slotreck/pickle huggingface dataset:
The cyclic derivative of 13(S)-hydroperoxolinolenic acid , 12-oxophytodienoic acid , serves as a signal transducer in higher plants , mediating mechanotransductory processes and plant defenses against a variety of pathogens , and also serves as a precursor for the biosynthesis of jasmonic acid , a mediator of plant herbivore defense . Biosynthesis of 12-oxophytodienoic acid from alpha-linolenic acid occurs in plastids , mainly in chloroplasts , and is thought to start with free linolenic acid liberated from membrane lipids by lipase action . In Arabidopsis thaliana , the glycerolipid fraction contains esterified 12-oxophytodienoic acid , which can be released enzymatically by sn1-specific , but not by sn2-specific , lipases . The 12-oxophytodienoyl glycerolipid fraction was isolated , purified , and characterized . Enzymatic , mass spectrometric , and NMR spectroscopic data allowed us to establish the structure of the novel oxylipin as sn1-O-(12-oxophytodienoyl)-sn2-O-(hexadecatrienoyl)-monogalactosyl diglyceride . The novel class of lipids is localized in plastids . Purified monogalactosyl diglyceride was not converted to the sn1-(12-oxophytodienoyl ) derivative by the combined action of ( soybean ) lipoxygenase and ( A. thaliana ) allene oxide synthase , an enzyme ensemble that converts free alpha-linolenic acid to free 12-oxophytodienoic acid . When leaves were wounded , a significant and transient increase in the level of (12-oxophytodienoyl)-monogalactosyl diglyceride was observed . In A. thaliana , the major fraction of 12-oxophytodienoic acid occurs esterified at the sn1 position of the plastid-specific glycerolipid , monogalactosyl diglyceride .
The rice pathogenesis-related protein OsPR10a was scarcely expressed in OsCDPK1-silenced ( Ri-1 ) rice , which was highly sensitive to pathogen infection . After inoculating the leaves with bacterial blight ( Xanthomonas oryzae pv . oryzae ; Xoo ) , we found that the expression of OsPR10a was up- and down-regulated in OEtr-1 ( overexpression of the constitutively active truncated form of OsCDPK1 ) and Ri-1 rice plants , respectively . OsPR10a and OsCDPK1 showed corresponding expression patterns and were up-regulated in response to the jasmonic acid , salicylic acid and Xoo treatments , and OsPR1 and OsPR4 were significantly up-regulated in OEtr-1 . These results suggest that OsCDPK1 may be an upstream regulator involved in rice innate immunity and conferred broad-spectrum of disease resistance . Following the Xoo inoculation , the OEtr-1 and Ri-1 seedlings showed enhanced and reduced disease resistance , respectively . The dihybrid rice Ri-1/OsPR10a-Ox not only bypassed the effect of OsCDPK1 silencing on the susceptibility to Xoo but also showed enhanced disease resistance and , consistent with Ri-1 phenotypes , increased plant height and grain size . Our results reveal that OsCDPK1 plays novel key roles in the cross-talk and mediation of the balance between stress response and development and provides a clue for improving grain yield and disease resistance simultaneously in rice .
Gibberellic acid (GA)-mediated cell expansion initiates the seed-to-seedling transition in plants and is repressed by DELLA proteins . Using digital single-cell analysis , we identified a cellular subdomain within the midhypocotyl , whose expansion drives the final step of this developmental transition under optimal conditions . Using network inference , the transcription factor ATHB5 was identified as a genetic factor whose localized expression promotes GA-mediated expansion specifically within these cells . Both this protein and its putative growth-promoting target EXPANSIN3 are repressed by DELLA , and coregulated at single-cell resolution during seed germination . The cellular domains of hormone sensitivity were explored within the Arabidopsis ( Arabidopsis thaliana ) embryo by putting seeds under GA-limiting conditions and quantifying cellular growth responses . The middle and upper hypocotyl have a greater requirement for GA to promote cell expansion than the lower embryo axis . Under these conditions , germination was still completed following enhanced growth within the radicle and lower axis . Under GA-limiting conditions , the athb5 mutant did not show a phenotype at the level of seed germination , but it did at a cellular level with reduced cell expansion in the hypocotyl relative to the wild type . These data reveal that the spatiotemporal cell expansion events driving this transition are not determinate , and the conditional use of GA-ATHB5-mediated hypocotyl growth under optimal conditions may be used to optionally support rapid seedling growth . This study demonstrates that multiple genetic and spatiotemporal cell expansion mechanisms underlie the seed to seedling transition in Arabidopsis .
