Jack Wang
Jack P. Wang is Associate Professor in the Forest Biotechnology Group, Department of Forestry and Environmental Resources, College of Natural Resources at North Carolina State University. Jack received his B.S. degree in Biology and Chemistry from Waikato University, New Zealand in 2006, and completed his Ph.D. at North Carolina State University in 2012, under the mentorship of Dr. Vincent Chiang and Dr. Ron Sederoff. Jack is a forestry scientist with research experience in molecular genetics and biotechnology, particularly the integrative genomic and genetic analysis of plant metabolism for tree growth, development, and defense against biotic and abiotic stresses. Some highlights of his recent research include an unprecedented quantitative systematic analysis of the response to genetic regulation in the model tree species (Populus trichocarpa), with important immediate implications for plant growth and adaptation, as well as biofuels and biomaterials (published in 2018 in Nature Communications); demonstrating that protein phosphorylation acts as an on/off switch for AldOMT, a central enzyme in monolignol biosynthesis (published in 2015 in PNAS); characterizing the hetero-tetrameric 4CL enzyme complex formation, regulation and numerical modeling (published in 2014 in Plant Cell); and establishing a proteomic-based predictive kinetic metabolic-flux (PKMF) model of the monolignol biosynthetic pathway (published in 2014 in Plant Cell). This PKMF model predicts how monolignol pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolignol subunit ratios in lignin, and reveals novel mechanisms involved in the regulation of lignin biosynthesis.
Works (52)
Updated: November 28th, 2024 05:01
2024 journal article
Beyond low lignin: Identifying the primary barrier to plant biomass conversion by fermentative bacteria
SCIENCE ADVANCES, 10(42).
open access via doi.org (publisher)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: November 1, 2024
2023 article
A COMPASS histone H3K4 trimethyltransferase pentamer transactivates drought tolerance and growth/biomass production in <i>Populus trichocarpa</i>
Zhang, B., Wang, Z., Dai, X., Gao, J., Zhao, J., Ma, R., … Li, W. (2023, December 14). NEW PHYTOLOGIST.
author keywords: biomass production; drought tolerance; growth; Populus trichocarpa; PtrAREB1-2; PtrCOMPASS-like complex; PtrSDG2-1
TL;DR:
The identity of the underlying H3K4 trimethyltransferase and its interactive arrangement with the COMPASS for catalysis specificity and efficiency is revealed and the study uncovered how the H3K4 trimethyltransferase-COMPASS complex is recruited to the effector genes for improved drought tolerance and growth/biomass production in plants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Source: Web Of Science
Added: January 2, 2024
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)
UN Sustainable Development Goal Categories
Source: Web Of Science
Added: January 23, 2023
2023 journal article
Multiplex CRISPR editing of wood for sustainable fiber production
SCIENCE, 381(6654), 216-+.
TL;DR:
This work demonstrates that genome editing can be harnessed for breeding more efficient trees, which will provide timely opportunities for sustainable forestry and a more efficient bioeconomy.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: ORCID, Web Of Science, NC State University Libraries
Added: August 9, 2023
2023 article
Woody plant cell walls: Fundamentals and utilization
Li, W., Lin, Y.-C. J., Chen, Y.-L., Zhou, C., Li, S., De Ridder, N., … Chiang, V. L. (2024, January 1). MOLECULAR PLANT, Vol. 17, pp. 112–140.
author keywords: regulation of cell wall formation; biosynthesis of cell wall components; lignin; cellulose; hemicellulose; cell wall utilization
TL;DR:
Opportunities and challenges in future research to better understand cell type biogenesis for more efficient wood cell-wall modification and utilization for biomaterials or for enhanced carbon capture and storage are outlined.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: Web Of Science
Added: February 26, 2024
2022 journal article
<p>Plant biomass fermentation by the extreme thermophile Caldicellulosiruptor bescii for co-production of green hydrogen and acetone: Technoeconomic analysis</p>
BIORESOURCE TECHNOLOGY, 348.
