Lin, Y.-C., Wang, J., Delhomme, N., Schiffthaler, B., Sundström, G., Zuccolo, A., Nystedt, B., Hvidsten, T. R., de la Torre, A., Cossu, R. M., Hoeppner, M. P., Lantz, H., Scofield, D. G., Zamani, N., Johansson, A., Mannapperuma, C., Robinson, K. M., Mähler, N., Leitch, I. J., Pellicer, J., Park, E.-J., Van Montagu, M., Van de Peer, Y., Grabherr, M., Jansson, S., Ingvarsson, P. K. and Street, N. R. (2018) Functional and evolutionary genomic inferences in Populus through genome and population sequencing of American and European aspen. PNAS published ahead of print October 29, 2018
We performed de novo, full-genome sequence analysis of two Populus species, North American quaking and Eurasian trembling aspen, that contain striking levels of genetic variation. Our results showed that positive and negative selection broadly affects patterns of genomic variation, but to varying degrees across coding and noncoding regions. The strength of selection and rates of sequence divergence were strongly related to differences in gene expression and coexpression network connectivity. These results highlight the importance of both positive and negative selection in shaping genome-wide levels of genetic variation in an obligately outcrossing, perennial plant. The resources we present establish aspens as a powerful study system enabling future studies for understanding the genomic determinants of adaptive evolution. To maximize the community utility of these resources, we have integrated all presented data within the PopGenIE web resource (PopGenIE.org).
Lin W-Y, Lin Y-Y, Chiang S-F, Syu C, Hsieh L-C*, Chiou T-J* (2018) Evolution of microRNA827 targeting in the plant kingdom. New Phytologist 217: 1712-1725
Unlike most ancient microRNAs, which conservatively target homologous genes across species, microRNA827 (miR827) targets two different types of SPX (SYG1/PHO81/XPR1)-domain-containing genes, NITROGEN LIMITATION ADAPTATION (NLA) and PHOSPHATE TRANSPORTER 5 (PHT5), in Arabidopsis thaliana and Oryza sativa to regulate phosphate (Pi) transport and storage, respectively. However, how miR827 shifted its target preference and its evolutionary history are unknown. Based on target prediction analysis, we found that in most angiosperms, miR827 conservatively targets PHT5 homologs, but in Brassicaceae and Cleomaceae it preferentially targets NLA homologs, and we provide evidence for the transition of target preference during Brassicales evolution. Intriguingly, we found a lineage-specific loss of the miR827-regulatory module in legumes. Analysis of miR827-mediated cleavage efficiency and the expression of PHT5 in A. thaliana indicated that accumulation of mutations in the target site and the exclusion of the target site by alternative transcriptional initiation eliminated PHT5 targeting by miR827. * Here, we identified a transition of miR827 target preference during plant evolution and revealed the uniqueness of miR827-mediated regulation among conserved plant miRNAs. Despite the change in its target preference, upregulation of miR827 by Pi starvation and its role in regulating cellular Pi homeostasis were retained.
Leong, S. J., Lu, W.-C. and Chiou, T.-J.* (2018) Phosphite-Mediated Suppression of Anthocyanin Accumulation Regulated by Mitochondrial ATP Synthesis and Sugar in Arabidopsis. Plant & Cell Physiology 59: 1158-1169
Despite the essential role of phosphate (Pi) in plant growth and development, how plants sense and signal the change of Pi supply to adjust its uptake and utilization is not yet well understood. Pi itself has been proposed to be a signaling molecule that regulates Pi starvation responses (PSRs) because phosphite (Phi), a non-metabolized Pi analog, suppresses several PSRs. In this study, we identified a phosphite-insensitive1 (phi1) mutant which retained anthocyanin, a visible PSR, in Phi-containing but Pi-deficient medium. phi1 mutants were impaired in the gene encoding an FAd subunit of mitochondrial F1Fo-ATP synthase and showed a reduced mitochondrial ATP level in roots, growth hypersensitivity to oligomycin and an increased mitochondrial membrane potential, suggesting that this gene has a crucial role in mitochondrial ATP synthesis. phi1 mutants accumulated a high level of sugars in shoots, which may account for the increased accumulation of anthocyanin and starch in Phi-containing conditions. Gene expression analysis showed that a subset of genes involved in carbohydrate metabolism in phi1 was misregulated in response to Phi. The majority of genes were repressed by Pi starvation and, unlike wild-type plants, their repression in phi1 was not affected by the addition of Phi. Our findings show that defective mitochondrial ATP synthesis results in sugar accumulation, leading to alteration of Phi-mediated suppression of PSRs. This study reinforces the role of sugars, and also reveals a cross-talk among ATP, sugars and Pi/Phi molecules in mediating PSRs.
