國立台灣大學 | 生命科學院
 
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Using Silicon Polymer Impression Technique and Scanning Electron Microscopy to Measure Stomatal Aperture, Morphology, and Density.

Wu HC, Huang YC, Liu CH, Jinn TL*
Bio-protocol. 2017 Aug 20;7: e2449. DOI: 10.21769/BioProtoc.2449.

The number of stomata on leaves can be affected by intrinsic development programming and various environmental factors, in addition the control of stomatal apertures is extremely important for the plant stress response. In response to elevated temperatures, transpiration occurs through the stomatal apertures, allowing the leaf to cool through water evaporation. As such, monitoring of stomata behavior to elevated temperatures remains as an important area of research. The protocol allows analysis of stomatal aperture, morphology, and density through a non-destructive imprint of Arabidopsis thaliana leaf surface. Stomatal counts were performed and observed under a scanning electron microcopy. more....


HISTONE DEACETYLASE6 Acts in Concert with Histone Methyltransferases SUVH4, SUVH5, and SUVH6 to Regulate Transposon Silencing.

Yu CW, Tai R, Wang SC, Yang P, Luo M, Yang S, Cheng K, Wang WC, Cheng YS, Wu K*
Plant Cell. 2017 Aug 4. pii: tpc.00570.2016. doi: 10.1105/tpc.16.00570. [Epub ahead of print]

Histone deacetylases (HDACs) play important roles in regulating gene expression. In yeast and animals, HDACs act as components of multiprotein complexes that modulate transcription during various biological processes. However, little is known about the interacting proteins of plant HDACs. To identify the plant HDAC complexes and interacting proteins, we developed an optimized workflow using immunopurification coupled to mass spectrometry-based proteomics in Arabidopsis thaliana. We found that the histone deacetylase HDA6 can interact with the histone methyltransferases SUVH4, SUVH5, and SUVH6 (SUVH4/5/6). Domain analysis revealed that the C-terminal regions of HDA6 and SUVH5 are important for their interaction. Furthermore, HDA6 interacts with SUVH4/5/6 and co-regulates a subset of transposons through histone H3K9 methylation and H3 deacetylation. In addition, two phosphorylated serine residues, S427 and S429, were unambiguously identified in the C-terminal region of HDA6. Phosphomimetics (amino acid substitutions that mimic a phosphorylated protein) of HDA6 resulted in increased enzymatic activity, whereas the mutation of Ser427 to alanine in HDA6 abolished its interaction with SUVH5 and SUVH6, suggesting that the phosphorylation of HDA6 is important for its activity and function. more....


Pectin methylesterase is required for guard cell function in response to heat.

Wu HC, Huang YC, Stracovsky L.,Jinn TL*
Plant Signal Behav. 2017 Jun 3. 12(6):e1338227. doi: 10.1080/15592324

Pectin is an important cell wall polysaccharide required for cellular adhesion, extension, and plant growth. The pectic methylesterification status of guard cell walls influences the movement of stomata in response to different stimuli. Pectin methylesterase (PME) has a profound effect on cell wall modification, especially on the degree of pectic methylesterification during heat response. The Arabidopsis thaliana PME34 gene is highly expressed in guard cells and in response to the phytohormone abscisic acid. The genetic data highlighted the significant role of PME34 in heat tolerance through the regulation of stomatal movement. Thus, the opening and closure of stomata is mediated by changes in response to a given stimulus, could require a specific cell wall modifying enzyme to function properly. more....


Identification of HDA15-PIF1 as a key repression module directing the transcriptional network of seed germination in the dark.

Gu D, Chen CY, Zhao M, Zhao L, Duan X, Duan J*, Wu K*, Liu X*.
Nucleic Acids Res. 2017 Apr 21. doi: 10.1093/nar/gkx283. [Epub ahead of print]

Light is a major external factor in regulating seed germination. Photoreceptor phytochrome B (PHYB) plays a predominant role in promoting seed germination in the initial phase after imbibition, partially by repressing phytochrome-interacting factor1 (PIF1). However, the mechanism underlying the PHYB-PIF1-mediated transcription regulation remains largely unclear. Here, we identified that histone deacetylase15 (HDA15) is a negative component of PHYB-dependent seed germination. Overexpression of HDA15 in Arabidopsis inhibits PHYB-dependent seed germination, whereas loss of function of HDA15 increases PHYB-dependent seed germination. Genetic evidence indicated that HDA15 acts downstream of PHYB and represses seed germination dependent on PIF1. Furthermore, HDA15 interacts with PIF1 both in vitro and in vivo. Genome-wide transcriptome analysis revealed that HDA15 and PIF1 co-regulate the transcription of the light-responsive genes involved in multiple hormonal signaling pathways and cellular processes in germinating seeds in the dark. In addition, PIF1 recruits HDA15 to the promoter regions of target genes and represses their expression by decreasing the histone H3 acetylation levels in the dark. Taken together, our analysis uncovered the role of histone deacetylation in the light-regulated seed germination process and identified that HDA15-PIF1 acts as a key repression module directing the transcription network of seed germination. more....


PECTIN METHYLESTERASE34 contributes to Heat tolerance through its role in promoting stomatal movement.

Huang YC, Wu HC, Wang YD, Liu CH, Lin CC, Luo DL, Jinn TL*
Plant Physiol. 2017 Apr 5. 174(2):748-763. doi: 10.1104/pp.17.00335.?

Pectin, a major component of the primary cell wall, is synthesized in the Golgi apparatus and exported to the cell wall in a highly methylesterified form, then is partially demethylesterified by pectin methylesterases (PMEs, EC 3.1.1.11). PMEs activity on the status of pectin methylesterification profoundly affects the properties of pectin, and thereby is critical for plant development and plant defense response, although the roles of PMEs under heat stress (HS) are poorly understood. Functional genome annotation predicts that at least 66 potential PME genes are contained in Arabidopsis (Arabidopsis thaliana). Thermotolerance assays of PME genes T-DNA insertion lines revealed two null-mutant alleles of PME34 (At3g49220) that both consistently showed reduced thermotolerance. Nevertheless, their impairment was independently associated with the expression of HS-responsive genes. It was also observed that PME34 transcription was induced by abscisic acid and highly expressed in guard cells. We showed that the PME34 mutation has a defect in the control of stomatal movement and greatly altered PME and polygalacturonase (PG, EC 3.2.1.15) activity, resulting in a heat-sensitive phenotype. PME34 has a role in the regulation of transpiration through control of stomatal aperture, due to its cell wall modifying enzyme activity during HS response. Hence, PME34 is required for regulating guard cell-wall flexibility to mediate heat response in Arabidopsis. more....


