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Yang S-Y, Huang T-K, Kuo H-F, Chiou T-J (2017) Role of vacuoles in phosphorus storage and remobilization Journal of Experimental Botany: erw481
TJC Vacuoles play a fundamental role in storage and remobilization of various nutrients, including phosphorus (P), an essential element for cell growth and development. Cells acquire P primarily in the form of inorganic orthophosphate (Pi). However, the form of P stored in vacuoles varies by organism and tissue. Algae and yeast store polyphosphates (polyPs), whereas plants store Pi and inositol phosphates (InsPs) in vegetative tissues and seeds, respectively. In this review, we summarize how vacuolar P molecules are stored and reallocated and how these processes are regulated and co-ordinated. The roles of SYG1/PHO81/XPR1 (SPX)-domain-containing membrane proteins in allocating vacuolar P are outlined. We also highlight the importance of vacuolar P in buffering the cytoplasmic Pi concentration to maintain cellular homeostasis when the external P supply fluctuates, and present additional roles for vacuolar polyP and InsP besides being a P reserve. Furthermore, we discuss the possibility of alternative pathways to recycle Pi from other P metabolites in vacuoles. Finally, future perspectives for researching this topic and its potential application in agriculture are proposed.
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Yao-Pin Lin, Meng-Chen Wu, and Yee-yung Charng* (2016) Identification of Chlorophyll Dephytylase Involved in Chlorophyll Turnover.The Plant Cell, 2016, 28, 2974-2990
YYChanrng In photosynthesis, chlorophylls absorb light energy, which is transformed into chemical energy by the multi-protein-pigment complex called photosystem. The photosystem, composing of chlorophylls and proteins, tends to be damaged during the process of photosynthesis. The plant cells must repair the damaged photosystem to maintain the photosynthetic efficiency, causing the bound chlorophylls to turnover. Previous studies suggest that chlorophylls in damaged photosystem would be salvaged by two successive steps: 1. Dephytylation of chlorophylls; 2. Rephytylation of the dephytylated chlorophylls (or chlorophyllides). The latter is catalyzed by chlorophyll synthase, but the enzyme involved in the first reaction has been enigmatic. More than a century, chlorophyllase has been the only enzyme known to hydrolyze chlorophyll into chlorophyllide in vitro. However, the role of chlorophyllase in chlorophyll catabolism remains controversial. In an effort in cloning the mutant gene responsible for a heat sensitive phenotype in Arabidopsis, we identified a novel chloroplast protein capable of hydrolyzing chlorophylls and named it chlorophyll dephytylase1 (CLD1). The results from genetic and biochemical experiments suggested that CLD1 is involved in the first step of the chlorophyll salvage cycle. Plants lacking CLD1 significantly reduced the photosynthetic efficiency and viability under prolonged heat stress, underscoring the importance of the chlorophyll salvage cycle for plant thermotolerance. The discovery of CLD1 fills the gap in chlorophyll metabolism and facilitates further studies in the understanding of photosystem repair and its regulation.
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Choun-Sea Lin, Jeremy JW Chen, Chi-Chou Chiu, Han C.W. Hsiao, Chen-Jui Yang, Xiao-Hua Jin, James Leebens-Mack, Claude W. dePamphilis ,Yao-Ting Huang, Ling-Hung Yang, Wan-Jung Chang, Ling Kui, Gane Ka-Shu Wong, Jer-Ming Hu, Wen Wang, Ming-Che Shih (2017) Concomitant loss of NDH complex-related genes within chloroplast and nuclear genomes in some orchids. The Plant Journal. DOI: 10.1111/tpj.13525
cslin Chloroplast NAD(P)H dehydrogenase-like (NDH) complex consists of ~30 subunits from both the nuclear and chloroplast genomes and is ubiquitous across most land plants. In some orchids, such as Phalaenopsis equestris, Dendrobium officinale and D. catenatum, most of the 11 chloroplast genome encoded ndh genes (cp-ndh) have been lost. Here we investigated whether functional cp-ndh genes have been completely lost in these orchids or whether they have been transferred and retained in the nuclear genomes. Further, we assessed whether both cp-ndh genes and nucleus-encoded NDH-related genes can be lost resulting in the absence of the NDH complex. Comparative analyses of the genome of Apostasia odorata, an orchid species with a complete complement of cp-ndh genes which represents the sister lineage to all other orchids, and three published orchid genome sequences for Phalaenopsis equestris, D. officinale and D. catenatum which are all missing cp-ndh genes, indicated that copies of cp-ndh genes are not present in any of these four nuclear genomes. This observation suggests that the NDH complex is not necessary for some plants. Comparative genomic/transcriptomic analyses of currently available plastid genome sequences and nuclear transcriptome data showed that 47 out of 660 photoautotrophic plants and all the heterotrophic plants are missing plastid encoded cp-ndh genes and exhibit no evidence for maintenance of a functional NDH complex. Our data indicate that the NDH complex can be lost in photoautotrophic plant species. Further, the loss of the NDH complex may increase the probability of transition from a photoautotrophic to a heterotrophic life history.
