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1.  Airborne signals from salt-stressed Arabidopsis plants trigger salinity tolerance in neighboring plants 
Plant Signaling & Behavior  2014;9:e28392.
Plants have evolved sophisticated defense mechanisms to overcome their sessile nature. One remarkable strategy is the inter-plant communication mediated by volatile organic compounds (VOCs). Quantity and quality of plant VOCs are intricately regulated by biotic and abiotic stresses, and the alterations facilitate plant community to optimize their growth, development, and endogenous physiology to environmental fluctuations. Here, we report that Arabidopsis thaliana plants that experience high salinity emit VOCs and trigger induction of high salt resistance in neighboring plants. VOC emission of emitter plants is likely correlative to the plant damages to high salt, and VOC-fumigated receiver plants acquire high salt tolerance. The VOC-induced stress tolerance is independent of conventional abscisic acid (ABA) and salt stress signaling pathways. Together, this study demonstrates that salt-induced Arabidopsis VOCs are relevant in priming stress tolerance in neighboring plants. In addition, it also provides insight into how VOCs elicit stress responses in plant community.
doi:10.4161/psb.28392
PMCID: PMC4091499  PMID: 24603614
Arabidopsis; chemical ecology; priming; salt stress; volatile organic compound
2.  A Competitive Peptide Inhibitor KIDARI Negatively Regulates HFR1 by Forming Nonfunctional Heterodimers in Arabidopsis Photomorphogenesis 
Molecules and Cells  2012;35(1):25-31.
Dynamic dimer formation is an elaborate means of modulating transcription factor activities in diverse cellular processes. The basic helix-loop-helix (bHLH) transcription factor LONG HYPOCOTYL IN FAR-RED 1 (HFR1), for example, plays a role in plant photomorphogenesis by forming non-DNA binding heterodimers with PHYTOCHROME-INTERACTING FACTORS (PIFs). Recent studies have shown that a small HLH protein KIDARI (KDR) negatively regulates the HFR1 activity in the process. However, molecular mechanisms underlying the KDR control of the HFR1 activity are unknown. Here, we demonstrate that KDR attenuates the HFR1 activity by competitively forming nonfunctional heterodimers, causing liberation of PIF4 from the transcriptionally inactive HFR1-PIF4 complex. Accordingly, the photomorphogenic hypocotyl growth of the HFR1-overexpres-sing plants can be suppressed by KDR coexpression, as observed in the HFR1-deficient hfr1-201 mutant. These results indicate that the PIF4 activity is modulated through a double layer of competitive inhibition by HFR1 and KDR, which could in turn ensure fine-tuning of the PIF4 activity under fluctuating light conditions.
doi:10.1007/s10059-013-2159-2
PMCID: PMC3887847  PMID: 23224238
Arabidopsis; competitive inhibition; KIDARI (KDR); light signaling; LONG HYPOCOTYL IN FAR-RED 1 (HFR1); PHYTOCHROME-INTERACTING FACTOR (PIF)
3.  Natural variation in floral nectar proteins of two Nicotiana attenuata accessions 
BMC Plant Biology  2013;13:101.
Background
Floral nectar (FN) contains not only energy-rich compounds to attract pollinators, but also defense chemicals and several proteins. However, proteomic analysis of FN has been hampered by the lack of publically available sequence information from nectar-producing plants. Here we used next-generation sequencing and advanced proteomics to profile FN proteins in the opportunistic outcrossing wild tobacco, Nicotiana attenuata.
Results
We constructed a transcriptome database of N. attenuata and characterized its nectar proteome using LC-MS/MS. The FN proteins of N. attenuata included nectarins, sugar-cleaving enzymes (glucosidase, galactosidase, and xylosidase), RNases, pathogen-related proteins, and lipid transfer proteins. Natural variation in FN proteins of eleven N. attenuata accessions revealed a negative relationship between the accumulation of two abundant proteins, nectarin1b and nectarin5. In addition, microarray analysis of nectary tissues revealed that protein accumulation in FN is not simply correlated with the accumulation of transcripts encoding FN proteins and identified a group of genes that were specifically expressed in the nectary.
