@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{wang_matthews_williams_shi_yang_tunlaya-anukit_chen_li_liu_lin_et al._2018, title={Improving wood properties for wood utilization through multi-omics integration in lignin biosynthesis}, volume={9}, ISSN={2041-1723}, url={http://dx.doi.org/10.1038/s41467-018-03863-z}, DOI={10.1038/s41467-018-03863-z}, abstractNote={Abstract}, number={1}, journal={Nature Communications}, publisher={Springer Science and Business Media LLC}, author={Wang, Jack P. and Matthews, Megan L. and Williams, Cranos M. and Shi, Rui and Yang, Chenmin and Tunlaya-Anukit, Sermsawat and Chen, Hsi-Chuan and Li, Quanzi and Liu, Jie and Lin, Chien-Yuan and et al.}, year={2018}, month={Apr}, pages={1579} }
 @article{samykutty_grizzle_fouts_mcnally_chuong_thomas_chiba_otali_woloszynska_said_et al._2018, title={Optoacoustic imaging identifies ovarian cancer using a microenvironment targeted theranostic wormhole mesoporous silica nanoparticle}, volume={182}, ISSN={["1878-5905"]}, DOI={10.1016/j.biomaterials.2018.08.001}, abstractNote={At the intersection of the newly emerging fields of optoacoustic imaging and theranostic nanomedicine, promising clinical progress can be made in dismal prognosis of ovarian cancer. An acidic pH targeted wormhole mesoporous silica nanoparticle (V7-RUBY) was developed to serve as a novel tumor specific theranostic nanoparticle detectable using multispectral optoacoustic tomographic (MSOT) imaging. We report the synthesis of a small, < 40 nm, biocompatible asymmetric wormhole pore mesoporous silica core particle that has both large loading capacity and favorable release kinetics combined with tumor-specific targeting and gatekeeping. V7-RUBY exploits the acidic tumor microenvironment for tumor-specific targeting and tumor-specific release. In vitro, treatment with V7-RUBY containing either paclitaxel or carboplatin resulted in increased cell death at pH 6.6 in comparison to drug alone (p < 0.0001). In orthotopic ovarian xenograft mouse models, V7-RUBY containing IR780 was specifically detected within the tumor 7X and 4X higher than the liver and >10X higher than in the kidney using both multispectral optoacoustic tomography (MSOT) imaging with secondary confirmation using near infrared fluorescence imaging (p < 0.0004). The V7-RUBY system carrying a cargo of either contrast agent or an anti-neoplastic drug has the potential to become a theranostic nanoparticle which can improve both diagnosis and treatment of ovarian cancer.}, journal={BIOMATERIALS}, author={Samykutty, Abhilash and Grizzle, William E. and Fouts, Benjamin L. and McNally, Molly W. and Chuong, Phillip and Thomas, Alexandra and Chiba, Akiko and Otali, Dennis and Woloszynska, Anna and Said, Neveen and et al.}, year={2018}, month={Nov}, pages={114–126} }
 @article{jiang_liu_du_hu_chang_jameel_2018, title={Phenolation to Improve Lignin Reactivity toward Thermosets Application}, volume={6}, ISSN={["2168-0485"]}, DOI={10.1021/acssuschemeng.8b00369}, abstractNote={Phenolation can be used to improve the reactivity and decrease the molecular weight of lignin, thereby making it more useful for various applications. We report an effective phenolation process with only a catalytic amount of sulfuric acid and using phenol as solvent. The optimum phenolation conditions for pine kraft lignin and sweetgum biorefinery lignin were determined to be lignin/phenol (L/P, wt/wt) of 3/5, 5% acid charge at 90 °C for 2 h and L/P of 2/5, 5% acid charge at 110 °C for 2 h, respectively. Phenolation resulted in introducing 30 wt % of phenol onto pine kraft lignin and 60 wt % of phenol onto sweetgum biorefinery lignin and significantly decreasing in the molecular weight of lignin. Phenol was incorporated onto both the side chains and aromatic nuclei of lignin. All lignin substructures of β-O-4′, β-5′/α-O-4′, β–β′, α-carbonyl, etc. were reacted, resulting in a significant decrease in aliphatic hydroxyl groups and increase in the phenolic hydroxyl groups. The comprehensive characterization ...}, number={4}, journal={ACS SUSTAINABLE CHEMISTRY & ENGINEERING}, author={Jiang, Xiao and Liu, Jie and Du, Xueyu and Hu, Zhoujian and Chang, Hou-min and Jameel, Hasan}, year={2018}, month={Apr}, pages={5504–5512} }