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Ya-Ting Chao, Shao-Hua Yen, Jen-Hau Yeh, Wan-Chieh Chen, Ming-Che Shih*(2017) Orchidstra 2.0—A Transcriptomics Resource for the Orchid Family Plant & Cell Physiol DOI:10.1093/pcp/pcw220
MCS Orchidaceae, the orchid family, encompasses more than 25,000 species and five subfamilies. Due to their beautiful and exotic flowers, distinct biological and ecological features, orchids have aroused wide interest among both researchers and the general public. We constructed the Orchidstra database, a resource for orchid transcriptome assembly and gene annotations. The Orchistra database has been under active development since 2013. To accommodate the increasing amount of orchid transcriptome data and house more comprehensive information, Orchidstra 2.0 has been built with a new database system to store the annotations of 510,947 protein-coding genes and 161,826 noncoding transcripts, covering 18 orchid species belonging to 12 genera in five subfamilies of Orchidaceae. We have improved the N50 size of protein-coding genes, provided new functional annotations (including protein-coding gene annotations, protein domain/family information, pathways analysis, Gene Ontology term assignments, orthologous genes across orchid species, cross-links to the database of model species, and miRNA information), and improved the user interface with better website performance. We also provide new database functionalities for database searching and sequence retrieval. Moreover, the Orchidstra 2.0 database incorporates detailed RNA-Seq gene expression data from various tissues and developmental stages in different orchid species. The database will be useful for gene prediction and gene family studies, and for exploring gene expression in orchid species. The Orchidstra 2.0 database is freely accessible at http://orchidstra2.abrc.sinica.edu.tw.
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Maria Karmella Apaya, Meng-Ting Chang, and Lie-Fen Shyur* (2016) Phytomedicine polypharmacology: Cancer therapy through modulating the tumor microenvironment and oxylipin dynamics.Pharmacology & Therapeutics 162:58-68
lfs Integrative approaches in cancer therapy have recently been extended beyond the induction of cytotoxicity to controlling the tumor microenvironment and modulating inflammatory cascades and pathways such as lipid mediator biosynthesis and their dynamics. Profiling of important lipid messengers, such as oxylipins, produced as part of the physiological response to pharmacological stimuli, provides a unique opportunity to explore drug pharmacology and the possibilities for molecular management of cancer physiopathology. Whereas single targeted chemotherapeutic drugs commonly lack efficacy and invoke drug resistance and/or adverse effects in cancer patients, traditional herbal medicines are seen as bright prospects for treating complex diseases, such as cancers, in a systematic and holistic manner. Understanding the molecular mechanisms of traditional medicine and its bioactive chemical constituents may aid the modernization of herbal remedies and the discovery of novel phytoagents for cancer management. In this review, systems-based polypharmacology and studies to develop multi-target drugs or leads from phytomedicines and their derived natural products that may overcome the problems of current anti-cancer drugs, are proposed and summarized.