Conclusions
Natural variation of identified FN proteins in the ecological model plant N. attenuata suggests that nectar chemistry may have a complex function in plant-pollinator-microbe interactions.
doi:10.1186/1471-2229-13-101
PMCID: PMC3728157  PMID: 23848992
LC-MS/MS; Nectar protein; Nectarin; Nicotiana attenuata
4.  Alternative splicing of transcription factors in plant responses to low temperature stress: mechanisms and functions 
Planta  2013;237(6):1415-1424.
Transcription factors play a central role in the gene regulatory networks that mediate various aspects of plant developmental processes and responses to environmental changes. Therefore, their activities are elaborately regulated at multiple steps. In particular, accumulating evidence illustrates that post-transcriptional control of mRNA metabolism is a key molecular scheme that modulates the transcription factor activities in plant responses to temperature fluctuations. Transcription factors have a modular structure consisting of distinct protein domains essential for DNA binding, dimerization, and transcriptional regulation. Alternative splicing produces multiple proteins having different structural domain compositions from a single transcription factor gene. Recent studies have shown that alternative splicing of some transcription factor genes generates small interfering peptides (siPEPs) that negatively regulate the target transcription factors via peptide interference (PEPi), constituting self-regulatory circuits in plant cold stress response. A number of splicing factors, which are involved in RNA binding, splice site selection, and spliceosome assembly, are also affected by temperature fluctuations, supporting the close association of alternative splicing of transcription factors with plant responses to low temperatures. In this review, we summarize recent progress on the temperature-responsive alternative splicing of transcription factors in plants with emphasis on the siPEP-mediated PEPi mechanism.
doi:10.1007/s00425-013-1882-4
PMCID: PMC3664756  PMID: 23624977
Alternative splicing; Arabidopsis; Cold stress; Peptide interference (PEPi); Small interfering peptide (siPEP); Splicing factor; Transcription factor
5.  CCA1 alternative splicing as a way of linking the circadian clock to temperature response in Arabidopsis 
Plant Signaling & Behavior  2012;7(9):1194-1196.
Most living organisms on the earth have the circadian clock to synchronize their biochemical processes and physiological activities with environmental changes to optimize their propagation and survival. CIRCADIAN CLOCK-ASSOCIATED1 (CCA1) is one of the core clock components in Arabidopsis. Notably, it is also associated with cold acclimation. However, it is largely unknown how CCA1 activity is modulated by low temperatures. We found that the CCA1 activity is self-regulated by a splice variant CCA1β and the CCA1β production is modulated by low temperatures, linking the circadian clock with cold acclimation. CCA1β competitively inhibits the activities of functional CCA1α and LATE ELONGATED HYPOCOTYL (LHY) transcription factors by forming nonfunctional CCA1α-CCA1β and LHY-CCA1β heterodimers. Consequently, CCA1β-overexpressing plants (35S:CCA1β) exhibit shortened circadian periods as observed in cca1 lhy double mutants. In addition, elongated hypocotyls and petioles and delayed flowering of CCA1α-overexpressing plants (35S:CCA1α) were rescued by coexpression of CCA1β. Interestingly, low temperatures suppress CCA1 alternative splicing and thus derepress the CCA1α activity in inducing cold tolerance. These observations indicate that a cold-responsive self-regulatory circuit of CCA1 plays a role in plant responses to low temperatures.
doi:10.4161/psb.21300
PMCID: PMC3489659  PMID: 22899064
alternative splicing; Arabidopsis; CCA1; circadian clock; cold acclimation; freezing tolerance
6.  The Floral Repressor BROTHER OF FT AND TFL1 (BFT) Modulates Flowering Initiation under High Salinity in Arabidopsis 
Molecules and Cells  2011;32(3):295-303.