 @article{lin_li_tunlaya-anukit_shi_sun_wang_liu_loziuk_edmunds_miller_et al._2016, title={A cell wall-bound anionic peroxidase, PtrPO21, is involved in lignin polymerization in Populus trichocarpa}, volume={12}, ISSN={1614-2942 1614-2950}, url={http://dx.doi.org/10.1007/S11295-016-0978-Y}, DOI={10.1007/s11295-016-0978-y}, number={2}, journal={Tree Genetics & Genomes}, publisher={Springer Science and Business Media LLC}, author={Lin, Chien-Yuan and Li, Quanzi and Tunlaya-Anukit, Sermsawat and Shi, Rui and Sun, Ying-Hsuan and Wang, Jack P. and Liu, Jie and Loziuk, Philip and Edmunds, Charles W. and Miller, Zachary D. and et al.}, year={2016}, month={Mar} }
 @article{hu_du_liu_chang_jameel_2016, title={Structural Characterization of Pine Kraft Lignin: BioChoice Lignin vs Indulin AT}, volume={36}, ISSN={["1532-2319"]}, DOI={10.1080/02773813.2016.1214732}, abstractNote={BioChoice lignin (BCL) is a newly commercialized pine kraft lignin from Plymouth Mill of Domtar, which is precipitated from black liquor of bleachable-grade pulp. Indulin AT is a pine kraft lignin commercialized by Meadwestvaco for the past 60 years, which is precipitated from black liquor of linerboard-grade pulp. Thus, the two technical lignins are produced under quite different conditions in terms of alkali charge and pulping time/temperature. While the chemical structure of Indulin AT is well documented, that of BCL is totally unknown. In this study, chemical structures of BCL and Indulin AT are characterized using modern analytical techniques and compared with those of pine milled wood lignin (MWL) in order to elucidate the structural changes that occur during kraft pulping and the structural differences, if any, between BCL and Indulin AT. Both BCL and Indulin AT are structurally very different from the native lignin (MWL) in wood, indicating drastic structural modification during the kraft pulping process. Surprisingly, BCL and Indulin AT are structurally very similar, in spite of the fact that they are produced under different process conditions. However, there are subtle structural differences between BCL and Indulin AT. BCL has higher phenolic hydroxyl, catechol, enol ether, and stilbene contents, but lower methoxyl and β-O-4 contents. These differences are explained by the different pulping conditions under which the two technical lignins are produced.}, number={6}, journal={JOURNAL OF WOOD CHEMISTRY AND TECHNOLOGY}, author={Hu, Zhoujian and Du, Xueyu and Liu, Jie and Chang, Hou-min and Jameel, Hasan}, year={2016}, pages={432–446} }
 @article{lin_wang_li_chen_liu_loziuk_song_williams_muddiman_sederoff_et al._2015, title={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}, volume={8}, ISSN={["1752-9867"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84925201417&partnerID=MN8TOARS}, DOI={10.1016/j.molp.2014.12.003}, abstractNote={Downregulation of 4-coumaric acid:coenzyme A ligase (4CL) can reduce lignin content in a number of plant species. In lignin precursor (monolignol) biosynthesis during stem wood formation in Populus trichocarpa, two enzymes, Ptr4CL3 and Ptr4CL5, catalyze the coenzyme A (CoA) ligation of 4-coumaric acid to 4-coumaroyl-CoA and caffeic acid to caffeoyl-CoA. CoA ligation of 4-coumaric acid is essential for the 3-hydroxylation of 4-coumaroyl shikimic acid. This hydroxylation results from sequential reactions of 4-hydroxycinnamoyl-CoA:shikimic acid hydroxycinnamoyl transferases (PtrHCT1 and PtrHCT6) and 4-coumaric acid 3-hydroxylase 3 (PtrC3H3). Alternatively, 3-hydroxylation of 4-coumaric acid to caffeic acid may occur through an enzyme complex of cinnamic acid 4-hydroxylase 1 and 2 (PtrC4H1 and PtrC4H2) and PtrC3H3. We found that 4-coumaroyl and caffeoyl shikimic acids are inhibitors of Ptr4CL3 and Ptr4CL5. 