Plants respond to stresses by producing a broad spectrum of bioactive specialized metabolites . Hormonal elicitors , such as jasmonates , trigger a complex signaling circuit leading to the concerted activation of specific metabolic pathways . However , for many specialized metabolic pathways , the transcription factors involved remain unknown . Here , we report on two homologous jasmonate-inducible transcription factors of the basic helix-loop-helix family , TRITERPENE SAPONIN BIOSYNTHESIS ACTIVATING REGULATOR1 ( TSAR1 ) and TSAR2 , which direct triterpene saponin biosynthesis in Medicago truncatula . TSAR1 and TSAR2 are coregulated with and transactivate the genes encoding 3-HYDROXY-3-METHYLGLUTARYL-COENZYME A REDUCTASE1 ( HMGR1 ) and MAKIBISHI1 , the rate-limiting enzyme for triterpene biosynthesis and an E3 ubiquitin ligase that controls HMGR1 levels , respectively . Transactivation is mediated by direct binding of TSARs to the N-box in the promoter of HMGR1 . In transient expression assays in tobacco ( Nicotiana tabacum ) protoplasts , TSAR1 and TSAR2 exhibit different patterns of transactivation of downstream triterpene saponin biosynthetic genes , hinting at distinct functionalities within the regulation of the pathway . Correspondingly , overexpression of TSAR1 or TSAR2 in M. truncatula hairy roots resulted in elevated transcript levels of known triterpene saponin biosynthetic genes and strongly increased the accumulation of triterpene saponins . TSAR2 overexpression specifically boosted hemolytic saponin biosynthesis , whereas TSAR1 overexpression primarily stimulated nonhemolytic soyasaponin biosynthesis . Both TSARs also activated all genes of the precursor mevalonate pathway but did not affect sterol biosynthetic genes , pointing to their specific role as regulators of specialized triterpene metabolism in M. truncatula .
Thellungiella , an Arabidopsis ( Arabidopsis thaliana)-related halophyte , is an emerging model species for studies designed to elucidate molecular mechanisms of abiotic stress tolerance . Using a cDNA microarray containing 3,628 unique sequences derived from previously described libraries of stress-induced cDNAs of the Yukon ecotype of Thellungiella salsuginea , we obtained transcript profiles of its response to cold , salinity , simulated drought , and rewatering after simulated drought . A total of 154 transcripts were differentially regulated under the conditions studied . Only six of these genes responded to all three stresses of drought , cold , and salinity , indicating a divergence among the end responses triggered by each of these stresses . Unlike in Arabidopsis , there were relatively few transcript changes in response to high salinity in this halophyte . Furthermore , the gene products represented among drought-responsive transcripts in Thellungiella associate a down-regulation of defense-related transcripts with exposure to water deficits . This antagonistic interaction between drought and biotic stress response may demonstrate Thellungiella 's ability to respond precisely to environmental stresses , thereby conserving energy and resources and maximizing its survival potential . Intriguingly , changes of transcript abundance in response to cold implicate the involvement of jasmonic acid . While transcripts associated with photosynthetic processes were repressed by cold , physiological responses in plants developed at low temperature suggest a novel mechanism for photosynthetic acclimation . Taken together , our results provide useful starting points for more in-depth analyses of Thellungiella 's extreme stress tolerance .
The hormone jasmonate ( JA ) , which functions in plant immunity , regulates resistance to pathogen infection and insect attack through triggering genome-wide transcriptional reprogramming in plants . We show that the basic helix-loop-helix transcription factor ( TF ) MYC2 in tomato ( Solanum lycopersicum ) acts downstream of the JA receptor to orchestrate JA-mediated activation of both the wounding and pathogen responses . Using chromatin immunoprecipitation sequencing ( ChIP-seq ) coupled with RNA sequencing ( RNA-seq ) assays , we identified 655 MYC2-targeted JA-responsive genes . These genes are highly enriched in Gene Ontology categories related to TFs and the early response to JA , indicating that MYC2 functions at a high hierarchical level to regulate JA-mediated gene transcription . We also identified a group of MYC2-targeted TFs ( MTFs ) that may directly regulate the JA-induced transcription of late defense genes . Our findings suggest that MYC2 and its downstream MTFs form a hierarchical transcriptional cascade during JA-mediated plant immunity that initiates and amplifies transcriptional output . As proof of concept , we showed that during plant resistance to the necrotrophic pathogen Botrytis cinerea , MYC2 and the MTF JA2-Like form a transcription module that preferentially regulates wounding-responsive genes , whereas MYC2 and the MTF ETHYLENE RESPONSE FACTOR.C3 form a transcription module that preferentially regulates pathogen-responsive genes .