Kuo, H.-F., Hsu, Y.-Y., Lin, W.-C., Chen, K.-Y., Munnik, T., Brearley, C. A.* and Chiou, T.-J.* (2018) Arabidopsis inositol phosphate kinases, IPK1 and ITPK1, constitute a metabolic pathway in maintaining phosphate homeostasis. The Plant J. (doi:10.1111/tpj.13974)
Emerging studies have implicated a close link between inositol phosphate (InsP) metabolism and cellular phosphate (Pi) homeostasis in eukaryotes; however, whether a common InsP species is deployed as an evolutionarily conserved metabolic messenger to mediate Pi signaling remains unknown. Here, using genetics and InsP profiling combined with Pi starvation response (PSR) analysis in Arabidopsis thaliana, we showed that the kinase activity of inositol pentakisphosphate 2-kinase (IPK1), an enzyme required for phytate (inositol hexakisphosphates; InsP6) synthesis, is indispensable for maintaining Pi homeostasis under Pi-replete conditions, and inositol 1,3,4-trisphosphate 5/6-kinase 1 (ITPK1) plays an equivalent role. Although both ipk1-1 and itpk1 mutants exhibited decreased levels of InsP6 and diphosphoinositol pentakisphosphate (PP-InsP5; InsP7), disruption of another ITPK family enzyme, ITPK4, which correspondingly caused depletion of InsP6 and InsP7, did not display similar Pi-related phenotypes, which precludes these InsP species as effectors. Notably, the level of D/L-Ins(3,4,5,6) P4 was concurrently elevated in both ipk1-1 and itpk1 mutants, which showed a specific correlation to the misregulated Pi phenotypes. However, the level of D/L-Ins(3,4,5,6)P4 is not responsive to Pi starvation that instead manifests a shoot-specific increase in InsP7 level. This study demonstrates a more nuanced picture of the intersection of InsP metabolism and Pi homeostasis and PSR than has previously been elaborated and additionally establishes intermediate steps to phytate biosynthesis in plant vegetative tissues.
Hsiang-chin Liu†, Jörn Lämke†, Siou-ying Lin†, Meng-Ju Hung, Kuan-Ming Liu, Yee-yung Charng*, Isabel Bäurle* (2018) Distinct heat shock factors and chromatin modifications mediate the organ-autonomous transcriptional memory of heat stress. Plant J. https://doi.org/10.1111/tpj.13958
Plants can be primed by a stress cue to mount a faster or stronger activation of defense mechanisms upon a subsequent stress. A crucial component of such stress priming is the modified reactivation of genes upon recurring stress; however, the underlying mechanisms are poorly understood. Here, we report that dozens of Arabidopsis thaliana genes display transcriptional memory, i.e. stronger upregulation after a recurring heat stress, that lasts for at least three days. We define a set of transcription factors involved in this memory response and show that the transcriptional memory results in enhanced transcriptional activation within minutes after the onset of a heat stress cue. Further, we show that the transcriptional memory is active in all tissues. It may last for up to a week, and is associated with histone H3 lysine 4 hyper-methylation during this time. This transcriptional memory is cis-encoded, as we identify a promoter fragment that confers memory onto a heterologous gene. In summary, heat-induced transcriptional memory is a widespread and sustained response, and our study provides a framework for future mechanistic studies of somatic stress memory in higher plants.