Young inversion with multiple linked QTLs under selection in a hybrid zone.

Lee CR*, Wang B, Mojica JP, Mandakova T, Prasad KVSK, Goicoechea JL, Perera N, Hellsten U, Hundley HN, Johnson J, Grimwood J, Barry K, Fairclough S, Jenkins JW, Yu Y, Kudrna D, Zhang J, Talag J, Golser W, Ghattas K, Schranz ME, Wing R, Lysak MA, Schmutz J, Rokhsar DS and Mitchell-Olds T*
Nature Ecology & Evolution. 2017 April 3.

Fixed chromosomal inversions can reduce gene flow and promote speciation in two ways: by suppressing recombination and by carrying locally favoured alleles at multiple loci. However, it is unknown whether favoured mutations slowly accumulate on older inversions or if young inversions spread because they capture pre-existing adaptive quantitative trait loci (QTLs). By genetic mapping, chromosome painting and genome sequencing, we have identified a major inversion controlling ecologically important traits in Boechera stricta. The inversion arose since the last glaciation and subsequently reached local high frequency in a hybrid speciation zone. Furthermore, the inversion shows signs of positive directional selection. To test whether the inversion could have captured existing, linked QTLs, we crossed standard, collinear haplotypes from the hybrid zone and found multiple linked phenology QTLs within the inversion region. These findings provide the first direct evidence that linked, locally adapted QTLs may be captured by young inversions during incipient speciation. more....


Structural basis of jasmonate-amido synthetase FIN219 in complex with glutathione S-transferase FIP1 during the JA signal regulation.

Chen CY, Ho SS, Kuo TY, Hsieh HL, Cheng YS*
Proc Natl Acad Sci U S A. 2017 Mar 7;114(10):E1815-E1824. doi: 10.1073/pnas.1609980114. Epub 2017 Feb 21.

Far-red (FR) light-coupled jasmonate (JA) signaling is necessary for plant defense and development. FR insensitive 219 (FIN219) is a member of the Gretchen Hagen 3 (GH3) family of proteins in Arabidopsis and belongs to the adenylate-forming family of enzymes. It directly controls biosynthesis of jasmonoyl-isoleucine in JA-mediated defense responses and interacts with FIN219-interacting protein 1 (FIP1) under FR light conditions. FIN219 and FIP1 are involved in FR light signaling and are regulators of the interplay between light and JA signaling. However, how their interactions affect plant physiological functions remains unclear. Here, we demonstrate the crystal structures of FIN219-FIP1 while binding with substrates at atomic resolution. Our results show an unexpected FIN219 conformation and demonstrate various differences between this protein and other members of the GH3 family. We show that the rotated C-terminal domain of FIN219 alters ATP binding and the core structure of the active site. We further demonstrate that this unique FIN219-FIP1 structure is crucial for increasing FIN219 activity and determines the priority of substrate binding. We suggest that the increased FIN219 activity resulting from the complex form, a conformation for domain switching, allows FIN219 to switch to its high-affinity mode and thereby enhances JA signaling under continuous FR light conditions. more....


On the post-glacial spread of human commensal Arabidopsis thaliana
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Lee CR*, Svardal H, Farlow A, Exposito-Alonso M, Ding W, Novikova P, Alonso-Blanco C, Weigel D, Nordborg M*
Nat Commun. 2017 Feb 9;8:14458. doi: 10.1038/ncomms14458.

Recent work has shown that Arabidopsis thaliana contains genetic groups originating from different ice age refugia, with one particular group comprising over 95% of the current worldwide population. In Europe, relicts of other groups can be found in local populations along the Mediterranean Sea. Here we provide evidence that these 'relicts' occupied post-glacial Eurasia first and were later replaced by the invading 'non-relicts', which expanded through the east-west axis of Eurasia, leaving traces of admixture in the north and south of the species range. The non-relict expansion was likely associated with human activity and led to a demographic replacement similar to what occurred in humans. Introgressed genomic regions from relicts are associated with flowering time and enriched for genes associated with environmental conditions, such as root cap development or metal ion trans-membrane transport, which suggest that admixture with locally adapted relicts helped the non-relicts colonize new habitats. more....


UBC18 mediates ERF1 degradation under light-dark cycles.

Cheng MC, Kuo WC, Wang YM, Chen HY, Lin TP*
New Phytol. 2017 Feb;213(3):1156-1167.

Ethylene Response Factor 1(ERF1) plays a crucial role in biotic and abiotic stress responses. Previous studies have shown that ERF1 regulates stress-responsive gene expression by binding to different cis-acting elements in response to various stress signals. ERF1 was also reported to be unstable in the dark, and it regulates hypocotyl elongation. Here, we elucidated the mechanism underlying degradation of ERF1. Yeast two-hybrid screening showed that UBIQUITIN-CONJUGATING ENZYME 18 (UBC18) interacted with ERF1. The interaction between ERF1 and UBC18 was verified using pull-down assays and coimmunoprecipitation analyses. We then compared the ERF1 protein abundance in the UBC18 mutant and overexpression plants. Based on the results of protein degradation and in vivo ubiquitination assays, we proposed that UBC18 mediates ERF1 ubiquitination and degradation. ERF1 was more stable in UBC18 mutants and less stable in UBC18 overexpression lines compared with that in wild-type plants. ERF1 was degraded by the 26S proteasome system via regulation of UBC18 and promotes dark-repression of downstream genes and proline accumulation. UBC18 negatively regulated drought and salt stress responses by altering the abundance of ERF1 and the expression of genes downstream of ERF1. more....


A Chinese cabbage (Brassica campetris subsp. Chinensis) τ-type glutathione-S-transferase stimulates Arabidopsis development and primes against abiotic and biotic stress.