Floral transition is coordinately regulated by both endogenous and exogenous cues to ensure reproductive success under fluctuating environmental conditions. Abiotic stress conditions, including drought and high salinity, also have considerable influence on this developmental process. However, the signaling components and molecular mechanisms underlying the regulation of floral transition by environmental factors have not yet been defined. In this work, we show that the Arabidopsis BROTHER OF FT AND TFL1 (BFT) gene, which encodes a member of the FLOWERING LOCUS T (FT)/TERMINAL FLOWER 1 (TFL1) family, regulates floral transition under conditions of high salinity. The BFT gene was transcriptionally induced by high salinity in an abscisic acid (ABA)-dependent manner. Transgenic plants overexpressing the BFT gene (35S:BFT) and BFT-deficient mutant (bft-2) plants were phenotypically indistinguishable from Col-0 plants in seed germination and seedling growth under high salinity. In contrast, although the floral transition was delayed significantly in Col-0 plants under high salinity, that of the bft-2 mutant was not affected by high salinity. We also observed that expression of the APETALA1 (AP1) gene was suppressed to a lesser degree in the bft-2 mutant than in Col-0 plants. Taken together, our observations suggest that BFT mediates salt stress-responsive flowering, providing an adaptive strategy that ensures reproductive success under unfavorable stress conditions.
doi:10.1007/s10059-011-0112-9
PMCID: PMC3887636  PMID: 21809215
abscisic acid; Arabidopsis; BFT; flowering; salt stress
7.  Identification and characterization of circadian clock genes in a native tobacco, Nicotiana attenuata 
BMC Plant Biology  2012;12:172.
Background
A plant’s endogenous clock (circadian clock) entrains physiological processes to light/dark and temperature cycles. Forward and reverse genetic approaches in Arabidopsis have revealed the mechanisms of the circadian clock and its components in the genome. Similar approaches have been used to characterize conserved clock elements in several plant species. A wild tobacco, Nicotiana attenuata has been studied extensively to understand responses to biotic or abiotic stress in the glasshouse and also in their native habitat. During two decades of field experiment, we observed several diurnal rhythmic traits of N. attenuata in nature. To expand our knowledge of circadian clock function into the entrainment of traits important for ecological processes, we here report three core clock components in N. attenuata.
Results
Protein similarity and transcript accumulation allowed us to isolate orthologous genes of the core circadian clock components, LATE ELONGATED HYPOCOTYL (LHY), TIMING OF CAB EXPRESSION 1/PSEUDO-RESPONSE REGULATOR 1 (TOC1/PRR1), and ZEITLUPE (ZTL). Transcript accumulation of NaLHY peaked at dawn and NaTOC1 peaked at dusk in plants grown under long day conditions. Ectopic expression of NaLHY and NaZTL in Arabidopsis resulted in elongated hypocotyl and late-flowering phenotypes. Protein interactions between NaTOC1 and NaZTL were confirmed by yeast two-hybrid assays. Finally, when NaTOC1 was silenced in N. attenuata, late-flowering phenotypes under long day conditions were clearly observed.
Conclusions
We identified three core circadian clock genes in N. attenuata and demonstrated the functional and biochemical conservation of NaLHY, NaTOC1, and NaZTL.
doi:10.1186/1471-2229-12-172
PMCID: PMC3489836  PMID: 23006446
Circadian clock; Flowering time; NaLHY; NaTOC1; NaZTL; Nicotiana attenuata; Protein interaction
8.  Activation of a Mitochondrial ATPase Gene Induces Abnormal Seed Development in Arabidopsis 
Molecules and Cells  2011;31(4):361-369.
The ATPases associated with various cellular activities (AAA) proteins are widespread in living organisms. Some of the AAA-type ATPases possess metalloprotease activities. Other members constitute the 26S proteasome complexes. In recent years, a few AAA members have been implicated in vesicle-mediated secretion, membrane fusion, cellular organelle biogenesis, and hypersensitive responses (HR) in plants. However, the physiological roles and biochemical activities of plant AAA proteins have not yet been defined at the molecular level, and regulatory mechanisms underlying their functions are largely unknown. In this study, we showed that overexpression of an Arabidopsis gene encoding a mitochondrial AAA protein, ATPase-in-Seed-Development (ASD), induces morphological and anatomical defects in seed maturation. The ASD gene is expressed at a high level during the seed maturation process and in mature seeds but is repressed rapidly in germinating seeds. Transgenic plants overexpressing the ASD gene are morphologically normal. However, seed formation is severely disrupted in the transgenic plants. The ASD gene is induced by abiotic stresses, such as low temperatures and high salinity, in an abscisic acid (ABA)- dependent manner. The ASD protein possesses ATPase activity and is localized into the mitochondria. Our observations suggest that ASD may play a role in seed maturation by influencing mitochondrial function under abiotic stress.