4-Coumaroyl shikimic acid strongly inhibits the formation of 4-coumaroyl-CoA and caffeoyl-CoA. Caffeoyl shikimic acid inhibits only the formation of 4-coumaroyl-CoA. 4-Coumaroyl and caffeoyl shikimic acids both act as competitive and uncompetitive inhibitors. Metabolic flux in wild-type and PtrC3H3 downregulated P. trichocarpa transgenics has been estimated by absolute protein and metabolite quantification based on liquid chromatography–tandem mass spectrometry, mass action kinetics, and inhibition equations. Inhibition by 4-coumaroyl and caffeoyl shikimic acids may play significant regulatory roles when these inhibitors accumulate.}, number={1}, journal={MOLECULAR PLANT}, author={Lin, Chien-Yuan and Wang, Jack P. and Li, Quanzi and Chen, Hsi-Chuan and Liu, Jie and Loziuk, Philip and Song, Jina and Williams, Cranos and Muddiman, David C. and Sederoff, Ronald R. and et al.}, year={2015}, month={Jan}, pages={176–187} }
 @article{min_xiang_liu_jameel_chiang_jin_chang_2014, title={Improved Protocol for Alkaline Nitrobenzene Oxidation of Woody and Non-Woody Biomass}, volume={35}, ISSN={0277-3813 1532-2319}, url={http://dx.doi.org/10.1080/02773813.2014.902965}, DOI={10.1080/02773813.2014.902965}, abstractNote={The protocol of alkaline nitrobenzene oxidation was investigated to improve its ability to identify the different lignin structures for both woody and non-woody biomass. The survival factors of all six oxidation products—syringaldehde (Sr), vanillin (V), p-hydroxybenzaldehyde (B) and their corresponding acids, syringic acid (Sa), vanillic acid (Va), and p-hydroxybenzoic acid (Ba)—were studied at 170, 180, and 190°C for several residence times. Under similar conditions, various lignin model compounds—a softwood (loblolly pine), a hardwood (red maple), and a non-wood raw material (corn stover)—were oxidized. Molar yields of oxidation products were determined and the ratios of (Sr+Sa)/(V+Va), (Sr/V), and B/(V+Va) (B/V) were calculated. All oxidation products were relatively stable at 170 and 180°C but showed some degradation at 190°C, especially at long residence time. In all cases, p-hydroxybenzoic acid was barely detectable. While yields of oxidation products reach a maximum at 170°C for pine and maple, maximal yields of corn stover require 190°C. Consequently, we recommend that nitrobenzene oxidation be carried out at 170°C for 2.5 h for softwood and hardwood, but at 190°C and 4 h with correction for the survival factors for corn stover and other non-woody biomass. Alternatively, a protocol of oxidation at two temperatures is recommended for non-woody biomass.}, number={1}, journal={Journal of Wood Chemistry and Technology}, publisher={Informa UK Limited}, author={Min, Douyong and Xiang, Zhouyang and Liu, Jie and Jameel, Hasan and Chiang, Vincent and Jin, Yongcan and Chang, Hou-min}, year={2014}, month={Sep}, pages={52–61} }
 @article{chen_song_wang_lin_ducoste_shuford_liu_li_shi_nepomuceno_et al._2014, title={Systems Biology of Lignin Biosynthesis in Populus trichocarpa: Heteromeric 4-Coumaric Acid:Coenzyme A Ligase Protein Complex Formation, Regulation, and Numerical Modeling}, volume={26}, ISSN={1040-4651 1532-298X}, url={http://dx.doi.org/10.1105/tpc.113.119685}, DOI={10.1105/tpc.113.119685}, abstractNote={This work shows that 4CL, an enzyme in monolignol biosynthesis, is found as a heterotetrameric complex of two isoforms in Populus trichocarpa. The activity of the heterotetramer can be described by a mathematical model that explains the effects of each isoform with mixtures of substrates and three types of inhibition, providing insights into the regulation of metabolic flux for this pathway. As a step toward predictive modeling of flux through the pathway of monolignol biosynthesis in stem differentiating xylem of Populus trichocarpa, we discovered that the two 4-coumaric acid:CoA ligase (4CL) isoforms, 4CL3 and 4CL5, interact in vivo and in vitro to form a heterotetrameric protein complex. This conclusion is based on laser microdissection, coimmunoprecipitation, chemical cross-linking, bimolecular fluorescence complementation, and mass spectrometry. The tetramer is composed of three subunits of 4CL3 and one of 4CL5. 