Ming-Jung Liu*, Koichi Sugimoto, Sahra Uygun, Nicholas Panchy, Michael S. Campbell, Mark Yandell, Gregg A. Howe and Shin-Han Shiu* (2018). Regulatory divergence in wound-responsive gene expression between domesticated and wild tomato. Plant Cell DOI: http://www.plantcell.org/content/early/2018/05/09/tpc.18.00194
Background: Two related species accumulate differences between each other over time. If one of the species is domesticated due to human selection of desirable traits, the domesticated species experiences a "bottleneck" where many traits present in the related wild species are lost because only a few individuals are targeted for selection. For example, domesticated tomato has a weaker defense response to wounding and insect feeding compared to wild tomato species that separated from the domesticated tomato ~3-7 million years ago. One of the major reasons for this difference lies with genes that are turned on and off differently due to evolution of short DNA sequences that are like molecular switches.
Question: We wanted to know how wounding leads to different genes being turned on and off in domesticated and wild tomatoes, which DNA sequence "switches" are important for this response, and how these sequence switches differ between species.
Findings: We found that thousands of genes were turned on or off differently in response to wounding between domesticated and wild tomato species. We found hundreds of potential DNA switches associated with this set of genes, and nearly half of them were unique to one species or the other. Our findings indicate a large difference in how these two plant species turn genes on/off in response to wounding; for example this difference is much greater than similar comparisons between human and mouse genes, which were separated from a common ancestor roughly 100 million years ago.
Sakthivel Kailasam, Ying Wang, Jing-Chi Lo, Hsin-Fang Chang and Kuo-Chen Yeh* (2018) S-nitrosoglutathione works downstream of nitric oxide to mediate iron deficiency signaling in Arabidopsis The Plant Journal, DOI: 10.1111/tpj.13850
Several studies elucidated the transcriptional responses to iron (Fe) starvation, however, the Fe sensing and signal transduction machineries are poorly resolved thus far in plants. With this focus, by using chemical biology approach, we identified a small molecule R7, whose use inhibited the physiological and molecular responses of Fe starvation in Arabidopsis. R7 blocked the Fe starvation signaling from nitric oxide (NO) to the central transcription factor, FER-LIKE IRON-DEFICIENCY-INDUCED TRANSCRIPTION FACTOR (FIT). Exogenous applications of NO abduct, S-nitrosoglutathione (GSNO) were able to attenuate the R7 effect. R7 directly or indirectly decreased the endogenous GSNO levels in roots but not the NO levels. Our finding reveals that, under Fe limited situation the starvation signal from NO is passed to FIT through GSNO.
Choun-Sea Lin*,Chen-Tran Hsu, Ling-Hung Yang, Lan-Ying Lee, Jin-Yuan Fu, Qiao-Wei Cheng, Fu-Hui Wu, Han Chen-Wei Hsiao, Yesheng Zhang, Ru Zhang, Wan-Jung Chang, Chen-Ting Yu, Wen Wang, Li-Jen Liao, Stanton B. Gelvin*,Ming-Che Shih*. (2018) Application of protoplast technology to CRISPR/Cas9 mutagenesis: From single cell mutation detection to mutant plant regeneration. Plant Biotechnol J. 2017 Dec 12. doi: 10.1111/pbi.12870
Plant protoplasts are useful for assessing the efficiency of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)/CRISPR Associated Protein 9 (Cas9) mutagenesis. We improved the process of protoplast isolation and transfection of several plant species. We also developed a method to isolate and regenerate single mutagenized Nicotianna tabacum protoplasts into mature plants. Following transfection of protoplasts with constructs encoding Cas9 and sgRNAs, target gene DNA could be amplified for further analysis to determine mutagenesis efficiency. We investigated N. tabacum protoplasts and derived regenerated plants for targeted mutagenesis of the phytoene desaturase (NtPDS) gene. Genotyping of albino regenerants indicated that all four NtPDS alleles were mutated in amphidiploid tobacco, and no Cas9 DNA could be detected in most regenerated plants.