doi:10.1007/s10059-011-0048-0
PMCID: PMC3933970  PMID: 21359673
AAA-type ATPase; abiotic stress; abscisic acid; Arabidopsis; seed development
9.  Signaling linkage between environmental stress resistance and leaf senescence in Arabidopsis 
Plant Signaling & Behavior  2011;6(10):1564-1566.
Plants possess versatile strategies that permit efficient use of limited nutrient resources during senescing process. This metabolic adjustment is critical for prevention of diverse cellular damage and thus for reproductive success and offspring production, particularly under environmental stress conditions. However, it is largely unknown how age-dependent resistance to cellular damages is established and how it is influenced by environmental stress signals during senescing process. We found that the VNI2 (VND-INTERACTING 2) transcription factor, which belongs to the NAC (NAM/ATAF1, 2/CUC2) transcription factor family, plays a role in the age-dependent induction of stress resistance. The VNI2 transcription factor is transcriptionally induced during senescing process and regulates COR/RD genes by binding directly to their promoters. The COR/RD proteins play a role in the protection from diverse cellular damages during senescing process. Notably, the transcriptional activation activity of VNI2 is further elevated under high salinity. These results indicate that plants increase environmental stress resistance by inducing the VNI2 gene to assure their reproductive success, supporting signaling crosstalk between stress resistance response and senescing process.
doi:10.4161/psb.6.10.17003
PMCID: PMC3256385  PMID: 21921691
abscisic acid; arabidopsis; COR/RD; salt stress; senescence; VNI2
10.  Cuticular wax biosynthesis as a way of inducing drought resistance 
Plant Signaling & Behavior  2011;6(7):1043-1045.
Plants have evolved diverse adaptive strategies to cope with drought or water deficit conditions, such as stomatal closure, maintenance of root growth and water uptake, and biosynthesis of osmoprotectants. Accumulation of cuticular waxes also contributes to drought resistance. However, it is still unclear how cuticular wax biosynthesis is regulated in response to drought and how it is associated with plant responses to drought at the molecular level. The abscisic acid (ABA)-inducible MYB96 transcription factor plays a role in drought resistance. Notably, it also regulates cuticular wax biosynthesis by binding directly to the promoters of genes encoding fatty acid elongating enzymes, such as KCS, KCR and ECR that constitute a rate-limiting step in cuticular wax biosynthesis. In the myb96-1D mutant that constitutively express the MYB96 gene, many of genes involved in cuticular wax biosynthesis are upregulated and accordingly, cuticular wax accumulation is greatly elevated. In contrast, cuticular wax accumulation is reduced in the myb96-1 mutant, linking drought with cuticular wax biosynthesis. It is evident that the MYB96 transcription factor incorporates drought stress signals into a gene regulatory network that modulates cuticular wax biosynthesis under drought stress conditions, providing a first molecular mechanism by which cuticular wax biosynthesis contributes to drought resistance and protection from pathogenic and mechanical damages as well.
doi:10.4161/psb.6.7.15606
PMCID: PMC3257791  PMID: 21617381
abscisic acid; alkane biosynthesis; arabidopsis; cuticular wax; drought; MYB96
11.  Auxin homeostasis during lateral root development under drought condition 
Plant Signaling & Behavior  2009;4(10):1002-1004.