Kao CW, Bakshi M, Sherameti I, Dong S, Reichelt M, Oelmuller R, Yeh KW*
Plant Mol Biol. 2016 Oct 31. [Epub ahead of print]

The beneficial root-colonizing fungus Piriformospora indica stimulates root development of Chinese cabbage (Brassica campestris subsp. Chinensis) and this is accompanied by the up-regulation of a τ-class glutathione (GSH)-S-transferase gene (BcGSTU) (Lee et al. 2011) in the roots. BcGSTU expression is further promoted by osmotic (salt and PEG) and heat stress. Ectopic expression of BcGSTU in Arabidopsis under the control of the 35S promoter results in the promotion of root and shoot growth as well as better performance of the plants under abiotic (150 mM NaCl, PEG, 42?°C) and biotic (Alternaria brassicae infection) stresses. Higher levels of glutathione, auxin and stress-related (salicylic and jasmonic acid) phytohormones as well as changes in the gene expression profile result in better performance of the BcGSTU expressors upon exposure to stress. Simultaneously the plants are primed against upcoming stresses. We propose that BcGSTU is a target of P. indica in Chinese cabbage roots because the enzyme participates in balancing growth and stress responses, depending on the equilibrium of the symbiotic interaction. A comparable function of BcGST in transgenic Arabidopsis makes the enzyme a valuable tool for agricultural applications. more....


The Sweet Potato NAC-Domain Transcription Factor IbNAC1 Is Dynamically Coordinated by the Activator IbbHLH3 and the Repressor IbbHLH4 to Reprogram the Defense Mechanism against Wounding.

Chen SP, Kuo CH, Lu HH, Lo HS, Yeh KW*
PLoS Genet. 2016 Oct 25;12(10): e1006397

IbNAC1 is known to activate the defense system by reprogramming a genetic network against herbivory in sweet potato. This regulatory activity elevates plant defense potential but relatively weakens plants by IbNAC1-mediated JA response. The mechanism controlling IbNAC1 expression to balance plant vitality and survival remains unclear. In this study, a wound-responsive G-box cis-element in the IbNAC1 promoter from -1484 to -1479 bp was identified. From a screen of wound-activated transcriptomic data, one transcriptional activator, IbbHLH3, and one repressor, IbbHLH4, were selected that bind to and activate or repress, respectively, the G-box motif in the IbNAC1 promoter to modulate the IbNAC1-mediated response. In the early wound response, the IbbHLH3-IbbHLH3 protein complex binds to the G-box motif to activate IbNAC1 expression. Thus, an elegant defense network is activated against wounding stress. Until the late stages of wounding, IbbHLH4 interacts with IbbHLH3, and the IbbHLH3-IbbHLH4 heterodimer competes with the IbbHLH3-IbbHLH3 complex to bind the G-box and suppress IbNAC1 expression and timely terminates the defense network. Moreover, the JAZs and IbEIL1 proteins interact with IbbHLH3 to repress the transactivation function of IbbHLH3 in non-wounded condition, but their transcription is immediately inhibited upon early wounding. Our work provides a genetic model that accurately switches the regulatory mechanism of IbNAC1 expression to adjust wounding physiology and represents a delicate defense regulatory network in plants. more....


Nitric oxide participates in plant flowering repression by ascorbate.

Senthil Kumar R, Shen CH, Wu PY, Suresh Kumar S, Hua MS, Yeh KW*
Sci. Rep. 2016 Oct 12;6:35246. doi: 10.1038/srep35246.

In Oncidium, redox homeostasis involved in flowering is mainly due to ascorbic acid (AsA). Here, we discovered that Oncidium floral repression is caused by an increase in AsA-mediated NO levels,which is directed by the enzymatic activities of nitrate reductase (NaR) and nitrite reducatase (NiR).Through Solexa transcriptomic analysis of two libraries, 'pseudobulb with inflorescent bud' (PIB)and 'pseudobulb with axillary bud' (PAB), we identified differentially expressed genes related to NO metabolism. Subsequently, we showed a significant reduction of NaR enzymatic activities and NO levels during bolting and blooming stage, suggesting that NO controlled the phase transition and flowering process. Applying AsA to Oncidium PLB (protocorm-like bodies) significantly elevated the NO content and enzyme activities. Application of sodium nitroprusside (-NO donor) on Arabidopsis vtc1 mutant caused late flowering and expression level of flowering-associated genes (CO, FT and LFY) were reduced, suggesting NO signaling is vital for flowering repression. Conversely, the flowering time of noa1, an Arabidopsis NO-deficient mutant, was not altered after treatment with L-galacturonate, a precursor of AsA, suggesting AsA is required for NO-biosynthesis involved in the NO-mediated flowering-repression pathway. Altogether, Oncidium bolting is tightly regulated by AsA-mediated NO level and downregulation of transcriptional levels of NO metabolism genes. more....


The heat-stress factor HSFA6b connects ABA signaling and ABA-mediated heat responses.

Huang YC, Niu CY, Yang CR, Jinn TL*
Plant Physiol. 2016 Aug 4. pii: pp.00860.2016.[Epub ahead of print]

Heat stress response (HSR) is a conserved mechanism developed to increase the expression of heat shock proteins (HSPs) via a heat shock factor (HSF)-dependent mechanism. Signaling by the stress phytohormone abscisic acid (ABA) is involved in acquired thermotolerance as well. Analysis of Arabidopsis thaliana microarray databases revealed that the expression of HSFA6b, a class-A HSF, extensively increased with salinity, osmotic, and cold stresses, but not heat. Here, we show that HSFA6b plays a pivotal role in the response to ABA and in thermotolerance. Salt-inducible HSFA6b expression was downregulated in ABA insensitive and deficient mutants; however exogenous ABA application restored expression in ABA-deficient, but not insensitive plants. Thus, ABA signaling is required for proper HSFA6b expression. A transcriptional activation assay of protoplasts revealed that ABA treatment and coexpression of an ABA-signaling master effector, ABA-RESPONSIVE ELEMENT-BINDING PROTEIN1, could activate the HSFA6b promoter. In addition, HSFA6b directly bound to the promoter of DEHYDRATION-RESPONSIVE ELEMENT-BINDING PROTEIN2A and enhanced its expression. Analysis of ABA responses in seed germination, cotyledon greening, and root growth as well as salt and drought tolerance in HSFA6b-null, overexpression, and dominant-negative mutants revealed that HSFA6b is a positive regulator participating in ABA mediated salt and drought resistance. Thermoprotection tests showed that HSFA6b was required for thermotolerance acquisition. Our study reveals a network in which HSFA6b operates as a downstream regulator of the ABA-mediated stress response and is required for HS resistance. This new ABA-signaling pathway is integrated into the complex HSR network in planta. more....