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Kyoko Nakagawa-Goto*, Jo-Yu Chen, Yu-Ting Cheng, Wai-Leng Lee, Munehisa Takeya, Yohei Saito, Kuo-Hsiung Lee*, and Lie-Fen Shyur* (2016) Novel sesquiterpene lactone analogues as potent anti-breast cancer agents. Molecular Oncology, 2016, 10(6):921-937
lfs Triple-negative breast cancer (TNBC) is associated with high grade, metastatic phenotype, younger patient age, and poor prognosis. The discovery of an effective anti-TNBC agent has been a challenge in oncology. In this study, fifty-eight ester derivatives (DETDs) with a novel sesquiterpene dilactone skeleton were organically synthesized from a bioactive natural product deoxyelephantopin (DET). Among them, DETD-35 showed potent antiproliferative activities against a panel of breast cancer cell lines including TNBC cell line MDA-MB-231, without inhibiting normal mammary cells M10. DETD-35 exhibited a better effect than parental DET on inhibiting migration, invasion, and motility of MDA-MB-231 cells in a concentration-dependent manner. Comparative study of DETD-35, DET and chemotherapeutic drug paclitaxel (PTX) showed that PTX mainly caused a typical time-dependent G2/M cell-cycle arrest, while DETD-35 or DET treatment induced cell apoptosis. In vivo efficacy of DETD-35 was evaluated using a lung metastatic MDA-MB-231 xenograft mouse model. DETD-35 significantly suppressed metastatic pulmonary foci information along with the expression level of VEGF and COX-2 in SCID mice. DETD-35 also showed a synergistic antitumor effect with PTX in vitro and in vivo. This study suggests that the novel compound DETD-35 may have a potential to be further developed into a therapeutic or adjuvant agent for chemotherapy against metastatic TNBC.
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Jia-Hua Feng, Kyoko Nakagawa-Goto, Kuo-Hsiung Lee, and Lie-Fen Shyur* (2016) A novel plant sesquiterpene lactone derivative DETD-35 suppresses BRAFV600E mutant melanoma growth and overcomes acquired vemurafenib resistance in mice. Molecular Cancer Therapeutics, 15(6):1163-1176
lfs Acquired resistance to vemurafenib (PLX4032), a chemotherapeutic drug targeting BRAFV600E mutant melanoma, is developed frequently through reactivation of RAF/MEK/ERK signaling or bypass mechanisms. Current combination therapy (e.g., MEK inhibitor plus vemurafenib) shows improvement in major clinical end points but percentage of patients with adverse toxic events are higher than vemurafenib monotherapy and most patients relapse ultimately. It is therefore an urgent need to develop new anti-melanoma drug and/or adjuvant agent for vemurafenib therapy. We created a novel semi-organically modified derivative DETD-35 from a plant sesquiterpene lactone deoxyelephantopin (DET), which showed potent effect against both parental human BRAFV600E mutant melanoma (A375) and vemurafenib resistance melanoma (A375-R) cell proliferation in vitro and no cytotoxicity to normal melanocyte. DETD-35 inhibited BRAFV600E mutant melanoma growth as effective as FDA approval drug vemurafenib and overcame both intrinsic and acquired vemurafenib resistance in mouse xenograft. Notably, the combination of DETD-35 and vemurafenib exhibited synergism and showed the most significant effects in both in vitro and xenograft mouse models compared to the monotherapy. Mechanistic studies revealed that DETD-35 triggered ROS-induced apoptotic cell death in both A375 and A375-R melanoma cells and overcamed acquired vemurafenib resistance through inhibition of the MEK-ERK, Akt, and STAT3 signaling pathways. Overall, our data suggest the great therapeutic or adjuvant potential of DETD-35 in management of melanoma patients with BRAFV600E mutation. The published article was selected as the “Highlights” of the issue in the journal “Molecular Cancer Therapeutics”; in addition, one ROC patent is issued and USA/PCT patents are pending.
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H.-F. Chang, S.-L. Wang and K.-C. Yeh* (2017) Effect of gallium exposure in Arabidopsis thaliana is similar to aluminum stress. Environmental Science & Technology: Accepted DOI: 10.1021/acs.est.6b05760
kcyeh The manuscript describes the first thorough exploration of gallium exposure in the model plant Arabidopsis. Gallium, a rare element, is one of the major elements in semiconductor compounds that are used in integrated circuits and optoelectronic devices. As one of major producers of semiconductor in the world, Hsinchu and Taichung Science Parks in Taiwan has been contaminated with gallium. The contamination of gallium in soil and water may lead to its uptake by plants and accumulation of gallium in the food chain. To our best knowledge, the harmful effects of gallium in plants are not yet investigated. Therefore, we investigated the accumulation, possible toxicity and defense systems of gallium exposure in plants. We found high similarities of exposure effects between gallium and aluminum. The Ga induced root secretion of citrate and malate play an important role for the protection from Ga toxicity.
