Formation in Populus trichocarpa
PLANT CELL, 25(11), 4324–4341.
MeSH headings : Algorithms; Cell Wall / genetics; Chromatin Immunoprecipitation; Gene Expression Regulation, Plant; Gene Ontology; Gene Regulatory Networks; High-Throughput Nucleotide Sequencing; Models, Genetic; Plant Proteins / genetics; Plant Proteins / metabolism; Plants, Genetically Modified; Polymerase Chain Reaction / methods; Populus / genetics; Populus / metabolism; Protoplasts; Reproducibility of Results; Transcription Factors / genetics; Transcription Factors / metabolism; Transfection; Wood / genetics; Wood / metabolism; Xylem / cytology; Xylem / genetics
TL;DR:
A genome-wide high-throughput system for the discovery and validation of specific transcription factor (TF)–directed hierarchical gene regulatory networks (hGRNs) in wood formation is developed and may be particularly useful to study hGRNs in complex processes in plant species resistant to stable genetic transformation and where mutants are unavailable.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2013 journal article
Understanding the Role of Proteolytic Digestion on Discovery and Targeted Proteomic Measurements Using Liquid Chromatography Tandem Mass Spectrometry and Design of Experiments
JOURNAL OF PROTEOME RESEARCH, 12(12), 5820–5829.
Contributors: P. Loziuk n, J. Wang n , n, R. Sederoff n, V. Chiang n & D. Muddiman n
author keywords: design of experiments; proteolytic digestion; LC-MS/MS; Populus trichocarpa
MeSH headings : Amino Acid Sequence; Animals; Cattle; Chromatography, Liquid / standards; Factor Analysis, Statistical; Hydrogen-Ion Concentration; Isotope Labeling; Molecular Sequence Annotation; Molecular Sequence Data; Peptide Fragments / chemistry; Peptide Fragments / isolation & purification; Plant Proteins / chemistry; Plant Proteins / isolation & purification; Populus / chemistry; Protein Stability; Proteolysis; Proteomics / methods; Proteomics / standards; Research Design; Swine; Tandem Mass Spectrometry / standards; Trypsin / chemistry; Xylem / chemistry
TL;DR:
The tryptic digest optimization described here has eliminated this previously observed peptide decay as well as provided a greater understanding and standardization for a common but critical sample treatment used across the field of proteomics.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2012 journal article
A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities
PLANTA, 236(3), 879–885.
author keywords: Monolignols; Enzyme activity; Populus trichocarpa; Pinus taeda; Angiosperm; Gymnosperm
MeSH headings : Biosynthetic Pathways; Chromatography, High Pressure Liquid; Enzyme Assays; Lignin / biosynthesis; Methyltransferases / metabolism; Mixed Function Oxygenases / metabolism; Oxidoreductases / metabolism; Pinus taeda / enzymology; Plant Proteins / analysis; Plant Stems / enzymology; Populus / enzymology; Substrate Specificity; Xylem / enzymology
TL;DR:
This work developed a method using a total protein extract (soluble and microsomal) for the comprehensive and simultaneous analysis of these ten enzyme activities in a single target tissue, stem differentiating xylem (SDX) of Populustrichocarpa.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2012 journal article
Comprehensive Quantification of Monolignol-Pathway Enzymes in Populus trichocarpa by Protein Cleavage Isotope Dilution Mass Spectrometry
Journal of Proteome Research, 11(6), 3390–3404.
Contributors: C. Shuford n, n, Y. Sun n, H. Chen n, J. Wang n , R. Shi n, R. Sederoff n, V. Chiang n, D. Muddiman n
author keywords: quantification; isotope dilution mass spectrometry; selected reaction monitoring; filter-aided sample preparation; monolignol biosynthesis
MeSH headings : Amino Acid Sequence; Biosynthetic Pathways; Isotope Labeling; Molecular Sequence Data; Plant Proteins / chemistry; Plant Proteins / metabolism; Populus / enzymology; Proteome / chemistry; Proteome / metabolism; Reference Standards; Spectrometry, Mass, Electrospray Ionization / standards; Xylem / enzymology
TL;DR:
This represents the most comprehensive assay for quantification of proteins regulating monolignol biosynthesis and will lead to a better understanding of lignin formation at a systems level.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, Crossref
Added: August 6, 2018
2012 journal article
Functional redundancy of the two 5-hydroxylases in monolignol biosynthesis of Populus trichocarpa: LC-MS/MS based protein quantification and metabolic flux analysis
PLANTA, 236(3), 795–808.