The Arabidopsis Malectin-Like/LRR-RLK IOS1 Is Critical for BAK1-Dependent and BAK1-Independent Pattern-Triggered Immunity.

Yeh YH, Panzeri D, Kadota Y, Huang YC, Huang PY, Tao CN, Roux M, Chien HC, Chin TC, Chu PW, Zipfel C, Zimmerli L*
Plant Cell. 2016 Jul;28(7):1701-21.

Plasma membrane-localized pattern recognition receptors (PRRs) such as FLAGELLIN SENSING2 (FLS2), EF-TU RECEPTOR (EFR), and CHITIN ELICITOR RECEPTOR KINASE1 (CERK1) recognize microbe-associated molecular patterns (MAMPs) to activate pattern-triggered immunity (PTI). A reverse genetics approach on genes responsive to the priming agent β-aminobutyric acid (BABA) revealed IMPAIRED OOMYCETE SUSCEPTIBILITY1 (IOS1) as a critical PTI player. Arabidopsis thaliana ios1 mutants were hypersusceptible to Pseudomonas syringae bacteria. Accordingly, ios1 mutants showed defective PTI responses, notably delayed upregulation of the PTI marker gene FLG22-INDUCED RECEPTOR-LIKE KINASE1, reduced callose deposition, and mitogen-activated protein kinase activation upon MAMP treatment. Moreover, Arabidopsis lines overexpressing IOS1 were more resistant to bacteria and showed a primed PTI response. In vitro pull-down, bimolecular fluorescence complementation, coimmunoprecipitation, and mass spectrometry analyses supported the existence of complexes between the membrane-localized IOS1 and BRASSINOSTEROID INSENSITIVE1-ASSOCIATED KINASE1 (BAK1)-dependent PRRs FLS2 and EFR, as well as with the BAK1-independent PRR CERK1. IOS1 also associated with BAK1 in a ligand-independent manner and positively regulated FLS2-BAK1 complex formation upon MAMP treatment. In addition, IOS1 was critical for chitin-mediated PTI. Finally, ios1 mutants were defective in BABA-induced resistance and priming. This work reveals IOS1 as a novel regulatory protein of FLS2-, EFR-, and CERK1-mediated signaling pathways that primes PTI activation. more....


Pathogen-induced ERF68 regulates hypersensitive cell death in tomato.

Liu AC, Cheng CP*
Mol Plant Pathol. 2016 Jul 14. doi: 10.1111/mpp.12460.

Ethylene response factors (ERFs) are a large plant-specific transcription factor family and play diverse important roles in various plant functions. However, most tomato ERFs have not been characterized. In this study, we showed that the expression of an uncharacterized member of the tomato ERF-IX subgroup, ERF68, was significantly induced by treatments with different bacterial pathogens, ethylene (ET) and salicylic acid (SA), but only slightly induced by bacterial mutants defective in the type III secretion system (T3SS) or non-host pathogens. The ERF68-green fluorescent protein (ERF68-GFP) fusion protein was localized in the nucleus. Transactivation and electrophoretic mobility shift assays (EMSAs) further showed that ERF68 was a functional transcriptional activator and was bound to the GCC-box. Moreover, transient overexpression of ERF68 led to spontaneous lesions in tomato and tobacco leaves and enhanced the expression of genes involved in ET, SA, jasmonic acid (JA) and hypersensitive response (HR) pathways, whereas silencing of ERF68 increased tomato susceptibility to two incompatible Xanthomonas spp. These results reveal the involvement of ERF68 in the effector-triggered immunity (ETI) pathway. To identify ERF68 target genes, chromatin immunoprecipitation combined with high-throughput sequencing (ChIP-seq) was performed. Amongst the confirmed target genes, a few genes involved in cell death or disease defence were differentially regulated by ERF68. Our study demonstrates the function of ERF68 in the positive regulation of hypersensitive cell death and disease defence by modulation of multiple signalling pathways, and provides important new information on the complex regulatory function of ERFs. more....


Sweet potato NAC transcription factor, IbNAC1, upregulates sporamin gene expression by binding the SWRE motif against mechanical wounding and herbivore attack.

Chen SP, Lin IW, Chen X, Huang YH, Chang HC, Lo HS, Lu HH, Yeh KW*
Plant J. 2016 Mar 21. doi: 10.1111/tpj.13171. [Epub ahead of print]

Sporamin is a tuberous storage protein with trypsin inhibitory activity in sweet potato (Ipomoea batatas Lam.), which accounts for 85% of the soluble protein in tubers. It is constitutively expressed in tuberousroots but is expressed in leaves only after wounding. Thus far, its wound-inducible signal transductionmechanisms remain unclear. In the present work, a 53-bp DNA region,sporamin wound-response cis-element (SWRE), was identi?ed in the sporamin promoter and was determined to be responsible for the wounding response. Using yeast one-hybrid screening, a NAC domain protein, IbNAC1, that speci?cally bound to the 5'-TACAATATC-3' sequence in SWRE was isolated from a cDNA library from wounded leaves.IbNAC1 was constitutively expressed in root tissues and was induced earlier than sporamin following thewounding of leaves. Transgenic sweet potato plants overexpressing IbNAC1 had greatly increased sporamin expression, increased trypsin inhibitory activity, and elevated resistance against Spodoptera litura. We further demonstrated that IbNAC1 has multiple biological functions in the jasmonic acid (JA) response, includ-ing the inhibition of root formation, accumulation of anthocyanin, regulation of aging processes, reductionof abiotic tolerance, and overproduction of reactive oxygen species (ROS). Thus, IbNAC1 is a core transcription factor that reprograms the transcriptional response to wounding via the JA-mediated pathway in sweet potato. more....


Signal transduction and regulation of IbpreproHypSys in sweet potato.

Li YC, Wan WL, Lin JS, Kuo YW, King YC, Chen YC, Jeng ST*
Plant Cell Environ. 2016 Feb 29. doi: 10.1111/pce.12729.