4CL5 appears to have a regulatory role. This protein–protein interaction affects the direction and rate of metabolic flux for monolignol biosynthesis in P. trichocarpa. A mathematical model was developed for the behavior of 4CL3 and 4CL5 individually and in mixtures that form the enzyme complex. The model incorporates effects of mixtures of multiple hydroxycinnamic acid substrates, competitive inhibition, uncompetitive inhibition, and self-inhibition, along with characteristic of the substrates, the enzyme isoforms, and the tetrameric complex. Kinetic analysis of different ratios of the enzyme isoforms shows both inhibition and activation components, which are explained by the mathematical model and provide insight into the regulation of metabolic flux for monolignol biosynthesis by protein complex formation.}, number={3}, journal={The Plant Cell}, publisher={Oxford University Press (OUP)}, author={Chen, Hsi-Chuan and Song, Jina and Wang, Jack P. and Lin, Ying-Chung and Ducoste, Joel and Shuford, Christopher M. and Liu, Jie and Li, Quanzi and Shi, Rui and Nepomuceno, Angelito and et al.}, year={2014}, month={Mar}, pages={876–893} }
 @article{chen_song_williams_shuford_liu_wang_li_shi_gokce_ducoste_et al._2013, title={Monolignol Pathway 4-Coumaric Acid: Coenzyme A Ligases in Populus trichocarpa: Novel Specificity, Metabolic Regulation, and Simulation of Coenzyme A Ligation Fluxes}, volume={161}, ISSN={["0032-0889"]}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84874626790&partnerID=MN8TOARS}, DOI={10.1104/pp.112.210971}, abstractNote={Abstract}, number={3}, journal={PLANT PHYSIOLOGY}, author={Chen, Hsi-Chuan and Song, Jina and Williams, Cranos M. and Shuford, Christopher M. and Liu, Jie and Wang, Jack P. and Li, Quanzi and Shi, Rui and Gokce, Emine and Ducoste, Joel and et al.}, year={2013}, month={Mar}, pages={1501–1516} }
 @article{lu_li_wei_chang_tunlaya-anukit_kim_liu_song_sun_yuan_et al._2013, title={Ptr-miR397a is a negative regulator of laccase genes affecting lignin content in Populus trichocarpa}, volume={110}, ISSN={0027-8424 1091-6490}, url={http://dx.doi.org/10.1073/PNAS.1308936110}, DOI={10.1073/pnas.1308936110}, abstractNote={
            Laccases, as early as 1959, were proposed to catalyze the oxidative polymerization of monolignols. Genetic evidence in support of this hypothesis has been elusive due to functional redundancy of laccase genes. An
            Arabidopsis
            double mutant demonstrated the involvement of laccases in lignin biosynthesis. We previously identified a subset of laccase genes to be targets of a microRNA (miRNA) ptr-miR397a in
            Populus trichocarpa
            . To elucidate the roles of ptr-miR397a and its targets, we characterized the laccase gene family and identified 49 laccase gene models, of which 29 were predicted to be targets of ptr-miR397a. We overexpressed
            Ptr-MIR397a
            in transgenic
            P. trichocarpa
            . In each of all nine transgenic lines tested, 17
            PtrLAC
            s were down-regulated as analyzed by RNA-seq. Transgenic lines with severe reduction in the expression of these laccase genes resulted in an ∼40% decrease in the total laccase activity. Overexpression of
            Ptr-MIR397a
            in these transgenic lines also reduced lignin content, whereas levels of all monolignol biosynthetic gene transcripts remained unchanged. 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. Full transcriptome–based differential gene expression in the overexpressed transgenics and protein domain analyses implicate previously unidentified transcription factors and their targets in an extended hierarchical GRN including ptr-miR397a and laccases that coregulate lignin biosynthesis in wood formation. Ptr-miR397a, laccases, and other regulatory components of this network may provide additional strategies for genetic manipulation of lignin content.
