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
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.
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
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.
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
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.
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
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.
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
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.
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
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.
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
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.
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.
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.
Hsing-Yi Cho, Tuan-Nan Wen, Ying-Tsui Wang, and Ming-Che Shih. (2016) Quantitative Phosphoproteomics of Protein Kinase SnRK1 regulated protein phosphorylation in Arabidopsis under Submergence. J. Exp. Bot. (2016)doi: 10.1093/jxb/erw107
SNF1 RELATED PROTEIN KINASE 1 (SnRK1) is proposed to be a central integrator of plant stress and energy starvation signaling-related regulatory pathways. We observed in this study that the Arabidopsis SnRK1.1 dominant negative mutant (SnRK1.1K48M) had lower tolerance to submergence than the wild-type, suggesting that SnRK1.1-dependent phosphorylation of target proteins is important in energy starvation signaling triggered by submergence. We conducted quantitative phosphoproteomics and found that the phosphorylation levels of 57 proteins increased and the levels of 27 proteins decreased in Col-0 within 0.5–3 h of submergence. Among the 57 proteins with increased phosphorylation in Col-0, 38 did not show increased phosphorylation levels in SnRK1.1K48M under submergence. These proteins are involved mainly in sugar synthesis and protein synthesis. In particular, the phosphorylation of MPK6, which is involved in regulating ROS responses under different abiotic stresses, was disrupted in the SnRK1.1K48M mutant. In addition, PTP1, a negative regulator of MPK6 activity that directly dephosphorylates MPK6, was also regulated by SnRK1.1.. We further showed that the energy conservation was disrupted in SnRK1.1K48M, mpk6 and PTP1S7AS8A under submergence. These results reveal insights into the function of SnRK1 and the downstream signaling factors related to submergence.
Chin-Hsien Tsai, Sheue-Fen Tzeng, Tai-Kuang Chao, Chia-Yun Tsai, Yu-Chih Yang, Ming-Ting Lee, Jiuan-Jiuan Hwang, Yu-Ching Chou, Mong-Hsun Tsai, Tai-Lung Cha and Pei-Wen Hsiao* (2016) Metastatic progression of prostate cancer is mediated by autonomous binding of galectin-4-O-glycans to cancer cells. Cancer Research 76(19); 5756-67, 2016
Metastatic prostate cancer (PCa) continues to pose a difficult therapeutic challenge. PCa progression is associated with aberrant O-glycosylation of cancer cell surface receptors, but the functional impact of such events are uncertain. Here we report spontaneous metastasis of human PCa xenografts which express high levels of galectin-4 along with genetic signatures of EGFR-HER2 signaling and O-glycosylation. Galectin-4 expression in clinical specimens of PCa correlated with poor patient survival. Galectin-4 binding to multiple receptor tyrosine kinases stimulated their autophosphorylation, activated expression of pERK, pAkt, fibronectin and Twist1, and lowered expression of E-cadherin, thereby faciliating epithelial-mesenchyme transition, invasion and metastasis. In vivo investigations established that galectin-4 expression enabled PCa cells to repopulate tumors in orthotopic and heterotopic tissues. Notably, these effects of galectin-4 relied upon O-glycosylation mediated by C1GALT1, a galactosyltransferase implicated in other cancers. Parallel changes in galectin-4 and O-glycosylation triggered aberrant receptor signaling and more aggressive invasive character in PCa cells, which through better survival in the circulation also contributed to the bulk cell progeny of distal tumors. Our findings establish galectin-4 and C1GALT1-mediated glycosylation in a signaling axis that is activated during CaP progression, with implications for therapeutic targeting of advanced metastatic disease.
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2018/01/22 10:30 AM
Dr. Chung-Jui Tsai (Haynes Professor and Eminent Scholar, School of Forestry and Natural Resources, Department of Genetics, Department of Plant Biology, University of Georgia, USA)
CRISPR Genome Editing in Outcrossing Species: from knockout to allelic series mutagenesis (and dose-dependent tradeoffs of lignin reduction)
Auditorium A134, Agricultural Technology Building, Agricultural Biotechnology Research Center 2018/02/05 10:00 AM
Dr. Jungnam Cho (Postdoctoral Research Associate, The Sainsbury Laboratory, University of Cambridge, UK)
Taming and hunting retrotransposons in plants
Auditorium A134, Agricultural Technology Building, Agricultural Biotechnology Research Center