Hydroxyproline-rich glycopeptides (HypSys) are small signaling peptides containing 18-20 amino acids. The expression of IbpreproHypSys, encoding the precursor of IbHypSys, was induced in sweet potato (Ipomoea batatas cv. Tainung 57) through wounding and IbHypSys treatments by using jasmonate and H2 O2 . Transgenic sweet potatoes overexpressing (OE) and silencing (RNAi) IbpreproHypSys were created. The expression of the wound-inducible gene ipomoelin (IPO) in the local and systemic leaves of OE plants was stronger than the expression in wild-type (WT) and RNAi plants after wounding. Furthermore, grafting experiments indicated that IPO expression was considerably higher in WT stocks receiving wounding signals from OE than from RNAi scions. However, wounding WT scions highly induced IPO expression in OE stocks. These results indicated that IbpreproHypSys expression contributed toward sending and receiving the systemic signals that induced IPO Hydroxyproline-rich glycopeptides (HypSys) are small signaling peptides containing 18-20 amino acids. The expression of IbpreproHypSys, encoding the precursor of IbHypSys, was induced in sweet potato (Ipomoea batatas cv. Tainung 57) through wounding and IbHypSys treatments by using jasmonate and H2 O2 . Transgenic sweet potatoes overexpressing (OE) and silencing (RNAi) IbpreproHypSys were created. The expression of the wound-inducible gene ipomoelin (IPO) in the local and systemic leaves of OE plants was stronger than the expression in wild-type (WT) and RNAi plants after wounding. Furthermore, grafting experiments indicated that IPO expression was considerably higher in WT stocks receiving wounding signals from OE than from RNAi scions. However, wounding WT scions highly induced IPO expression in OE stocks. These results indicated that IbpreproHypSys expression contributed toward sending and receiving the systemic signals that induced IPO expression. Analyzing the genes involved in the phenylpropanoid pathway demonstrated that lignin biosynthesis was activated after synthetic IbHypSys treatment. IbpreproHypSys expression in sweet potato suppressed Spodoptera litura growth. In conclusion, wounding induced the expression of IbpreproHypSys, whose protein product was processed into IbHypSys. IbHypSys stimulated IbpreproHypSys and IPO expression and enhanced lignin biosynthesis, thus protecting plants from insects. This article is protected by copyright. All rights reserved. more....


The Arabidopsis glutamate receptor-like gene GLR3.6 controls root development by repressing the Kip-related protein gene KRP4.

Singh SK, Chien CT, Chang IF*
J Exp Bot. 2016 Apr;67(6):1853-69. doi: 10.1093/jxb/erv576. Epub 2016 Jan 15.

In Arabidopsis, 20 genes encode putative glutamate receptor-like proteins (AtGLRs). However, the functions of most genes are unknown. In this study, our results revealed that loss of function of AtGLR3.6 (atglr3.6-1) leads to reduced primary root growth and fewer lateral roots, whereas AtGLR3.6 overexpression induced both primary and lateral root growth. The glr3.6-1 mutant exhibited a smaller root meristem size compared with the wild type, indicating that AtGLR3.6 controls root meristem size. In addition, atglr3.6-1 roots show a decreased mitotic activity accounting for the reduced root meristem size. Furthermore, expression of a gene encoding a cell cycle inhibitor, the cyclin-dependent kinase (CDK) inhibitor Kip-related protein 4 (KRP4), was significantly up-regulated in the mutant and down-regulated in AtGLR3.6-overexpressing roots, suggesting a role for KRP4 in AtGLR3.6-mediated root meristem maintenance. Importantly, the atglr3.6-1 mutant recovered most of its root growth when KRP4 expression is down-regulated, whereas elevated KRP4 expression in AtGLR3.6-overexpressing plants phenocopied the wild-type root growth, implying an underlying relationship between AtGLR3.6 and KRP4 genes. Cytosolic Ca(2+) elevation is reduced in atglr3.6-1 roots, suggesting impaired calcium signaling. Moreover, calcium treatment reduced the level of KRP4 and hence induced root growth. Collectively, we reveal that AtGLR3.6 is required for primary and lateral root development, and KRP4 functions as a downstream signaling element in Arabidopsis thaliana.

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ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47) regulates jasmonic acid and abscisic acid biosynthesis and signaling through binding to a novel cis-element.

Chen HY, Hsieh EJ, Cheng MC, Chen CY, Hwang SY, Lin TP*
New Phytol. 2016 Mar 8. doi: 10.1111/nph.13914.

ORA47 (octadecanoid-responsive AP2/ERF-domain transcription factor 47) of Arabidopsis thaliana is an AP2/ERF domain transcription factor that regulates jasmonate (JA) biosynthesis and is induced by methyl JA treatment. The regulatory mechanism of ORA47 remains unclear. ORA47 is shown to bind to the cis-element (NC/GT)CGNCCA, which is referred to as the O-box, in the promoter of ABI2. We proposed that ORA47 acts as a connection between ABA INSENSITIVE1 (ABI1) and ABI2 and mediates an ABI1-ORA47-ABI2 positive feedback loop. PORA47:ORA47-GFP transgenic plants were used in a chromatin immunoprecipitation (ChIP) assay to show that ORA47 participates in the biosynthesis and/or signaling pathways of nine phytohormones. Specifically, many abscisic acid (ABA) and JA biosynthesis and signaling genes were direct targets of ORA47 under stress conditions. The JA content of the P35S:ORA47-GR lines was highly induced under wounding and moderately induced under water stress relative to that of the wild-type plants. The wounding treatment moderately increased ABA accumulation in the transgenic lines, whereas the water stress treatment repressed the ABA content. ORA47 is proposed to play a role in the biosynthesis of JA and ABA and in regulating the biosynthesis and/or signaling of a suite of phytohormone genes when plants are subjected to wounding and water stress. more....


A Low Glutathione Redox State Couples with a Decreased Ascorbate Redox Ratio to Accelerate Flowering in Oncidium Orchid

Chin DC, Hsieh CC, Lin HY, Yeh KW*
Plant Cell Physiol. 2016 Feb;57(2):423-36. doi: 10.1093/pcp/pcv206.