          }, number={26}, journal={Proceedings of the National Academy of Sciences}, publisher={Proceedings of the National Academy of Sciences}, author={Lu, S. and Li, Q. and Wei, H. and Chang, M.-J. and Tunlaya-Anukit, S. and Kim, H. and Liu, J. and Song, J. and Sun, Y.-H. and Yuan, L. and et al.}, year={2013}, month={Jun}, pages={10848–10853} }
 @article{shi_shuford_wang_sun_yang_chen_tunlaya-anukit_li_liu_muddiman_et al._2013, title={Regulation of phenylalanine ammonia-lyase (PAL) gene family in wood forming tissue of Populus trichocarpa}, volume={238}, url={http://www.scopus.com/inward/record.url?eid=2-s2.0-84882877816&partnerID=MN8TOARS}, DOI={10.1007/s00425-013-1905-1}, abstractNote={Phenylalanine ammonia-lyase (PAL) catalyzes the initial step of phenylpropanoid biosynthesis in plants. Five PAL genes (PtrPAL1 to 5) have been identified in Populus trichocarpa. These genes are classified into two subgroups according to their transcript sequence similarity and tissue specificity. However, the regulation of these genes and their protein functions are not well understood. In this study, enzymatic properties of each PtrPALs were characterized based on their recombinant proteins expressed in E.coli. Subcellular localizations of each PtrPALs in stem wood forming tissue were investigated and individual PtrPAL protein abundances in cytosol and membrane protein fractions were measured using protein cleavage-isotope dilution mass spectrometry (PC-IDMS). Protein/mRNA ratios of PtrPALs were further verified using RNA-Seq and gel-enhanced liquid chromatography mass spectrometry (GeLC-MS). All PtrPALs have similar catalytic properties for the deamination of L-phenylalanine, their major substrate. All PtrPALs have similar subcellular locations in stem wood forming tissue, with major amount in the cytosol (93-96 %) and less in the membrane (4-7 %). However, the protein/mRNA ratios of subgroup A (PtrPAL2, 4 and 5) are about five times that of subgroup B (PtrPAL1 and 3) in stem wood forming tissue, while all PtrPALs have similar transcript abundances. These results indicate a greater functional significance of subgroup A PtrPALs for stem wood formation, and highlight the role of gene post-transcriptional regulation.}, number={3}, journal={Planta}, author={Shi, R. and Shuford, C. M. and Wang, Jack P. and Sun, Y. H. and Yang, Z. C. and Chen, H. C. and Tunlaya-Anukit, S. and Li, Q. Z. and Liu, J. and Muddiman, David and et al.}, year={2013}, pages={487–497} }
 @article{albert_barbazuk_depamphilis_der_leebens-mack_ma_palmer_rounsley_sankoff_schuster_et al._2013, title={The Amborella Genome and the Evolution of Flowering Plants}, volume={342}, ISSN={["1095-9203"]}, url={http://science.sciencemag.org/content/342/6165/1241089.long}, DOI={10.1126/science.1241089}, abstractNote={Shaping Plant Evolution}, number={6165}, journal={Science}, author={Albert, Victor A. and Barbazuk, W. Bradley and dePamphilis, Claude W. and Der, Joshua P. and Leebens-Mack, James and Ma, Hong and Palmer, Jeffrey D. and Rounsley, Steve and Sankoff, David and Schuster, Stephan C. and et al.}, year={2013}, month={Dec}, pages={1456–1457} }
 @article{liu_shi_li_sederoff_chiang_2012, title={A standard reaction condition and a single HPLC separation system are sufficient for estimation of monolignol biosynthetic pathway enzyme activities}, volume={236}, ISSN={["0032-0935"]}, DOI={10.1007/s00425-012-1688-9}, abstractNote={Lignin content and composition are largely determined by the composition and quantity of the monolignol precursors. Individual enzymes of the monolignol biosynthetic pathway determine the composition and quantity of monolignols. Monolignol biosynthesis in angiosperms is mediated by ten enzyme families. We 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 Populus trichocarpa. As little as 300 mg fresh weight of SDX is sufficient for triplicate assays of all ten enzyme activities. To expand the effectiveness of the analysis, we quantified the reaction products directly by HPLC and developed a universal method that can separate the substrates and products of all enzymes. The specific activities measured with this simple approach are similar to those obtained with the optimum conditions previously established for each individual enzyme. This approach is applicable to the enzyme activity analysis for both P. trichocarpa (angiosperm) and Pinus taeda (gymnosperm) and is particularly useful when a large number of samples need to be analyzed for all monolignol biosynthetic enzymes.}, number={3}, journal={PLANTA}, author={Liu, Jie and Shi, Rui and Li, Quanzi and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2012}, month={Sep}, pages={879–885} }