Chin-Hsien Tsai, Sheue-Fen Tzeng, Shih-Chuan Hsieh, Chia-Jui Tsai, Yu-Chih Yang, Mong-Hsun Tsai and Pei-Wen Hsiao (2017) A Standardized Wedelia chinensis Extract Overcomes the Feedback Activation of HER2/3 Signaling upon Androgen-Ablation in Prostate Cancer. Frontiers in Pharmacology 2017 Oct; 8:721
Androgen receptor (AR)-mediated signaling play an essential role in prostate cancer for survival, growth, and invasion. Crosstalk between the AR and other signaling pathways in prostate cancer (PCa) severely affects the therapeutic outcome of hormonal therapy. Although anti-androgen therapy prolongs overall survival in PCa patients, resistance rapidly develops and is often associated with increased AR expression and upregulation of the HER2/3-AKT signaling pathway. However, single-agent therapy targeting AR, HER2/3 or AKT usually fails due to the reciprocal feedback loop. Here, we demonstrated that a standardized herbal extract, named WCE, effectively disrupted the AR, HER2/3, and AKT signaling networks and therefore enhanced the therapeutic efﬁcacy of androgen ablation in PCa. Furthermore, WCE remained effective in suppressing AR and HER2/3 signaling in an in vivo adapted castration-resistant PCa cells that were insensitive to androgen withdrawal and a second-line antiandrogen, enzalutamide. This study provides preclinical evidence that the use of a deﬁned, single plant-derived extract can augment the therapeutic efﬁcacy of castration with signiﬁcantly prolonged progression-free survival. These data also establish a solid basis for using WCE as a candidate agent in clinical studies.
Chin-Hsien Tsai, Sheue-Fen Tzeng, Shih-Chuan Hsieh, Yu-Chih Yang, Yi-Wen Hsiao, Mong-Hsun Tsai, and Pei-Wen Hsiao (2017) A standardized herbal extract mitigates tumor inflammation and augments chemotherapy effect of docetaxel in prostate cancer. Scientific Reports 2017 Nov; 7: 15624
Docetaxel remains the standard treatment for castration-resistant prostate cancer by improving overall survival but having severe adverse toxicity. Inflammatory cytokines in the tumor microenvironment promote docetaxel resistance through activation of IKKα/β-NFκB pathways. To tackle such chemotherapy-elicited adverse effects, this study demonstrates the standardized Wedelia chinensis herbal extract effectively inhibited the production of tumor-promoting cytokines, therefore inhibiting angiogenesis, tumor growth, and metastasis. Transcriptomic analysis of tumors revealed that WCE modulates inflammatory tumor microenvironment by suppressing the expression of HIF1α, IKKα/β phosphorylation and the downstream cytokines/chemokines, e.g., IL6, CXCL1, and CXCL8, thus reduced tumor-elicited chemotaxis and infiltration of MDSCs, TAMs, and endothelial cells into the tumors. Furthermore, WCE suppresses the expansion and activity of MDSCs by downregulating STAT3 activity and also prevents the differentiation of macrophages toward tumor-promoting M2 phenotype. On the other hand, co-treatment of docetaxel with this botanical preparation caused significant enhancement of the docetaxel-mediated therapeutic efficacy, while prevented the drug resistance and toxicity.
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2019/03/04 10:30 AM
Dr. Guido Grossmann (Group Leader, the Centre for Organismal Studies (COS) Heidelberg, Heidelberg University, Germany)
Auditorium A134, Agricultural Technology Building, Agricultural Biotechnology Research Center