Glutathione (GSH) plays multiple roles in plants, including stress defense and regulation of growth/development. Previous studies have demonstrated that the ascorbate (AsA) redox state is involved in flowering initiation in Oncidium orchid. In this study, we discovered that a significantly decreased GSH content and GSH redox ratio are correlated with a decline in the AsA redox state during flowering initiation and high ambient temperature-induced flowering. At the same time, the expression level and enzymatic activity of GSH redox-regulated genes, glutathione reductase (GR1), and the GSH biosynthesis genes γ-glutamylcysteine synthetase (GSH1) and glutathione synthase (GSH2), are down-regulated. Elevating dehydroascorbate (DHA) content in Oncidium by artificial addition of DHA resulted in a decreased AsA and GSH redox ratio, and enhanced dehydroascorbate reductase (DHAR) activity. This demonstrated that the lower GSH redox state could be influenced by the lower AsA redox ratio. Moreover, exogenous application of buthionine sulfoximine (BSO), to inhibit GSH biosynthesis, and glutathione disulfide (GSSG), to decrease the GSH redox ratio, also caused early flowering. However, spraying plants with GSH increased the GSH redox ratio and delayed flowering. Furthermore, transgenic Arabidopsis overexpressing Oncidium GSH1, GSH2 and GR1 displayed a high GSH redox ratio as well as delayed flowering under high ambient temperature treatment, while pad2, cad2 and gr1 mutants exhibited early flowering and a low GSH redox ratio. In conclusion, our results provide evidence that the decreased GSH redox state is linked to the decline in the AsA redox ratio and mediated by down-regulated expression of GSH metabolism-related genes to affect flowering time in Oncidium orchid.

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Ethylene response factors in Arabidopsis immunity.

Huang PY, Catinot J and Zimmerli L*
Journal of Experimental Botany. 2015 (online preview doi:10.1093/jxb/erv518)

Pathogen attack leads to transcriptional changes and metabolic modifications allowing the establishment of appropriate plant defences. Transcription factors (TFs) are key players in plant innate immunity. Notably, ethylene response factor (ERF) TFs are integrators of hormonal pathways and are directly responsible for the transcriptional regulation of several jasmonate (JA)/ethylene (ET)-responsive defence genes. Transcriptional activation or repression by ERFs is achieved through the binding to JA/ET-responsive gene promoters. In this review, we describe the regulation and mode of action at a molecular level of ERFs involved in Arabidopsis thaliana immunity. In particular, we focus on defence activators such as ERF1, ORA59, ERF6, and the recently described ERF96. more....


Modification of flower colour by suppressing β-ring carotene hydroxylase genes in Oncidium.

Wang HM, To KY, Lai HM and Jeng ST *
Plant Biol (Stuttg). 2015 Sep 25. doi: 10.1111/plb.12399.

Oncidium 'Gower Ramsey' (Onc. GR) is a popular cut flower, but its colour is limited to bright yellow. The β-ring carotene hydroxylase (BCH2) gene is involved in carotenoid biogenesis for pigment formation. However, the role of BCH2 in Onc. GR is poorly understood. Here, we investigated the functions of three BCH2 genes, BCH-A2, BCH-B2 and BCH-C2 isolated from Onc. GR, to analyse their roles in flower colour. RT-PCR expression profiling suggested that BCH2 was mainly expressed in flowers. The expression of BCH-B2 remained constant while that of BCH-A2 gradually decreased during flower development. Using Agrobacterium tumefaciens to introduce BCH2 RNA interference (RNAi), we created transgenic Oncidium plants with down-regulated BCH expression. In the transgenic plants, flower colour changed from the bright yellow of the wild type to light and white-yellow. BCH-A2 and BCH-B2 expression levels were significantly reduced in the transgenic flower lips, which make up the major portion of the Oncidium flower. Sectional magnification of the flower lip showed that the amount of pigmentation in the papillate cells of the adaxial epidermis was proportional to the intensity of yellow colouration. HPLC analyses of the carotenoid composition of the transgenic flowers suggested major reductions in neoxanthin and violaxanthin. In conclusion, BCH2 expression regulated the accumulation of yellow pigments in the Oncidium flower, and the down-regulation of BCH-A2 and BCH-B2 changed the flower colour from bright yellow to light and white-yellow. more....


Increased glutathione contributes to stress tolerance and global translational changes in Arabidopsis.

Cheng MC, Ko K, Chang WL, Kuo WC, Chen GH and Lin TP*.
Plant J. 2015 Sep;83(5):926-39. doi: 10.1111/tpj.12940.

Although glutathione is well known for its reactive oxygen species (ROS) scavenging function and plays a protective role in biotic stress, its regulatory function in abiotic stress still remains to be elucidated. Our previous study showed that exogenously applied reduced glutathione (GSH) could improve abiotic stress tolerance in Arabidopsis. Here, we report that endogenously increased GSH also conferred tolerance to drought and salt stress in Arabidopsis. Moreover, both exogenous and endogenous GSH delayed senescence and flowering time. Polysomal profiling results showed that global translation was enhanced after GSH treatment and by the induced increase of GSH level by salt stress. By performing transcriptomic analyses of steady-state and polysome-bound mRNAs in GSH-treated plants, we reveal that GSH has a substantial impact on translation. Translational changes induced by GSH treatment target numerous hormones and stress signaling molecules, which might contribute to the enhanced stress tolerance in GSH-treated plants. Our translatome analysis also revealed that abscisic acid (ABA), auxin and jasmonic acid (JA) biosynthesis, as well as signaling genes, were activated during GSH treatment, which has not been reported in previously published transcriptomic data. Together, our data suggest that the increased glutathione level results in stress tolerance and global translational changes. more....


Significance Statement
The mechanisms by which recued glutathione (GSH) treatment leads to increased abiotic stress are poorly understood. Here we show that GSH treatment leads to translational changes of numerous hormones and stress signaling molecules, which might contribute to enhanced stress tolerance and growth.


Functional Assignment to Positively Selected Sites in the Core Type III Effector RipG7 from Ralstonia solanacearum.

Wang K, Remigi P, Anisimova M, Lonjon F, Kars I, Kajava A, Li CH, Cheng CP, Vailleau F, Genin S and Peeters N.
Molecular Plant Pathology. 2015. (Accepted doi: 10.1111/mpp.12302)

The soil-borne pathogen Ralstonia solanacearum causes bacterial wilt in a broad range of plants. The main virulence determinants of R.?solanacearum are the Type III Secretion System (T3SS) and its associated Type III Effectors (T3Es), translocated into the host cells. Among the conserved T3Es among R.?solanacearum strains, The Fbox protein RipG7 is required for R.?solanacearum pathogenesis on Medicago truncatula. In this work we describe the existing natural ripG7 variability existing in the R.?solanacearum species complex. We show that eight representative ripG7 orthologs have different contributions to pathogenicity on M. truncatula: only ripG7 from Asian or African strains can complement the absence of ripG7 in GMI1000 (Asian reference strain). Nonetheless, RipG7 proteins from American and Indonesian strains can still interact with M.?truncatula SKP1-like/MSKa protein, essential for the function of RipG7 in virulence. This indicates that the absence of complementation is most likely due to variability in the leucine-rich repeat domain (LRR) of RipG7. We identified eleven sites under positive selection in the LRR domains of RipG7. By studying the functional impact of those 11 sites, we show the contribution of 5 positively selected sites for the function of RipG7CMR15 in Medicago truncatula colonization. This work reveals the genetic and functional variation of the essential core T3E RipG7 from R.?solanacearum. This analysis is the first of its kind on an essential disease-controlling type III effector and sheds light on the co-evolutionary arms race between the bacterium and its hosts. more....