author keywords: Acetone; Green hydrogen; Caldicellulosiruptor bescii; Extreme thermophiles; Technoeconomic analysis
MeSH headings : Acetone; Biomass; Caldicellulosiruptor; Fermentation; Hydrogen; Lignin / chemistry
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, NC State University Libraries
Added: April 25, 2022
2022 article
Dimerization of PtrMYB074 and PtrWRKY19 mediates transcriptional activation of PtrbHLH186 for secondary xylem development in Populus trichocarpa
Liu, H., Gao, J., Sun, J., Li, S., Zhang, B., Wang, Z., … Li, W. (2022, March 3). NEW PHYTOLOGIST, Vol. 5.
author keywords: Populus trichocarpa; protein-protein interaction; secondary xylem development; transcription factor; wood formation
MeSH headings : Cell Wall / metabolism; Dimerization; Gene Expression Regulation, Plant; Plant Proteins / genetics; Plant Proteins / metabolism; Populus; Transcriptional Activation; Wood; Xylem / metabolism
TL;DR:
Knowledge of the PtrMYB074‐PtrWRKY19‐PtrbHLH186 regulation may help design genetic controls of optimal growth and wood formation to maximize beneficial wood properties while minimizing negative effects on growth.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: March 21, 2022
2022 journal article
Enhancing HR Frequency for Precise Genome Editing in Plants
FRONTIERS IN PLANT SCIENCE, 13.
author keywords: homologous recombination; homology-directed repair; gene targeting; donor template; programmable nucleases
TL;DR:
Various strategies implemented to increase the frequency of HDR in plant cells are summarized, including methods for targeting double-strand DNA breaks, optimizing donor sequences, altering plant DNA repair machinery, and environmental factors shown to influence HR frequency in plants.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
Sources: Web Of Science, ORCID
Added: May 31, 2022
2022 journal article
Fermentative conversion of unpretreated plant biomass: A thermophilic threshold for indigenous microbial growth
BIORESOURCE TECHNOLOGY, 367.
author keywords: Thermophiles; Lignocellulose; Consolidated bioprocessing; Caldicellulosiruptor bescii; Acetivibrio thermocellus
MeSH headings : Biomass; Fermentation; Lignin / chemistry; Clostridium thermocellum / metabolism; Plants / metabolism
TL;DR:
Thermophiles that naturally grow at and above 75°C offer specific advantages as platform microorganisms for biomass conversion into fuels and chemicals that prevents native microbes from competing with engineered microbes and forming undesirable by-products.
(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, NC State University Libraries
Added: January 17, 2023
2021 article
CRISPR-Cas9 editing of CAFFEOYL SHIKIMATE ESTERASE 1 and 2 shows their importance and partial redundancy in lignification in Populus tremula x P. alba
Vries, L., Brouckaert, M., Chanoca, A., Kim, H., Regner, M. R., Timokhin, V. I., … Boerjan, W. (2021, August 6). PLANT BIOTECHNOLOGY JOURNAL, Vol. 11.
author keywords: poplar; CRISPR-Cas9; CSE; lignin; phenylpropanoids; metabolic engineering
MeSH headings : CRISPR-Cas Systems / genetics; Carboxylesterase; Gene Expression Regulation, Plant; Lignin / metabolism; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; Populus / genetics; Populus / metabolism
TL;DR:
The results suggest an alternative path within the phenylpropanoid pathway at the level of the hydroxycinnamoyl‐shikimates, and show that CSE is a promising target to improve plants for the biorefinery.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 23, 2021
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, ORCID, NC State University Libraries
Added: November 8, 2021
2021 journal article
Thermophilic microbial deconstruction and conversion of natural and transgenic lignocellulose
Environmental Microbiology Reports, 13(3), 272–293.
MeSH headings : Biomass; Lignin / chemistry; Plants / metabolism
TL;DR:
Bioengineering plant properties to better fit the deconstruction capabilities of candidate consolidated bioprocessing microorganisms has potential to achieve the efficient lignocellulose deconstruction needed for industrial relevance.