Ozone layer depletion leads to elevated ultraviolet-B ( UV-B ) radiation , which affects plant growth ; however , little is known about the relationship between root growth and signaling molecules in roots . Therefore , in this work , simulated UV-B radiation was used to study the effects of elevated UV-B radiation on root growth of soybean seedlings and changes in the content of signaling molecules in roots . The results showed that compared with the control , the 2.63   kJ   m(-2 ) d(-1 ) and 6.17   kJ   m(-2 ) d(-1 ) elevated UV-B radiation treatments inhibited root growth , and root growth parameters ( total root length , root surface area , root volume , average diameter , root tip number , and root dry weight ) all decreased . For root signaling molecules , the content of nitric oxide , reactive oxygen species , abscisic acid , salicylic acid , and jasmonic acid increased , and the content of auxin , cytokinin , and gibberellin decreased . The above indices changed more significantly under the 6.17   kJ   m(-2 ) d(-1 ) treatment . After withdrawal of the exposure , the above indices could be restored to a certain extent . These data indicated that UV-B radiation interfered with root growth by affecting the content of signaling molecules in roots , and the degree of the effects was related to the intensity of UV-B radiation . The results from this study provide a theoretical basis for studying the preliminary mechanism of elevated UV-B radiation on root growth and possible pathways that can mitigate UV-B radiation damage for root growth . ONE SENTENCE SUMMARY : The effects of elevated UV-B on root growth of soybean seedlings were regulated by signaling molecules , and the degree of the effects was related to the intensity of UV-B radiation .
BACKGROUND : Plants respond to various stress stimuli by activating an enhanced broad-spectrum defensive ability . The development of novel resistance inducers represents an attractive , alternative crop protection strategy . In this regard , hexanoic acid ( Hxa , a chemical elicitor ) and azelaic acid ( Aza , a natural signaling compound ) have been proposed as inducers of plant defense , by means of a priming mechanism . Here , we investigated both the mode of action and the complementarity of Aza and Hxa as priming agents in Nicotiana tabacum cells in support of enhanced defense . RESULTS : Metabolomic analyses identified signatory biomarkers involved in the establishment of a pre-conditioned state following Aza and Hxa treatment . Both inducers affected the metabolomes in a similar manner and generated common biomarkers : caffeoylputrescine glycoside , cis-5-caffeoylquinic acid , feruloylglycoside , feruloyl-3-methoxytyramine glycoside and feruloyl-3-methoxytyramine conjugate . Subsequently , quantitative real time-PCR was used to investigate the expression of inducible defense response genes : phenylalanine ammonia lyase , hydroxycinnamoyl CoA quinate transferase and hydroxycinnamoyl transferase to monitor activation of the early phenylpropanoid pathway and chlorogenic acids metabolism , while ethylene response element-binding protein , small sar1 GTPase , heat shock protein 90 , RAR1 , SGT1 , non-expressor of PR genes 1 and thioredoxin were analyzed to report on signal transduction events . Pathogenesis-related protein 1a and defensin were quantified to investigate the activation of defenses regulated by salicylic acid and jasmonic acid respectively . The qPCR results revealed differential expression kinetics and , in general ( except for NPR1 , Thionin and PR1a ) , the relative gene expression ratios observed in the Hxa-treated cells were significantly greater than the expression observed in the cells treated with Aza . CONCLUSIONS : The results indicate that Aza and Hxa have a similar priming effect through activation of genes involved in the establishment of systemic acquired resistance , associated with enhanced synthesis of hydroxycinnamic acids and related conjugates .
