Works (13)
Updated: February 27th, 2024 08:30
2023 article
Cell-type-specific PtrWOX4a and PtrVCS2 form a regulatory nexus with a histone modification system for stem cambium development in Populus trichocarpa
Dai, X., Zhai, R., Lin, J., Wang, Z., Meng, D., Li, M., … Li, W. (2023, January 9). NATURE PLANTS.
MeSH headings : Cambium / genetics; Populus / genetics; Epigenesis, Genetic; Histone Code; Wood; Gene Expression Regulation, Plant
TL;DR:
A regulatory system in which transcription factor and histone acetylation functions are coordinated for maintaining normal stem vascular cambium development for wood formation in Populus trichocarpa is revealed.
(via Semantic Scholar)
open access via www.nature.com (publisher PDF)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: January 23, 2023
2021 journal article
Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa
FRONTIERS IN PLANT SCIENCE, 12.
author keywords: protein interaction; monolignol biosynthesis; wood formation; Populus trichocarpa; BiFC; metabolic flux
TL;DR:
It is proposed that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation in P. trichocarpa.
(via Semantic Scholar)
Sources: Web Of Science, NC State University Libraries, ORCID
Added: November 8, 2021
2021 journal article
Transcriptional reprogramming of xylem cell wall biosynthesis in tension wood
PLANT PHYSIOLOGY, 186(1), 250–269.
MeSH headings : Cell Wall / metabolism; Gene Expression Regulation, Plant; Populus / anatomy & histology; Populus / genetics; Transcription, Genetic; Wood / genetics; Wood / metabolism; Xylem / metabolism
TL;DR:
A transcriptional regulatory network is established in which PtrHSFB3-1 and PtrMYB092 directly activate 8 and 11 monolignol genes, respectively in P. trichocarpa, to further uncover how metabolism, growth, and stress adaptation are coordinately regulated in trees.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: May 27, 2021
2021 journal article
p A PtrLBD39-mediated transcriptional network regulates tension wood formation in Populus trichocarpa
PLANT COMMUNICATIONS, 3(1).
author keywords: tension wood; cellulose; lignin; transcriptional regulatory network; transcriptomics; chromatin immunoprecipitation sequencing
MeSH headings : Biomechanical Phenomena; Gene Expression Regulation, Plant / physiology; Gene Regulatory Networks / physiology; Genes, Plant / genetics; Genes, Plant / physiology; Laser Capture Microdissection; Populus / genetics; Populus / physiology; Wood / genetics; Wood / physiology; Xylem
TL;DR:
This work suggests that P trLBD39 and PtrLBD22 specifically control TW formation by mediating a TW-specific TRN in Populus by directly regulating 26 novel TW-responsive transcription factor genes.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: January 31, 2022
2019 journal article
A novel synthetic-genetic-array-based yeast one-hybrid system for high discovery rate and short processing time
GENOME RESEARCH, 29(8), 1343–1351.
MeSH headings : Animals; DNA / genetics; DNA / metabolism; Gene Expression Regulation; Gene Regulatory Networks; Genetic Markers; Humans; Meiosis; Microarray Analysis / instrumentation; Microarray Analysis / methods; Plasmids / chemistry; Plasmids / metabolism; Ploidies; Populus / cytology; Protein Binding; Protoplasts / cytology; Protoplasts / metabolism; Saccharomyces cerevisiae / genetics; Saccharomyces cerevisiae / metabolism; Time Factors; Transcription Factors / genetics; Transcription Factors / metabolism; Two-Hybrid System Techniques
TL;DR:
A high-throughput meiosis-directed yeast one-hybrid system using the Magic Markers of the synthetic genetic array analysis that has a transcription factor–DNA interaction discovery rate twice as high as the conventional diploid-mating approach and a processing time nearly one-tenth of the haploid-transformation method.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: September 16, 2019
2018 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, NC State University Libraries
Added: December 17, 2018
2017 journal article
Tissue and cell-type co-expression networks of transcription factors and wood component genes in Populus trichocarpa
PLANTA, 245(5), 927–938.
author keywords: Wood formation; Transcriptome; Fiber cells; Vessel elements; Cell wall biosynthesis; Co-expression network
MeSH headings : Cell Wall / metabolism; Cellulose / metabolism; Cluster Analysis; Gene Expression Regulation, Plant; Lignin / metabolism; Molecular Sequence Annotation; Organ Specificity; Phloem / genetics; Phloem / growth & development; Plant Leaves / genetics; Plant Leaves / growth & development; Plant Proteins / genetics; Populus / genetics; Populus / growth & development; Sequence Analysis, RNA; Transcription Factors / genetics; Transcriptome; Wood / genetics; Wood / growth & development; Xylem / genetics; Xylem / growth & development
TL;DR:
The co-expression networks revealed here suggest a well-structured transcriptional homeostasis for cell wall component biosynthesis during wood formation.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2015 journal article
Phosphorylation is an on/off switch for 5-hydroxyconiferaldehyde O-methyltransferase activity in poplar monolignol biosynthesis
Proceedings of the National Academy of Sciences, 112(27), 8481–8486.
Contributors: J. Wang n , L. Chuang n, P. Loziuk n, H. Chen n, n, R. Shi n, G. Qu *, D. Muddiman n , R. Sederoff n, V. Chiang n
author keywords: AldOMT; COMT; lignin; phosphoproteomics; phosphoregulation
MeSH headings : Acrolein / analogs & derivatives; Acrolein / metabolism; Amino Acid Sequence; Binding Sites / genetics; Biocatalysis; Catechols / metabolism; Chromatography, Liquid; Electrophoresis, Polyacrylamide Gel; Green Fluorescent Proteins / genetics; Green Fluorescent Proteins / metabolism; Isoenzymes / genetics; Isoenzymes / metabolism; Lignin / biosynthesis; Methyltransferases / genetics; Methyltransferases / metabolism; Microscopy, Confocal; Molecular Sequence Data; Mutation; Phosphoproteins / metabolism; Phosphorylation; Plant Proteins / genetics; Plant Proteins / metabolism; Populus / enzymology; Populus / genetics; Populus / metabolism; Proteomics / methods; Protoplasts / enzymology; Protoplasts / metabolism; Sequence Homology, Amino Acid; Tandem Mass Spectrometry
TL;DR:
It is shown that reversible monophosphorylation at Ser123 or Ser125 acts as an on/off switch for the activity of 5-hydroxyconiferaldehyde O-methyltransferase 2 (PtrAldOMT2), an enzyme central to monolignol biosynthesis for lignification in stem-differentiating xylem of Populus trichocarpa.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
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
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
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, Q. Li n, J. Song n, 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, NC State University Libraries
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
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