(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, Crossref, NC State University Libraries
Added: April 12, 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: ORCID, Web Of Science
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
2020 journal article
A multiscale model of lignin biosynthesis for predicting bioenergy traits in Populus trichocarpa
COMPUTATIONAL AND STRUCTURAL BIOTECHNOLOGY JOURNAL, 19, 168–182.
author keywords: Lignin biosynthesis; Multiscale modeling; Cross-regulatory influences; Random forests
Sources: Web Of Science, ORCID, NC State University Libraries
Added: September 20, 2021
2020 journal article
MYB Transcription Factor161 Mediates Feedback Regulation of Secondary wall-associated NAC-Domain1 Family Genes for Wood Formation
Plant Physiology, 9, pp.01033.2020.
MeSH headings : Cell Enlargement; Cell Proliferation; Cell Wall / metabolism; Gene Expression Regulation, Developmental; Gene Expression Regulation, Plant; Genes, Plant; Genetic Variation; Genotype; Plant Proteins / metabolism; Populus / genetics; Populus / growth & development; Populus / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism; Wood / growth & development; Xylem / metabolism
TL;DR:
It is demonstrated that PtrMYB161 binds to multiple sets of target genes, a feature that allows it to function as an activator as well as a repressor, and the balance of the two functions may be important to the establishment of regulatory homeostasis for normal growth and development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Source: ORCID
Added: November 3, 2020
2020 journal article
Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa
PLOS Computational Biology.
Ed(s): S. Roy
MeSH headings : Computational Biology / methods; Gene Expression Regulation, Plant / genetics; Gene Knockdown Techniques / methods; Lignin / biosynthesis; Lignin / genetics; Lignin / metabolism; Models, Theoretical; Populus / genetics; Wood / genetics
Source: ORCID
Added: April 11, 2020
2020 journal article
Monolignol Benzoates Incorporate into the Lignin of Transgenic Populus trichocarpa Depleted in C3H and C4H
ACS Sustainable Chemistry and Engineering, 8(9), 3644–3654.
Contributors: H. Kim *, Q. Li *, S. Karlen *, R. Smith *, R. Shi n, J. Liu n, C. Yang n, S. Tunlaya-Anukit n
author keywords: poplar; 2D NMR; HSQC; enzyme; p-hydroxybenzoate; biomass; cytochrome P450
TL;DR:
A large number of genetic modifications affecting monolignol biosynthesis, which produces lignin monom...
(via Semantic Scholar)
Source: ORCID
Added: April 2, 2020
2020 review
Regulation of Lignin Biosynthesis by Post-translational Protein Modifications
[Review of ]. FRONTIERS IN PLANT SCIENCE, 11.
author keywords: lignin; lignification; proteins; PTMs; SCW; trees; wood formation
TL;DR:
The main discoveries of post-translational modifications in lignin biosynthesis are discussed in this review.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 10, 2020
2020 journal article
Tracheid Associated Transcription Factors in Loblolly Pine.
Tree Physiology, 2.
MeSH headings : Pinus taeda; Transcription Factors / genetics
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Source: ORCID
Added: April 2, 2020
2020 journal article
Use of the lignocellulose-degrading bacterium Caldicellulosiruptor bescii to assess recalcitrance and conversion of wild-type and transgenic poplar
BIOTECHNOLOGY FOR BIOFUELS, 13(1).
author keywords: Caldicellulosiruptor; Extreme thermophiles; Lignocellulose; Biofuel; Poplar
TL;DR:
Utilizing C. bescii as a screening assay for recalcitrance, poplar lines with down-regulation of coumarate 3-hydroxylase 3 (C3H3) resulted in the highest degrees of solubilization and conversion by C. Bescii, suggesting that excellent digestibility can be achieved without compromising fitness of the tree.
(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, NC State University Libraries
Added: April 6, 2020
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
2019 review
Enzyme-Enzyme Interactions in Monolignol Biosynthesis
[Review of ]. FRONTIERS IN PLANT SCIENCE, 9.
Contributors: n , B. Liu *, Y. Sun *, V. Chiang n & R. Sederoff n
author keywords: monolignol biosynthesis; protein-protein interaction; lignin; enzyme kinetics; BiFC; co-immunoprecipitation
TL;DR:
Support for interactions comes from new studies of enzyme activity, co-immunoprecipitation, chemical crosslinking, bimolecular fluorescence complementation, yeast 2-hybrid functional screening, and cell type–specific gene expression based on light amplification by stimulated emission of radiation capture microdissection.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: January 28, 2019
2019 journal article
Hierarchical Transcription Factor and Chromatin Binding Network for Wood Formation in Populus trichocarpa
The Plant Cell, 31(3), 602–626.