Plants under stress from both biotic and abiotic sources produce increased levels of ethylene , which is perceived by ethylene receptors and triggers cellular responses further downstream . Protein phosphorylation and dephosphorylation were implicated in the regulation of ethylene induction by stresses based on studies using protein kinase and phosphatase inhibitors . However , the kinase(s ) involved remains to be determined . Using a conditional gain-of-function transgenic system , we demonstrate that the activation of SIPK , a tobacco mitogen-activated protein kinase ( MAPK ) , by NtMEK2DD , an active mutant of the upstream kinase of SIPK , resulted in a dramatic increase in ethylene production . The increase in ethylene after the activation of SIPK coincided with a dramatic increase in 1-aminocyclopropane-1-carboxylic acid ( ACC ) synthase ( ACS ) activity , which was followed by the activation of a subgroup of ACS and ACC oxidase ( ACO ) genes , suggesting that either the activation of unidentified ACS(s ) or post-transcriptional regulation is involved . Infection with Tobacco mosaic virus ( TMV ) , which is known to activate the SIPK cascade and induce ethylene biosynthesis , also induced the same ACSs and ACOs . After ethylene production in NtMEK2DD plants , strong activation of ETHYLENE-RESPONSE FACTOR ( ERF ) genes was observed , similar to the effect in NN tobacco plants infected with TMV . In contrast to previous reports , no major increase in jasmonic acid ( JA ) and methyl jasmonate ( MJ ) was detected after the activation of SIPK/WIPK in NtMEK2DD transgenic plants . These results suggest that the induction of ethylene but not JA/MJ is involved in plant defense responses mediated by the NtMEK2-SIPK/WIPK pathway .
The effects of phytohormones ( abscisic acid , gibberelic acid , and jasmonic acid ) and ambiol ( a synthetic growth regulator ) on processes of H+ transport across the plasmalemma were studied in membrane vesicles isolated from the parenchyma of potato ( Solanum tuberosum L. ) tubers . Phytohormones and ambiol were tested either individually or in combinations . Each of the substances tested changed the initial rate of H+ uptake by the vesicles . Two signaling substances added to the incubation medium simultaneously modified the activity of each other . It is suggested that the interaction of a signaling substance with components of the plasmalemma alters the responses of the membrane to other signaling molecules .
The necrotrophic fungus Botrytis cinerea causes devastating pre- and post-harvest yield losses in grapevine ( Vitis vinifera L. ) . Although B. cinerea has been well-studied in different plant species , there is limited information related to the resistance and susceptibility mechanisms of Vitis genotypes against B. cinerea infection . In the present study , leaves and berries of twenty four grape genotypes were evaluated against B. cinerea infection . According to the results , one genotype ( Ju mei gui ) was highly resistant ( HR ) , one genotype ( Kyoho ) was resistant ( R ) , eight genotypes were susceptible ( S ) , and fourteen genotypes were highly susceptible ( HS ) against infection of B. cinerea in leaves . Whereas in the case of B. cinerea infection in grape berry , three genotypes were found to be highly resistant , three resistant , eleven genotypes susceptible , and seven were highly susceptible . To further explore the mechanism of disease resistance in grapevine , we evaluated " Ju mei gui " and " Summer black " in terms of B. cinerea progression , reactive oxygen species reactions , jasmonic acid contents , and the activities of antioxidant enzymes in leaf and fruit . We surmise that the resistance of " Ju mei gui " is due to seized fungal growth , minor reactive oxygen species ( ROS ) production , elevated antioxidant enzyme activity , and more jasmonic acid ( JA ) contents . This study provides insights into the resistance and susceptibility mechanism of Vitis genotypes against B. cinerea . This will help for the selection of appropriate germplasm to explore the molecular basis of disease resistance mechanisms in grapevine .