 @article{liu_kurashiki_fukuta_kaneko_suimi_shimizu_kondo_2012, title={Quantitative determination of the representative triterpenoids in the extracts of Ganoderma lucidum with different growth stages using high-performance liquid chromatography for evaluation of their 5 alpha-reductase inhibitory properties}, volume={133}, ISSN={["1873-7072"]}, DOI={10.1016/j.foodchem.2012.01.034}, abstractNote={For quantitative determination of 5 triterpenoid constituents, including one ganoderma alcohol (ganodermatriol) and four ganoderma acids (ganoderic acid TR, DM, A, and D), in the products of Ganoderma lucidum, an analytical system was developed using high-performance liquid chromatography. The mobile phase was a linear gradient of 2% AcOH/H2O–CH3CN, and the elution profile was monitored at 243 and 252 nm for ganoderma alcohols and acids, respectively. This system was applied to a quantitative determination of the constituents in the different stage of G. lucidum (BMC9049 strain). The analytical results indicated that the quantity and composition of these triterpenoids differed appreciably among various stages. The stage that showed the highest concentration of ganoderic acid DM and TR also showed the strongest 5α-reductase inhibitory activity. This stage (stage 5 of 6) is thus the prime stage for harvesting this strain. Further, the contents of 5α-reductase inhibitors such as ganoderic acid TR and DM in G. lucidum extracts could be a very useful indicator to assess their 5α-reductase inhibitory activity and verify their potency.}, number={3}, journal={FOOD CHEMISTRY}, author={Liu, Jie and Kurashiki, Kenji and Fukuta, Atsuko and Kaneko, Shuhei and Suimi, Yoshitaro and Shimizu, Kuniyoshi and Kondo, Ryuichiro}, year={2012}, month={Aug}, pages={1034–1038} }
 @article{chen_li_shuford_liu_muddiman_sederoff_chiang_2011, title={Membrane protein complexes catalyze both 4-and 3-hydroxylation of cinnamic acid derivatives in monolignol biosynthesis}, volume={108}, ISSN={["0027-8424"]}, DOI={10.1073/pnas.1116416109}, abstractNote={
            The hydroxylation of 4- and 3-ring carbons of cinnamic acid derivatives during monolignol biosynthesis are key steps that determine the structure and properties of lignin. Individual enzymes have been thought to catalyze these reactions. In stem differentiating xylem (SDX) of
            Populus trichocarpa
            , two cinnamic acid 4-hydroxylases (PtrC4H1 and PtrC4H2) and a
            p
            -coumaroyl ester 3-hydroxylase (PtrC3H3) are the enzymes involved in these reactions. Here we present evidence that these hydroxylases interact, forming heterodimeric (PtrC4H1/C4H2, PtrC4H1/C3H3, and PtrC4H2/C3H3) and heterotrimeric (PtrC4H1/C4H2/C3H3) membrane protein complexes. Enzyme kinetics using yeast recombinant proteins demonstrated that the enzymatic efficiency (
            V
            max
            /
            k
            m
            ) for any of the complexes is 70–6,500 times greater than that of the individual proteins. The highest increase in efficiency was found for the PtrC4H1/C4H2/C3H3-mediated
            p
            -coumaroyl ester 3-hydroxylation. Affinity purification-quantitative mass spectrometry, bimolecular fluorescence complementation, chemical cross-linking, and reciprocal coimmunoprecipitation provide further evidence for these multiprotein complexes. The activities of the recombinant and SDX plant proteins demonstrate two protein-complex–mediated 3-hydroxylation paths in monolignol biosynthesis in
            P
            .