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Wen-Jen Chen, Tzu-Yen Kuo , Feng-Chia Hsieh, Pi-Yu Chen, Chang-Sheng Wang, Yu-Ling Shih, Ying-Mi Lai, Je-Ruei Liu, Yu-Liang Yang, Ming-Che Shih. (2016) Involvement of type VI secretion system in secretion of iron chelator pyoverdine in Pseudomonas taiwanensis Scientific Reports 6, Article number: 32950 doi:10.1038/srep32950
MCS Rice bacterial blight caused by Xanthomonas oryzae pv. oryzae (Xoo) is one of the most destructive rice diseases worldwide. Therefore, in addition to breeding disease-resistant rice cultivars, it is desirable to develop effective biocontrol agents against Xoo. Here, we report that a soil bacterium Pseudomonas taiwanensis displayed strong antagonistic activity against Xoo. Using matrix-assisted laser desorption/ionization imaging mass spectrometry, we identified an iron chelator, pyoverdine, secreted by P. taiwanensis that could inhibit the growth of Xoo. Through Tn5 mutagenesis of P. taiwanensis, we showed that mutations in genes that encode components of the type VI secretion system (T6SS) as well as biosynthesis and maturation of pyoverdine resulted in reduced toxicity against Xoo. Our results indicated that T6SS is involved in the secretion of endogenous pyoverdine. Mutations in T6SS component genes affected the secretion of mature pyoverdine from the periplasmic space into the extracellular medium after pyoverdine precursor is transferred to the periplasm by the inner membrane transporter PvdE. In addition, we also showed that other export systems, i.e., the PvdRT-OpmQ and MexAB-OprM efflux systems (for which there have been previous suggestions of involvement) and the type II secretion system (T2SS), are not involved in pyoverdine secretion.
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Kuen-Jin Tsai, Chih-Yu Lin, Chen-Yun Ting, Ming-Che Shih*(2016) Ethylene-regulated glutamate dehydrogenase fine-tunes metabolism during anoxia-reoxygenation in Arabidopsis. Plant Physiology doi: http:/​/​dx.​doi.​org/​10.​1104/​pp.​16.​00985.
MCS Ethylene is an essential hormone in plants that is involved in low oxygen and reoxygenation responses. As a key transcription factor in ethylene signaling, ETHYLENE INSENSITIVE 3 (EIN3) activates targets that trigger various responses. However, most of these targets are still poorly characterized. Through analyses of our microarray data and the published Arabidopsis EIN3 ChIP-seq dataset, we inferred the putative targets of EIN3 during anoxia-reoxygenation. Among them, GDH2, which encodes one subunit of glutamate dehydrogenase (GDH), was chosen for further studies for its role in TCA cycle replenishment. We demonstrated that both GDH1 and GDH2 are induced during anoxia and reoxygenation and that this induction is mediated via ethylene signaling. In addition, the results of enzymatic assays showed that the level of GDH during anoxia-reoxygenation decreased in the ethylene insensitive mutants ein2-5 and ein3eil1. Global metabolite analysis indicated that the deamination activity of GDH might regenerate 2-oxoglutarate that is a co-substrate that facilitates the breakdown of alanine by alanine aminotransferase (AlaAT) when reoxygenation occurs. Moreover, ineffective TCA cycle replenishment, disturbed carbohydrate metabolism, reduced phytosterol biosynthesis, and delayed energy regeneration were found in gdh1gdh2 and ethylene mutants during reoxygenation. Taken together, these data illustrate the essential role of EIN3-regulated GDH activity in metabolic adjustment during anoxia-reoxygenation.
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*2018/07/16 10:30 AM
Dr. Jeng-Yuan Shiau (Dr. Lie-Fen Shyur's Lab)
Molecular insights of phytoagent deoxyelephantopin and its derivative against human triple negative breast cancer cell activities
Auditorium A134, Agricultural Technology Building, Academia Sinica

*2018/08/22 10:30 AM
Dr. Nathaniel Robert Street (Associate Professor, Department of Plant Physiology, Umeå University, Sweden)
Systems genetics and genomics insights into complex traits in aspen and Norway spruce
Auditorium A134, Agricultural Technology Building, Agricultural Biotechnology Research Center

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