Lateral root formation is a critical agronomic trait in plant architecture that determines crop productivity and environmental stress adaptability. It is therefore tightly regulated both by intrinsic developmental cues, such as abscisic acid (ABA) and auxin, and by diverse environmental growth conditions, including water deficit and high salinity in the soil. We have recently reported that an Arabidopsis R2R3-type MYB transcription factor, MYB96, regulates lateral root meristem activation under drought conditions via an ABA-auxin signaling crosstalk. In this signaling scheme, the MYB96-mediated ABA signals are incorporated into an auxin signaling pathway that involves a subset of GH3 gene encoding auxin-conjugating enzymes. The MYB96-overexpressing, activation tagging mutant, which is featured by having dwarfed growth and reduced lateral root formation, exhibits an enhanced drought resistance. In the mutant, expression of the GH3 genes was significantly elevated, which is consistent with the reduced lateral root formation. In contrast, the MYB96-deficient knockout mutant produced more lateral roots and was more susceptible to drought stress. Our observations strongly support that MYB96 is a molecular link that integrates ABA and auxin signals in modulating auxin homeostasis during lateral root development, particularly under water deficit conditions. It is also envisioned that the MYB96-mediated signals are related with pathogen resistance response, which is also profoundly affected by water content in plant cells.
PMCID: PMC2801374  PMID: 19826230
arabidopsis; abscisic acid; auxin homeostasis; lateral root; MYB; GH3; drought
12.  Exploring valid reference genes for gene expression studies in Brachypodium distachyon by real-time PCR 
BMC Plant Biology  2008;8:112.
Background
The wild grass species Brachypodium distachyon (Brachypodium hereafter) is emerging as a new model system for grass crop genomics research and biofuel grass biology. A draft nuclear genome sequence is expected to be publicly available in the near future; an explosion of gene expression studies will undoubtedly follow. Therefore, stable reference genes are necessary to normalize the gene expression data.
Results
A systematic exploration of suitable reference genes in Brachypodium is presented here. Nine reference gene candidates were chosen, and their gene sequences were obtained from the Brachypodium expressed sequence tag (EST) databases. Their expression levels were examined by quantitative real-time PCR (qRT-PCR) using 21 different Brachypodium plant samples, including those from different plant tissues and grown under various growth conditions. Effects of plant growth hormones were also visualized in the assays. The expression stability of the candidate genes was evaluated using two analysis software packages, geNorm and NormFinder. In conclusion, the ubiquitin-conjugating enzyme 18 gene (UBC18) was validated as a suitable reference gene across all the plant samples examined. While the expression of the polyubiquitin genes (Ubi4 and Ubi10) was most stable in different plant tissues and growth hormone-treated plant samples, the expression of the S-adenosylmethionine decarboxylase gene (SamDC) ranked was most stable in plants grown under various environmental stresses.
Conclusion
This study identified the reference genes that are most suitable for normalizing the gene expression data in Brachypodium. These reference genes will be particularly useful when stress-responsive genes are analyzed in order to produce transgenic plants that exhibit enhanced stress resistance.
doi:10.1186/1471-2229-8-112
PMCID: PMC2588586  PMID: 18992143
13.  Exploring membrane-associated NAC transcription factors in Arabidopsis: implications for membrane biology in genome regulation 
Nucleic Acids Research  2006;35(1):203-213.
Controlled proteolytic cleavage of membrane-associated transcription factors (MTFs) is an intriguing activation strategy that ensures rapid transcriptional responses to incoming stimuli. Several MTFs are known to regulate diverse cellular functions in prokaryotes, yeast, and animals. In Arabidopsis, a few NAC MTFs mediate either cytokinin signaling during cell division or endoplasmic reticulum (ER) stress responses. Through genome-wide analysis, it was found that at least 13 members of the NAC family in Arabidopsis contain strong α-helical transmembrane motifs (TMs) in their C-terminal regions and are predicted to be membrane-associated. Interestingly, most of the putative NAC MTF genes are up-regulated by stress conditions, suggesting that they may be involved in stress responses. Notably, transgenic studies revealed that membrane release is essential for the function of NAC MTFs. Transgenic plants overexpressing partial-size NAC constructs devoid of the TMs, but not those overexpressing full-size constructs, showed distinct phenotypic changes, including dwarfed growth and delayed flowering. The rice genome also contains more than six NAC MTFs. Furthermore, the presence of numerous MTFs is predicted in the whole transcription factors in plants. We thus propose that proteolytic activation of MTFs is a genome-wide mechanism regulating plant genomes.
doi:10.1093/nar/gkl1068
PMCID: PMC1802569  PMID: 17158162

Results 1-13 (13)