MeSH headings : Cell Wall / metabolism; Chromatin / genetics; Chromatin / metabolism; Gene Expression Regulation, Developmental / genetics; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks / genetics; Plant Proteins / genetics; Plant Proteins / metabolism; Populus / genetics; Populus / growth & development; Populus / physiology; Transcription Factors / genetics; Transcription Factors / metabolism; Wood / growth & development
TL;DR:
This work suggests that wood formation may involve regulatory homeostasis determined by combinations of TF–DNA and TF–TF (protein–protein) regulations.
(via Semantic Scholar)
Source: ORCID
Added: April 18, 2019
2019 article
Modeling cross-regulatory influences on monolignol transcripts and proteins under single and combinatorial gene knockdowns in Populus trichocarpa
Matthews, M. L., Wang, J. P., Sederoff, R., Chiang, V. L., & Williams, C. M. (2019, June 19). (Vol. 6). Vol. 6.
TL;DR:
A computational model is developed that more accurately estimates transcript and protein abundances in differentiating xylem tissue when individual and families of monolignol genes were perturbed, and is an important addition to current models of lignin biosynthesis.
(via Semantic Scholar)
Source: ORCID
Added: June 20, 2019
2019 journal article
Quantitative fermentation of unpretreated transgenic poplar by Caldicellulosiruptor bescii
NATURE COMMUNICATIONS, 10(1).
Contributors: C. Straub n, P. Khatibi n, n , J. Conway n, A. Williams-Rhaesa *, I. Peszlen n , V. Chiang n, M. Adams *, R. Kelly n
MeSH headings : Biomass; Cellulose / metabolism; Clostridiales / genetics; Clostridiales / metabolism; Ethanol / metabolism; Fermentation; Industrial Microbiology; Lignin / metabolism; Metabolic Engineering; Plants, Genetically Modified / chemistry; Plants, Genetically Modified / genetics; Plants, Genetically Modified / metabolism; Polysaccharides / metabolism; Populus / chemistry; Populus / genetics; Populus / metabolism
TL;DR:
The authors pair transgenic lignin modified poplar lines with engineered Caldicellusiruptor bescii to achieve biomass solubilization and ethanol conversion without pretreatment and the nearly quantitative microbial conversion of the carbohydrate content of unpretreated transgen lignocellulosic biomass bodes well for full utilization of renewable biomass feedstocks.
(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, NC State University Libraries
Added: August 26, 2019
2019 review
Systems and Synthetic Biology of Forest Trees: A Bioengineering Paradigm for Woody Biomass Feedstocks
[Review of ]. FRONTIERS IN PLANT SCIENCE, 10.
Contributors: A. Myburg *, S. Hussey *, n , N. Street * & E. Mizrachi *
author keywords: synthetic biology (synbio); systems biology; systems genetics; woody biomass; biorefinery; bioeconomy; lignin biosynthesis; wood formation
TL;DR:
A bioengineering paradigm based on a deeper understanding and rational design of biological parts, devices, and integrated systems will be crucial for the development of a new generation of woody biorefinery crops.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: July 8, 2019
2018 journal article
Assessing the impact of the 4CL enzyme complex on the robustness of monolignol biosynthesis using metabolic pathway analysis
PLOS ONE, 13(3), e0193896.
Contributors: P. Naik n, n , R. Sederoff n, V. Chiang n, C. Williams n & J. Ducoste n
Ed(s): D. Cullen
MeSH headings : Biosynthetic Pathways; Homeostasis; Lignin / biosynthesis; Metabolic Networks and Pathways; Monte Carlo Method; Plant Proteins / metabolism; Populus / enzymology; Populus / metabolism
TL;DR:
Results from robustness and stability analyses suggest that the monolignol biosynthetic pathway is resilient to mild perturbations in the presence of the Ptr4CL3-Ptr4CL5 complex, which increased the stability of the pathway by 22%.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
7. Affordable and Clean Energy
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
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: ORCID, Web Of Science, NC State University Libraries
Added: December 17, 2018
2018 journal article
Flux modeling for monolignol biosynthesis
Current Opinion in Biotechnology, 56, 187–192.
