@article{sulis_jiang_yang_marques_matthews_miller_lan_cofre-vega_liu_sun_et al._2023, title={Multiplex CRISPR editing of wood for sustainable fiber production}, volume={381}, ISSN={["1095-9203"]}, url={http://europepmc.org/abstract/med/37440632}, DOI={10.1126/science.add4514}, abstractNote={The domestication of forest trees for a more sustainable fiber bioeconomy has long been hindered by the complexity and plasticity of lignin, a biopolymer in wood that is recalcitrant to chemical and enzymatic degradation. Here, we show that multiplex CRISPR editing enables precise woody feedstock design for combinatorial improvement of lignin composition and wood properties. By assessing every possible combination of 69,123 multigenic editing strategies for 21 lignin biosynthesis genes, we deduced seven different genome editing strategies targeting the concurrent alteration of up to six genes and produced 174 edited poplar variants. CRISPR editing increased the wood carbohydrate-to-lignin ratio up to 228% that of wild type, leading to more-efficient fiber pulping. The edited wood alleviates a major fiber-production bottleneck regardless of changes in tree growth rate and could bring unprecedented operational efficiencies, bioeconomic opportunities, and environmental benefits.}, number={6654}, journal={SCIENCE}, author={Sulis, Daniel B. and Jiang, Xiao and Yang, Chenmin and Marques, Barbara M. and Matthews, Megan L. and Miller, Zachary and Lan, Kai and Cofre-Vega, Carlos and Liu, Baoguang and Sun, Runkun and et al.}, year={2023}, month={Jul}, pages={216-+} }
 @article{lin_sun_song_chen_shi_yang_liu_tunlaya-anukit_liu_loziuk_et al._2021, title={Enzyme Complexes of Ptr4CL and PtrHCT Modulate Co-enzyme A Ligation of Hydroxycinnamic Acids for Monolignol Biosynthesis in Populus trichocarpa}, volume={12}, ISSN={["1664-462X"]}, url={http://europepmc.org/abstract/med/34691108}, DOI={10.3389/fpls.2021.727932}, abstractNote={Co-enzyme A (CoA) ligation of hydroxycinnamic acids by 4-coumaric acid:CoA ligase (4CL) is a critical step in the biosynthesis of monolignols. Perturbation of 4CL activity significantly impacts the lignin content of diverse plant species. InPopulus trichocarpa, two well-studied xylem-specific Ptr4CLs (Ptr4CL3 and Ptr4CL5) catalyze the CoA ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. Subsequently, two 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) mediate the conversion of 4-coumaroyl-CoA to caffeoyl-CoA. Here, we show that the CoA ligation of 4-coumaric and caffeic acids is modulated by Ptr4CL/PtrHCT protein complexes. Downregulation ofPtrHCTsreduced Ptr4CL activities in the stem-differentiating xylem (SDX) of transgenicP. trichocarpa. The Ptr4CL/PtrHCT interactions were then validatedin vivousing biomolecular fluorescence complementation (BiFC) and protein pull-down assays inP. trichocarpaSDX extracts. Enzyme activity assays using recombinant proteins of Ptr4CL and PtrHCT showed elevated CoA ligation activity for Ptr4CL when supplemented with PtrHCT. Numerical analyses based on an evolutionary computation of the CoA ligation activity estimated the stoichiometry of the protein complex to consist of one Ptr4CL and two PtrHCTs, which was experimentally confirmed by chemical cross-linking using SDX plant protein extracts and recombinant proteins. Based on these results, we propose that Ptr4CL/PtrHCT complexes modulate the metabolic flux of CoA ligation for monolignol biosynthesis during wood formation inP. trichocarpa.}, journal={FRONTIERS IN PLANT SCIENCE}, author={Lin, Chien-Yuan and Sun, Yi and Song, Jina and Chen, Hsi-Chuan and Shi, Rui and Yang, Chenmin and Liu, Jie and Tunlaya-Anukit, Sermsawat and Liu, Baoguang and Loziuk, Philip L. and et al.}, year={2021}, month={Oct} }
 @article{yan_liu_kim_liu_huang_yang_lin_chen_yang_wang_et al._2019, title={CAD1 and CCR2 protein complex formation in monolignol biosynthesis in Populus trichocarpa}, volume={222}, ISSN={["1469-8137"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-85055556739&partnerID=MN8TOARS}, DOI={10.1111/nph.15505}, abstractNote={Summary}, number={1}, journal={NEW PHYTOLOGIST}, author={Yan, Xiaojing and Liu, Jie and Kim, Hoon and Liu, Baoguang and Huang, Xiong and Yang, Zhichang and Lin, Ying-Chung Jimmy and Chen, Hao and Yang, Chenmin and Wang, Jack P. and et al.}, year={2019}, month={Apr}, pages={244–260} }