Far-red light-mediated seedling development in Arabidopsis involves FAR-RED INSENSITIVE 219/JASMONATE RESISTANT 1-dependent and –independent Pathways

Chen HJ, Chen CL and Hsieh HL *.
PLoS One. 2015 Jul 15;10(7):e0132723. doi: 10.1371/journal.pone.0132723.

Plant growth and development is often regulated by the interaction of environmental factors such as light and various phytohormones. Arabidopsis FAR-RED INSENSITIVE 219 (FIN219)/JASMONATE RESISTANT 1 (JAR1) participates in phytochrome A-mediated far-red (FR) light signaling and interacts with different light signaling regulators. FIN219/JAR1 is a jasmonic acid (JA)-conjugating enzyme responsible for the formation of JA-isoleucine. However, how FIN219/JAR1 integrates FR light and JA signaling remains largely unknown. We used a microarray approach to dissect the effect of fin219 mutation on the interaction of FR light and JA signaling. The fin219-2 mutant was less sensitive than the wild type to various concentrations of methyl jasmonate (MeJA) under low and high FR light. High FR light reduced the sensitivity of Arabidopsis seedlings to MeJA likely through FIN219. Intriguingly, in response to MeJA, FIN219 levels showed a negative feedback regulation. Further microarray assay revealed that FR light could regulate gene expression by FIN219-dependent or -independent pathways. The expression profiles affected in fin219-2 indicated that FIN219/JAR1 plays a critical role in the integration of multiple hormone-related signaling. In particular, FIN219 regulates a number of transcription factors (TFs), including 94 basic helix-loop-helix (bHLH) TFs, in response to FR light and MeJA. Loss-of-function mutants of some bHLH TFs affected by FIN219 showed altered responses to MeJA in the regulation of hypocotyl and root elongation. Thus, FIN219/JAR1 is tightly regulated in response to exogenous MeJA. It also interacts with multiple plant hormones to modulate hypocotyl and root elongation of Arabidopsis seedlings likely by regulating a group of TFs. more....


ETHYLENE RESPONSE FACTOR 96 positively regulates Arabidopsis resistance to necrotrophic pathogens by direct binding to GCC elements of jasmonate - and ethylene-responsive defence genes.

Catinot J, Huang JB, Huang PY, Tseng MY, Chen YL, Gu SY, Lo WS, Wang LC, Chen YR and Zimmerli L*.
Plant Cell Environ. (2015) 38, 2721-2734. doi: 10.1111/pce.12583.

The ERF (ethylene responsive factor) family is composed of transcription factors (TFs) that are critical for appropriate Arabidopsis thaliana responses to biotic and abiotic stresses. Here we identified and characterized a member of the ERF TF group IX, namely ERF96, that when overexpressed enhances Arabidopsis resistance to necrotrophic pathogens such as the fungus Botrytis cinerea and the bacterium Pectobacterium carotovorum. ERF96 is jasmonate (JA) and ethylene (ET) responsive and ERF96 transcripts accumulation was abolished in JA-insensitive coi1-16 and in ET-insensitive ein2-1 mutants. Protoplast transactivation and electrophoresis mobility shift analyses revealed that ERF96 is an activator of transcription that binds to GCC elements. In addition, ERF96 mainly localized to the nucleus. Microarray analysis coupled to chromatin immunoprecipitation-PCR of Arabidopsis overexpressing ERF96 revealed that ERF96 enhances the expression of the JA/ET defence genes PDF1.2a, PR-3 and PR-4 as well as the TF ORA59 by direct binding to GCC elements present in their promoters. While ERF96-RNAi plants demonstrated wild-type resistance to necrotrophic pathogens, basal PDF1.2 expression levels were reduced in ERF96-silenced plants. This work revealed ERF96 as a key player of the ERF network that positively regulates the Arabidopsis resistance response to necrotrophic pathogens. more....


Engineered xylose utilization enhances bio-products productivity in the cyanobacterium Synechocystis sp. PCC 6803.

Lee TC, Xiong W, Paddock T, Carrieri D, Chang IF, Chiu HF, Ungerer J, Juo SH*, Maness PC* and Yu J*.
Metabolic Engineering. 2015; 30: 179-189.

Hydrolysis of plant biomass generates a mixture of simple sugars that is particularly rich in glucose and xylose. Fermentation of the released sugars emits CO2 as byproduct due to metabolic inefficiencies. Therefore, the ability of a microbe to simultaneously convert biomass sugars and photosynthetically fix CO2 into target products is very desirable. In this work, the cyanobacterium, Synechocystis 6803, was engineered to grow on xylose in addition to glucose. Both the xylA (xylose isomerase) and xylB (xylulokinase) genes from Escherichia coli were required to confer xylose utilization, but a xylose-specific transporter was not required. Introduction of xylAB into an ethylene-producing strain increased the rate of ethylene production in the presence of xylose. Additionally, introduction of xylAB into a glycogen-synthesis mutant enhanced production of keto acids. Isotopic tracer studies found that nearly half of the carbon in the excreted keto acids was derived from the engineered xylose metabolism, while the remainder was derived from CO2 fixation. more....


The Arabidopsis SWI2/SNF2 chromatin remodeling ATPase BRAHMA targets directly to pins and is required for root stem cell niche maintenance.

Yang S, Li C, Zhao L, Gao S, Lu J, Zhao M, Chen C, Liu X, Luo M, Cui Yu, Yang C and Wu K*.
The Plant Cell. 2015 Jun;27(6):1670-80.