Contributors: n , M. Matthews n, P. Naik n, C. Williams n , J. Ducoste n , R. Sederoff n, V. Chiang n
MeSH headings : Biosynthetic Pathways; Kinetics; Lignin / biosynthesis; Metabolic Engineering; Metabolic Flux Analysis; Models, Biological
TL;DR:
This review summarizes the recent progress in flux modeling and its application to lignin engineering for improved plant development and utilization.
(via Semantic Scholar)
Sources: ORCID, Crossref, NC State University Libraries
Added: April 24, 2019
2018 journal article
Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis
Nature Communications, 9(1), 1579.
Contributors: n , M. Matthews n, C. Williams n , R. Shi n, C. Yang n, S. Tunlaya-Anukit n, H. Chen n, Q. Li *
MeSH headings : Gene Expression Regulation, Plant; Lignin / biosynthesis; Lignin / genetics; Plants, Genetically Modified / genetics; Populus / genetics; Populus / metabolism; Transcriptome / genetics; Trees / genetics; Trees / metabolism; Wood / chemistry; Wood / physiology; Xylem / metabolism
TL;DR:
A multi-omics quantitative integrative analysis of lignin biosynthesis can advance the strategic engineering of wood for timber, pulp, and biofuels and may lead to greater understanding of other pathways for improved growth and adaptation.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries, Crossref
Added: August 6, 2018
2018 journal article
The AREB1 Transcription Factor Influences Histone Acetylation to Regulate Drought Responses and Tolerance in Populus trichocarpa
Plant Cell, 31(3), 663–686.
Contributors: S. Li *, Y. Lin n, P. Wang *, B. Zhang *, M. Li *, S. Chen *, R. Shi n, S. Tunlaya-Anukit n
MeSH headings : Abscisic Acid / metabolism; Acetylation; Droughts; Gene Expression Regulation, Plant; Histone Acetyltransferases / genetics; Histone Acetyltransferases / metabolism; Histones / metabolism; Nucleotide Motifs; Phenotype; Plant Growth Regulators / metabolism; Plant Proteins / genetics; Plant Proteins / metabolism; Populus / genetics; Populus / physiology; Promoter Regions, Genetic / genetics; Protein Processing, Post-Translational; RNA Polymerase II / genetics; RNA Polymerase II / metabolism; Transcription Factors / genetics; Transcription Factors / metabolism; Transcriptional Activation
TL;DR:
The combinatorial function of the ternary proteins establishes a coordinated histone acetylation and transcription factor-mediated gene activation for drought response and tolerance in Populus species.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
3. Good Health and Well-being
(Web of Science)
14. Life Below Water
(OpenAlex)
Source: ORCID
Added: April 24, 2019
2017 journal article
Reciprocal cross-regulation of VND and SND multigene TF families for wood formation in Populus trichocarpa
PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA, 114(45), E9722–E9729.
author keywords: reciprocal cross-regulation; NAC transcription factors; alternative splicing; wood formation; Populus trichocarpa
MeSH headings : Alternative Splicing; Cell Wall / genetics; Cell Wall / metabolism; Cloning, Molecular; DNA, Plant; Gene Expression Regulation, Plant / genetics; Gene Regulatory Networks; Genes, Plant; Homeostasis; Multigene Family; Nuclear Proteins; Plant Leaves / genetics; Plant Leaves / metabolism; Plant Proteins / genetics; Plant Proteins / metabolism; Plant Shoots / genetics; Plant Shoots / metabolism; Populus / genetics; Populus / metabolism; Recombinant Proteins / genetics; Transcription Factors / genetics; Transcription Factors / metabolism; Transcriptional Activation / genetics; Transcriptome; Wood / genetics; Wood / growth & development; Xylem / genetics; Xylem / growth & development
TL;DR:
The results indicate that the splice variants from the PtrVND6 and PtrSND1 family may exert reciprocal cross-regulation for complete transcriptional regulation of these two families in wood formation, suggesting a general mechanism among NAC domain proteins and likely other transcription factors.