• Arsenic ( As ) contamination of rice ( Oryza sativa ) is a worldwide concern and elucidating the molecular mechanisms of As accumulation in rice may provide promising solutions to the problem . Previous studies using microarray techniques to investigate transcriptional regulation of plant responses to As stress have identified numerous differentially expressed genes . However , little is known about the metabolic and regulatory network remodelings , or their interactions with microRNA ( miRNA ) in plants upon As(III ) exposure . • We used Illumina sequencing to acquire global transcriptome alterations and miRNA regulation in rice under As(III ) treatments of varying lengths of time and dosages . • We found that the response of roots was more distinct when the dosage was varied , whereas that of shoots was more distinct when the treatment time was varied . In particular , the genes involved in heavy metal transportation , jasmonate ( JA ) biosynthesis and signaling , and lipid metabolism were closely related to responses of rice under As(III ) stress . Furthermore , we discovered 36 new As(III)-responsive miRNAs , 14 of which were likely involved in regulating gene expression in transportation , signaling , and metabolism . • Our findings highlight the significance of JA signaling and lipid metabolism in response to As(III ) stress and their regulation by miRNA , which provides a foundation for subsequent functional research .
BACKGROUND : Fusarium head blight ( FHB ) caused by Fusarium species like F. graminearum is a devastating disease of wheat ( Triticum aestivum ) worldwide . Mycotoxins such as deoxynivalenol produced by the fungus affect plant and animal health , and cause significant reductions of grain yield and quality . Resistant varieties are the only effective way to control this disease , but the molecular events leading to FHB resistance are still poorly understood . Transcriptional profiling was conducted for the winter wheat cultivars Dream ( moderately resistant ) and Lynx ( susceptible ) . The gene expressions at 32 and 72 h after inoculation with Fusarium were used to trace possible defence mechanisms and associated genes . A comparative qPCR was carried out for selected genes to analyse the respective expression patterns in the resistant cultivars Dream and Sumai 3 ( Chinese spring wheat ) . RESULTS : Among 2,169 differentially expressed genes , two putative main defence mechanisms were found in the FHB-resistant Dream cultivar . Both are defined base on their specific mode of resistance . A non-specific mechanism was based on several defence genes probably induced by jasmonate and ethylene signalling , including lipid-transfer protein , thionin , defensin and GDSL-like lipase genes . Additionally , defence-related genes encoding jasmonate-regulated proteins were up-regulated in response to FHB . Another mechanism based on the targeted suppression of essential Fusarium virulence factors comprising proteases and mycotoxins was found to be an essential , induced defence of general relevance in wheat . Moreover , similar inductions upon fungal infection were frequently observed among FHB-responsive genes of both mechanisms in the cultivars Dream and Sumai 3 . CONCLUSIONS : Especially ABC transporter , UDP-glucosyltransferase , protease and protease inhibitor genes associated with the defence mechanism against fungal virulence factors are apparently active in different resistant genetic backgrounds , according to reports on other wheat cultivars and barley . This was further supported in our qPCR experiments on seven genes originating from this mechanism which revealed similar activities in the resistant cultivars Dream and Sumai 3 . Finally , the combination of early-stage and steady-state induction was associated with resistance , while transcript induction generally occurred later and temporarily in the susceptible cultivars . The respective mechanisms are attractive for advanced studies aiming at new resistance and toxin management strategies .
The effect of elicitation with arachidonic and jasmonic acids on the production of phenolic compounds as well as the antioxidant and anti-inflammatory properties of phenolic extracts of wheatgrass was evaluated . The qualitative and quantitative analysis of phenolic compounds carried out with the UPLC-MS technique indicated that luteolin and apigenin derivatives were the dominant flavonoids , while ferulic acid derivatives and syringic acid were the main components in the phenolic acid fraction in the wheatgrass . No qualitative changes in the examined phenolic compounds were observed in the case of the control and elicited plants , while there was an increase in the content of some compounds . The antioxidant activity increased in the elicited samples ( with the exception of reducing power ) and this elevation was partially correlated with the increase in the polyphenol content in the studied plants . Elicitation with 0.01   µM arachidonic acid also caused improvement of potential anti-inflammatory properties of the wheatgrass .
Exposure of gibberellic acid-treated seedlings of a monoecious cucumber cultivar ; Chipper ' ( Cucumis sativus L. ) to ethylene caused thickening of the hypocotyl , inhibited longitudinal growth , and had no effect on fresh weight . Downward curvature of cotyledons was increased by the presence of ethylene . A gynoecious breeding line , ; Gy 3 , ' had thicker hypocotyls and displayed its cotyledons in a more downward position than ; Chipper ' . Excised hypocotyls of the gynoecious seedlings produced three times as much ethylene as did the monoecious Chipper hypocotyls . Thus , ethylene may play a role in the regulation of cucumber seedling morphology .