BRAHMA (BRM), a SWI/SNF chromatin remodeling ATPase, is essential for the transcriptional reprogramming associated with development and cell differentiation in Arabidopsis thaliana. In this study, we show that loss-of-function mutations in BRM led to defective maintenance of the root stem cell niche, decreased meristematic activity, and stunted root growth. Mutations of BRM affected auxin distribution by reducing local expression of several PIN-FORMED (PIN) genes in the stem cells and impaired the expression of the stem cell transcription factor genes PLETHORA (PLT1) and PLT2. Chromatin immunoprecipitation assays showed that BRM could directly target to the chromatin of PIN1, PIN2, PIN3, PIN4, and PIN7. In addition, genetic interaction assays indicate that PLTs acted downstream of BRM, and overexpression of PLT2 partially rescued the stem cell niche defect of brm mutants. Taken together, these results support the idea that BRM acts in the PLT pathway to maintain the root stem cell niche by altering the expression of PINs. more....


Regulation of flowering time by the histone deacetylase HDA5 in Arabidopsis.

Luo M, Tai R, Yu CW, Yang S, Chen C, Lin WD, Wolfgan S and Wu K*.
The Plant Journal. 2015 Jun;82(6):925-36.

The acetylation level of histones on lysine residues regulated by histone acetyltransferases and histone deacetylases plays an important but under-studied role in the control of gene expression in plants. With the aim of characterizing the Arabidopsis RPD3/HDA1 family histone deacetylase HDA5, we present evidence showing that HDA5 displays deacetylase activity. Mutants defective in the expression of HDA5 displayed a late-flowering phenotype. Expression of the flowering repressor genes FLC and MAF1 was up-regulated in hda5 mutants. Furthermore, the gene activation markers, histone H3 acetylation and H3K4 trimethylation on FLC and MAF1 chromatin were increased in hda5-1 mutants. Chromatin immunoprecipitation analysis showed that HDA5 binds to the chromatin of FLC and MAF1. Bimolecular fluorescence complementation assays and co-immunoprecipitation assays showed that HDA5 interacts with FVE, FLD and HDA6, indicating that these proteins are present in a protein complex involved in the regulation of flowering time. Comparing gene expression profiles of hda5 and hda6 mutants by RNA-seq revealed that HDA5 and HDA6 co-regulate gene expression in multiple development processes and pathways. more....


Enhanced Arabidopsis pattern-triggered immunity by overexpression of cysteine-rich receptor-like kinases.

Yeh YH, Chang YH, Huang PY, Huang JB and Zimmerli L*.
Front Plant Sci. 2015 May 12;6:322. doi: 10.3389/fpls.2015.00322. eCollection 2015.

Upon recognition of microbe-associated molecular patterns (MAMPs) such as the bacterial flagellin (or the derived peptide flg22) by pattern-recognition receptors (PRRs) such as the FLAGELLIN SENSING2 (FLS2), plants activate the pattern-triggered immunity (PTI) response. The L-type lectin receptor kinase-VI.2 (LecRK-VI.2) is a positive regulator of Arabidopsis thaliana PTI. Cysteine-rich receptor-like kinases (CRKs) possess two copies of the C-X8-C-X2-C (DUF26) motif in their extracellular domains and are thought to be involved in plant stress resistance, but data about CRK functions are scarce. Here, we show that Arabidopsis overexpressing the LecRK-VI.2-responsive CRK4, CRK6, and CRK36 demonstrated an enhanced PTI response and were resistant to virulent bacteria Pseudomonas syringae pv. tomato DC3000. Notably, the flg22-triggered oxidative burst was primed in CRK4, CRK6, and CRK36 transgenics and up-regulation of the PTI-responsive gene FLG22-INDUCED RECEPTOR-LIKE 1 (FRK1) was potentiated upon flg22 treatment in CRK4 and CRK6 overexpression lines or constitutively increased by CRK36 overexpression. PTI-mediated callose deposition was not affected by overexpression of CRK4 and CRK6, while CRK36 overexpression lines demonstrated constitutive accumulation of callose. In addition, Pst DC3000-mediated stomatal reopening was blocked in CRK4 and CRK36 overexpression lines, while overexpression of CRK6 induced constitutive stomatal closure suggesting a strengthening of stomatal immunity. Finally, bimolecular fluorescence complementation and co-immunoprecipitation analyses in Arabidopsis protoplasts suggested that the plasma membrane localized CRK4, CRK6, and CRK36 associate with the PRR FLS2. Association with FLS2 and the observation that overexpression of CRK4, CRK6, and CRK36 boosts specific PTI outputs and resistance to bacteria suggest a role for these CRKs in Arabidopsis innate immunity. more....


Molecular characterization of fruit-specific class III peroxidase genes in tomato (Solanum lycopersicum).

Chii-Jeng Wang, Yuan-Li Chan, Chin Hui Shien and Kai-Wun Yeh*.
Journal of Plant Physiology doi:10.1016/j.jplph.2015.01.011

In this study, expression of four peroxidase genes, LePrx09, LePrx17, LePrx35 and LePrxA, was identified in immature tomato fruits, and the function in the regulation of fruit growth was characterized. Analysis of amino acid sequences revealed that these genes code for class III peroxidases, containing B, D and F conserved domains, which bind heme groups, and a buried salt bridge motif. LePrx35 and LePrxA were identified as novel peroxidase genes in Solanum lycopersicum (L.). The temporal expression patterns at various fruit growth stages revealed that LePrx35 and LePrxA were expressed only in IMG fruits, whereas LePrx17 and LePrx09 were expressed in both immature and mature green fruits. Tissue-specific expression profiles indicated that only LePrx09 was expressed in the mesocarp but not the inner tissue of immature fruits. The effects of hormone treatments and stresses on the four genes were examined; only the expression levels of LePrx17 and LePrx09 were altered. Transcription of LePrx17 was up-regulated by jasmonic acid (JA) and pathogen infection and expression of LePrx09 was induced by ethephon, salicylic acid (SA) and JA, in particular, as well as wounding, pathogen infection and H2O2 stress. Tomato plants over-expressing LePrx09 displayed enhanced resistance to H2O2 stress, suggesting that LePrx09 may participate in the H2O2 signaling pathway to regulate fruit growth and disease resistance in tomato fruits. more....

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本所為首屈一指的植物科學研究與教學之重鎮,以建立本土性的植物科學與技術研究基礎為首務,並大步邁向國際級的科技研究水準,歡迎主動積極有志於植物科學的年輕學子加入研究陣容。


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