(via Semantic Scholar)
Sources: Web Of Science, ORCID
Added: August 6, 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
2016 chapter
A Proteomic-Based Quantitative Analysis of the Relationship Between Monolignol Biosynthetic Protein Abundance and Lignin Content Using TransgenicPopulus trichocarpa
In V. C. Kumi Yoshida & S. Quideau (Eds.), Recent Advances in Polyphenol Research (Vol. 5, pp. 89–107).
Contributors: * , S. Tunlaya-Anukit, R. Shi, T. Yeh, L. Chuang, F. Isik* , C. Yang, J. Liu
Ed(s): V. Kumi Yoshida & S. Quideau
UN Sustainable Development Goal Categories
2. Zero Hunger
(OpenAlex)
Sources: NC State University Libraries, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018
2016 journal article
A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa
Tree Genetics & Genomes, 12(2).
author keywords: Lignin polymerization; Populus trichocarpa; Lignin peroxidase; LC-MS/MS; Lignin systems biology
TL;DR:
Differentially expressed gene (DEG) analysis of PtrPO21 downregulated transgenics identified a significant overexpression of PtPrx35, suggesting a compensatory effect within the peroxidase family.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018
2015 journal article
4-Coumaroyl and Caffeoyl Shikimic Acids Inhibit 4-Coumaric Acid: Coenzyme A Ligases and Modulate Metabolic Flux for 3-Hydroxylation in Monolignol Biosynthesis of Populus trichocarpa
MOLECULAR PLANT, 8(1), 176–187.
author keywords: monolignol biosynthesis; Populus trichocarpa; metabolic flux; reaction and inhibition kinetics; LC-MS/MS; 4-coumaroyl and caffeoyl shikimic acids
MeSH headings : Acyl Coenzyme A / metabolism; Coenzyme A Ligases / metabolism; Coumaric Acids / metabolism; Coumaric Acids / pharmacology; Hydroxylation / drug effects; Plant Proteins / metabolism; Populus / drug effects; Populus / enzymology; Populus / metabolism; Propionates; Shikimic Acid / pharmacology
TL;DR:
4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr 4CL5, which can reduce lignin content in a number of plant species and play significant regulatory roles when these inhibitors accumulate.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, NC State University Libraries
Added: August 6, 2018
2015 journal article
Comparative proteomic analysis of Populus trichocarpa early stem from primary to secondary growth
JOURNAL OF PROTEOMICS, 126, 94–108.
author keywords: Proteomics; Early stem development; Secondary growth; Populus trichocarpa
MeSH headings : Plant Proteins / biosynthesis; Plant Stems / metabolism; Populus / metabolism; Proteome / biosynthesis; Proteomics
TL;DR:
The proteomic characteristics indicated that carbohydrate metabolism, oxido-reduction, protein degradation and secondary cell wall metabolism were the dominantly occurring biochemical processes during Populus early stem development.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
15. Life on Land
(OpenAlex)
Sources: Web Of Science, ORCID
Added: August 6, 2018
2015 journal article
Elucidation of Xylem-Specific Transcription Factors and Absolute Quantification of Enzymes Regulating Cellulose Biosynthesis in Populus trichocarpa
JOURNAL OF PROTEOME RESEARCH, 14(10), 4158–4168.
Contributors: P. Loziuk n, J. Parker n, W. Li n, C. Lin n, n , Q. Li *, R. Sederoff n, V. Chiang n, D. Muddiman n
author keywords: shotgun discovery proteomics; absolute quantification; PC-IDMS; cellulose biosynthesis; transcription factor; targeted mass spectrometiry; SRM
MeSH headings : Carbohydrate Metabolism; Cellulose / biosynthesis; Cellulose / genetics; Chromatography, Liquid; Gene Expression Regulation, Plant; Molecular Sequence Annotation; Plant Proteins / genetics; Plant Proteins / isolation & purification; Plant Proteins / metabolism; Populus / genetics; Populus / metabolism; Proteome / genetics; Proteome / isolation & purification; Proteome / metabolism; Proteomics; Tandem Mass Spectrometry; Transcription Factors / genetics; Transcription Factors / isolation & purification; Transcription Factors / metabolism; Wood / chemistry; Wood / metabolism; Xylem / genetics; Xylem / metabolism
TL;DR:
The study described herein sought to identify the proteins directly involved in cellulose biosynthesis during wood formation in Populus trichocarpa along with known xylem-specific transcription factors involved in regulating these key proteins.