            trichocarpa
            SDX; one converts
            p
            -coumaric acid to caffeic acid and the other converts
            p
            -coumaroyl shikimic acid to caffeoyl shikimic acid. Cinnamic acid 4-hydroxylation is also mediated by the same protein complexes. These results provide direct evidence for functional involvement of membrane protein complexes in monolignol biosynthesis.
          }, number={52}, journal={PROCEEDINGS OF THE NATIONAL ACADEMY OF SCIENCES OF THE UNITED STATES OF AMERICA}, author={Chen, Hsi-Chuan and Li, Quanzi and Shuford, Christopher M. and Liu, Jie and Muddiman, David C. and Sederoff, Ronald R. and Chiang, Vincent L.}, year={2011}, month={Dec}, pages={21253–21258} }
 @article{liu_shimizu_yu_zhang_jin_kondo_2010, title={Stereospecificity of hydroxyl group at C-20 in antiproliferative action of ginsenoside Rh2 on prostate cancer cells}, volume={81}, ISSN={["1873-6971"]}, DOI={10.1016/j.fitote.2010.05.020}, abstractNote={Prostate cancer is the fifth most common neoplasm worldwide, and the second most common cancer among men. Ginsenosides, the main component of ginseng, have been known for their medicinal effects such as anti-inflammatory and anti-proliferative activities. In this study, we investigated the inhibitory effects of ginsenosides (ginsenoside 20(R)-Rh2 and ginsenoside 20(S)-Rh2) on prostate cancer cells in vitro. Only ginsenoside 20(S)-Rh2 showed proliferation inhibition on androgen-dependent and -independent prostate cancer cells. These results implied that the stereochemistry of the hydroxyl group at C-20 may play an important role in antitumor activities.}, number={7}, journal={FITOTERAPIA}, author={Liu, Jie and Shimizu, Kuniyoshi and Yu, Hongshan and Zhang, Chunzhi and Jin, Fengxie and Kondo, Ryuichiro}, year={2010}, month={Oct}, pages={902–905} }
 @article{liu_shimizu_kondo_2010, title={The effects of ganoderma alcohols isolated from Ganoderma lucidum on the androgen receptor binding and the growth of LNCaP cells}, volume={81}, ISSN={["1873-6971"]}, DOI={10.1016/j.fitote.2010.06.029}, abstractNote={The effects of ganoderma alcohols isolated from ethanol extracts of Ganoderma lucidum (Fr.) Krast (Ganodermataceae) on the androgen receptor binding and the growth of LNCaP cells have been investigated. Less than two hydroxyl groups in 17β-side chain are needed for binding to androgen receptor. In the case of the ganoderma alcohols with the same number of hydroxyl groups in 17β-side chain, the one which has C-3 carbonyl group showed better binding activity to androgen receptor than that which has C-3 hydroxyl group. The unsaturation in 17β-side chain is needed for the inhibition of the cell proliferation of androgen-induced LNCaP cells growth.}, number={8}, journal={FITOTERAPIA}, author={Liu, Jie and Shimizu, Kuniyoshi and Kondo, Ryuichiro}, year={2010}, month={Dec}, pages={1067–1072} }