 @article{li_yeh_yang_song_chen_sederoff_chiang_2015, title={Populus trichocarpa}, volume={1224}, ISBN={["978-1-4939-1657-3"]}, ISSN={["1064-3745"]}, DOI={10.1007/978-1-4939-1658-0_28}, abstractNote={Populus trichocarpa Nisqually-1 is a clone of black cottonwood that is widely used as a model woody plant. It was the first woody plant to have a full genome sequence and remains today as the model for growth, metabolism, development, and adaptation for all woody dicotyledonous plants. It is one of the best-annotated plant genomes available. It is also currently studied to improve bioenergy feedstocks and to learn about responses to environmental variation that may result from climate change. It is the best characterized woody plant for lignin biosynthesis. In spite of its role as a model woody plant, many important genetic applications have been limited because it was particularly difficult for DNA transformation. The ability to transform P. trichocarpa is a central component of a systems biology approach to the study of metabolic and developmental processes, where in combination with genome and transcriptome sequencing, all the expressed genes for specific pathways can be defined, cloned, and characterized for biological function. We previously reported on a method for Agrobacterium-mediated genetic transformation in P. trichocarpa(Song et al. Plant Cell Physiol 47: 1582-1589, 2006). Since then, we have optimized the protocol based on many experiments that varied in tissue manipulation, media, DNA constructs and Agrobacterium strains. A modified step-by-step protocol for Agrobacterium-mediated transformation of stem explants is described here. The health of the tissue explants and the time of cocultivation are among the critical steps in the protocol for successful transformation. This updated protocol should be helpful to many laboratories that are currently carrying out P. trichocarpa transformation. It should also encourage many labs that have not yet had success with P. trichocarpa to try again.}, journal={AGROBACTERIUM PROTOCOLS, VOLUME 2, THIRD EDITION}, author={Li, Quanzi and Yeh, Ting-Feng and Yang, Chenmin and Song, Jingyuan and Chen, Zenn-Zong and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2015}, pages={357–363} }
 @article{stout_davis_domec_yang_shi_king_2014, title={Growth under field conditions affects lignin content and productivity in transgenic Populus trichocarpa with altered lignin biosynthesis}, volume={68}, ISSN={["1873-2909"]}, DOI={10.1016/j.biombioe.2014.06.008}, abstractNote={This study evaluated the potential of transgenic Populus trichocarpa with antisense 4CL for reduced total lignin and sense Cald5H for increased S/G ratio in a short rotation woody cropping (SRWC) system for bioethanol production in the Southeast USA. Trees produced from tissue-culture were planted in the Coastal Plain, Piedmont, and Mountain regions of North Carolina, USA. Trees were observed for growth differences and biomass recorded for two coppices. Insoluble lignin and S/G ratio were determined by molecular beam mass spectroscopy after the second coppice. Survival, growth form, and biomass were very consistent within construct lines. Higher total lignin content and S/G ratio were positively correlated with total aboveground biomass. The low-lignin phenotype was not completely maintained in the field, with total lignin content increasing on average more than 30.0% at all sites by the second coppice The capacity to upregulate lignin in the event of environmental stress may have helped some low-lignin lines to survive. More research focused on promising construct lines in appropriate environmental conditions is needed to clarify if a significant reduction in lignin can be achieved on a plantation scale, and whether that reduction will translate into increased efficiency of enzymatic hydrolysis.}, journal={BIOMASS & BIOENERGY}, author={Stout, Anna T. and Davis, Aletta A. and Domec, Jean-Christophe and Yang, Chenmin and Shi, Rui and King, John S.}, year={2014}, month={Sep}, pages={228–239} }