(via Semantic Scholar)
UN Sustainable Development Goal Categories
9. Industry, Innovation and Infrastructure
(OpenAlex)
Sources: Web Of Science, ORCID, NC State University Libraries
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: n , L. Chuang n, P. Loziuk n, H. Chen n, Y. Lin 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 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
Complete Proteomic-Based Enzyme Reaction and Inhibition Kinetics Reveal How Monolignol Biosynthetic Enzyme Families Affect Metabolic Flux and Lignin in Populus trichocarpa
The Plant Cell, 26(3), 894–914.
Contributors: n , P. Naik n, H. Chen n, R. Shi n, C. Lin n, J. Liu n, C. Shuford n, Q. Li n
MeSH headings : Kinetics; Lignin / metabolism; Mass Spectrometry; Plant Proteins / metabolism; Polymorphism, Single Nucleotide; Populus / metabolism; Proteome
TL;DR:
A proteomic-based predictive kinetic metabolic-flux model was developed for monolignol biosynthesis in Populus trichocarpa and predicts how pathway enzymes affect lignin content and composition, explains a long-standing paradox regarding the regulation of monolIGNol subunit ratios in lignIn, and reveals novel mechanisms involved in theregulation of lign in biosynthesis.
(via Semantic Scholar)
Sources: Web Of Science, ORCID, Crossref, NC State University Libraries
Added: August 6, 2018
2014 review
Plant biotechnology for lignocellulosic biofuel production
[Review of ]. PLANT BIOTECHNOLOGY JOURNAL, 12(9), 1174–1192.
Contributors: Q. Li *, J. Song *, S. Peng *, n , G. Qu *, R. Sederoff n, V. Chiang n
author keywords: biofuel; biotechnology; cell wall; lignocellulose
MeSH headings : Biofuels; Biotechnology / methods; Cell Wall / metabolism; Lignin / metabolism; Plants / enzymology; Plants / metabolism; Protein Engineering
TL;DR:
Transgenic plants can be engineered to reduce recalcitrance without any yield penalty, indicating that successful cell wall modification can be achieved without impacting cell wall integrity or plant development.
(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, n , Y. Lin n, J. Ducoste n , C. Shuford n, J. Liu n, Q. Li 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, NC State University Libraries, Crossref
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, n , Q. Li 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, NC State University Libraries
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, n , Y. Sun n, Z. Yang n, H. Chen n, S. Tunlaya-Anukit n, Q. Li 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, NC State University Libraries
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, n , Q. Li 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, NC State University Libraries
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, Q. Li n, Y. Sun n, H. Chen n, 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, NC State University Libraries
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: n , C. Shuford n, Q. Li 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, NC State University Libraries
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: Q. Li 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, NC State University Libraries
Added: August 6, 2018
2007 journal article
A novel O-methyl transferase-like gene with a drastic ectopic expression in response to tension wood formation in Populus trichocarpa
Cellulose Chemistry and Technology, 41(9-10), 521–528. http://www.scopus.com/inward/record.url?eid=2-s2.0-60749092120&partnerID=MN8TOARS
Source: ORCID
Added: December 17, 2018
2007 journal article
A novel O-methyl transferase-like gene with drastic ectopic expression in response to tension wood formation in Populus trichocarpa
Cellulose Chemistry and Technology, 41, 521–528.
Source: NC State University Libraries
Added: August 6, 2018
Employment
Updated: December 20th, 2024 11:05
2024 - present
North Carolina State University Raleigh, US
Associate Professor and Director
Forest Biotechnology Group
2018 - 2024
NC State University Raleigh, NC, US
Assistant Professor
Forest Biotechnology Group
Education
Updated: October 24th, 2016 13:50
2007 - 2012
North Carolina State University Raleigh, NC, US
Ph.D.
Forestry and Environmental Resources
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