Contributors: J. Wang n , C. Shuford n, n, J. Song n, Y. Lin n, Y. Sun n, H. Chen n, C. Williams n
author keywords: Lignin; Syringyl lignin; Angiosperm; Kinetics; Subcellular localization
MeSH headings : Cloning, Molecular; Gene Expression Regulation, Enzymologic; Gene Expression Regulation, Plant; Hydroxylation; Kinetics; Lignin / analysis; Lignin / biosynthesis; Mixed Function Oxygenases / metabolism; Plants, Genetically Modified; Populus / metabolism; Xylem / enzymology; Yeasts / metabolism
TL;DR:
The combination of genetic analysis, absolute protein quantitation-based enzyme kinetics, homologous CPR specificity, SNP characterization, and ER localization provides a more rigorous basis for a comprehensive systems understanding of 5-hydroxylation in lignin biosynthesis.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2012 journal article
Splice variant of the SND1 transcription factor is a dominant negative of SND1 members and their regulation in Populus trichocarpa
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 109(36), 14699–14704.
MeSH headings : Blotting, Western; Cloning, Molecular; DNA Primers / genetics; Dimerization; Electrophoresis, Polyacrylamide Gel; Gene Regulatory Networks / genetics; Homeostasis / physiology; Models, Biological; Plasmids / genetics; Populus / genetics; Protein Isoforms / genetics; Protein Transport; Real-Time Polymerase Chain Reaction; Transcription Factors / genetics
TL;DR:
A stem-differentiating xylem (SDX)-specific alternative SND1 splice variant, PtrSND1-A2IR, that acts as a dominant negative of S ND1 transcriptional network genes in Populus trichocarpa is discovered and may contribute to transcriptional homeostasis to avoid deleterious effects on xylogenesis and plant growth.
(via Semantic Scholar)
Source: Web Of Science
Added: August 6, 2018
2012 journal article
The Cellulase-Mediated Saccharification on Wood Derived from Transgenic Low-Lignin Lines of Black Cottonwood (Populus trichocarpa)
APPLIED BIOCHEMISTRY AND BIOTECHNOLOGY, 168(4), 947–955.
author keywords: Transgenic hardwood; Downregulated lignin; Pretreatment; Enzymatic saccharification
MeSH headings : Cellulase / metabolism; Down-Regulation; Hydrogen-Ion Concentration; Hydrolysis; Lignin / chemistry; Lignin / metabolism; Ozone / chemistry; Plants, Genetically Modified; Polysaccharides / chemistry; Populus / genetics; Populus / metabolism; Sulfuric Acids / chemistry; Wood / chemistry
TL;DR:
The results indicated that lignin is the main recalcitrance of biomass degradation, and pretreatment with ozone delignification had lower saccharification efficiency than the other pretreatment methods due to higher xylan content.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(Web of Science)
12. Responsible Consumption and Production
(Web of Science)
Source: Web Of Science
Added: August 6, 2018
2011 journal article
Down-regulation of glycosyltransferase 8D genes in Populus trichocarpa caused reduced mechanical strength and xylan content in wood
TREE PHYSIOLOGY, 31(2), 226–236.
Contributors: n, D. Min n, J. Wang n, I. Peszlen n , L. Horvath n, B. Horvath n, Y. Nishimura n, H. Jameel n, H. Chang n, V. Chiang n
author keywords: glycosyltransferase; Populus trichocarpa; wood formation; xylan
MeSH headings : Arabidopsis / genetics; Arabidopsis / metabolism; Cell Wall / metabolism; Down-Regulation; Elastic Modulus; Gene Expression Regulation, Plant; Genes, Plant; Genetic Variation; Glycosyltransferases / genetics; Glycosyltransferases / metabolism; Plant Stems / chemistry; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; Populus / genetics; Populus / metabolism; Stress, Mechanical; Transcription Factors; Wood / analysis; Xylans / biosynthesis; Xylans / genetics
TL;DR:
Results suggest that PtrGT8Ds play key roles in xylan biosynthesis in wood, and may be a more important factor than lignin affecting the stiffness and fracture strength of wood.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2011 journal article
Membrane protein complexes catalyze both 4-and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 108(52), 21253–21258.
MeSH headings : Carboxylic Ester Hydrolases / chemistry; Carboxylic Ester Hydrolases / metabolism; Chromatography, Liquid; Coumaric Acids; DNA Primers / genetics; Hydroxylation; Immunoprecipitation; Kinetics; Lignin / biosynthesis; Mass Spectrometry; Membrane Proteins / chemistry; Membrane Proteins / metabolism; Microscopy, Confocal; Molecular Structure; Multiprotein Complexes / chemistry; Multiprotein Complexes / metabolism; Phenols; Phenylpropionates; Plasmids / genetics; Populus / metabolism; Propionates; Trans-Cinnamate 4-Monooxygenase / chemistry; Trans-Cinnamate 4-Monooxygenase / metabolism; Xylem / metabolism; Yeasts
TL;DR:
Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for functional involvement of membrane protein complexes in monolignol biosynthesis.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 2018
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