 @article{min_yang_shi_jameel_chiang_chang_2013, title={The elucidation of the lignin structure effect on the cellulase-mediated saccharification by genetic engineering poplars (Populus nigra L. x Populus maximowiczii A.)}, volume={58}, ISSN={["1873-2909"]}, DOI={10.1016/j.biombioe.2013.08.019}, abstractNote={The lignin structure effect on the recalcitrance of biomass degradation was elucidated by twelve transgenic hybrid poplars (Populus nigra L. and Populus maximowiczii A.). Samples have different levels of the syringaldehyde (S) to vanillin (V) ratio from 0.1 to 2.6 and the lignin content from 10.5 to 24.3%, compared to the control (the S to V ratio 1.7 and the lignin content 22.0%). The dilute acid (0.1% sulfuric acid, 185 °C, and 30 min) and the green liquor (6% total titratable alkali (TTA), 25% sulfidity based on TTA, 185 °C and 15 min) were used as pretreatments. The enzymatic saccharification was performed at 5 FPU g−1 based on the substrate. The removal of lignin and hemicelluloses varied with pretreatments. The high delignification originated from the high S to V ratio. However, the high S to V ratio retarded the enzymatic saccharification. The decrease of the lignin and the hemicelluloses benefited the enzymatic saccharification with or without the pretreatment.}, journal={BIOMASS & BIOENERGY}, author={Min, Douyong and Yang, Chenmin and Shi, Rui and Jameel, Hasan and Chiang, Vincent and Chang, Houmin}, year={2013}, month={Nov}, pages={52–57} }
 @article{lu_yang_chiang_2011, title={Conservation and Diversity of MicroRNA-associated Copper-regulatory Networks in Populus trichocarpa}, volume={53}, ISSN={["1744-7909"]}, DOI={10.1111/j.1744-7909.2011.01080.x}, abstractNote={Plants develop important regulatory networks to adapt to the frequently-changing availability of copper (Cu). However, little is known about miRNA-associated Cu-regulatory networks in plant species other than Arabidopsis. Here, we report that Cu-responsive miRNAs in Populus trichocarpa (Torr. & Gray) include not only conserved miR397, miR398 and miR408, but also Populus-specific miR1444, suggesting the conservation and diversity of Cu-responsive miRNAs in plants. Copper-associated suppression of mature miRNAs is in company with the up-regulation of their target genes encoding Cu-containing proteins in Populus. The targets include miR397-targeted PtLAC5, PtLAC6 and PtLAC110a, miR398-targeted PtCSD1, PtCSD2a and PtCSD2b, miR408-targeted PtPCL1, PtPCL2, PtPCL3 and PtLAC4, and miR1444-targeted PtPPO3 and PtPPO6. Consistently, P. trichocarpa miR408 promoter-directed GUS gene expression is down-regulated by Cu in transgenic tobacco plants. Cu-response elements (CuREs) are found in the promoters of Cu-responsive miRNA genes. We identified 34 SQUAMOSA-promoter binding protein-like (SPL) genes, of which 17 are full-length PtSPL proteins or partial sequences with at least 300 amino acids. Phylogenetic analysis indicates that PtSPL3 and PtSPL4 are CuRE-binding proteins controlling Cu-responsive gene expression. Cu appears to be not involved in the regulation of these transcription factors because neither PtSPL3 nor PtSPL4 is Cu-regulated and no CuRE exists in their promoters.}, number={11}, journal={JOURNAL OF INTEGRATIVE PLANT BIOLOGY}, author={Lu, Shanfa and Yang, Chenmin and Chiang, Vincent L.}, year={2011}, month={Nov}, pages={879–891} }
 @article{shi_yang_lu_sederoff_chiang_2010, title={Specific down-regulation of PAL genes by artificial microRNAs in Populus trichocarpa}, volume={232}, ISSN={["0032-0935"]}, DOI={10.1007/s00425-010-1253-3}, abstractNote={Artificial microRNAs (amiRNAs) are similar to microRNAs (miRNAs) in that they are able to reduce the abundance of specific transcripts in plants by RNA-Induced Silencing Complex (RISC)-mediated cleavage and degradation, but differ in that they are designed for specific targets. The long generation times of forest trees have limited the discovery of mutations by conventional genetics. AmiRNAs can create gene-specific transcript reduction in transgenic trees in a single generation and may have broad application for functional genomics of trees. In this paper, we describe the specific down-regulation of multiple genes in the phenylalanine ammonia-lyase (PAL) gene family of Populus trichocarpa using amiRNA sequences incorporated in a P. trichocarpa miRNA-producing precursor, ptc-MIR408. Two different amiRNA constructs were designed to specifically down-regulate two different subsets of PAL genes, revealing differential regulation within the gene family. Down-regulation of subset A (PAL2, PAL4 and PAL5) by amiRNA-palA led to an increase in transcript abundance of subset B (PAL1 and PAL3). The reciprocal effect was not observed.}, number={6}, journal={PLANTA}, author={Shi, Rui and Yang, Chenmin and Lu, Shanfa and Sederoff, Ronald and Chiang, Vincent L.}, year={2010}, month={Nov}, pages={1281–1288} }