slotreck/pickle huggingface dataset:
In Nicotiana sylvestris , a set of nicotine biosynthesis genes were activated by exogenous application of methyl jasmonate , but the activation was effectively suppressed by simultaneous treatment with ethylene . When N. sylvestris transgenic hairy roots were treated with a natural ethylene precursor , the jasmonate-responsive expression of the promoter from a nicotine pathway enzyme gene was completely suppressed , and this suppressive effect was abolished when ethylene perception was blocked with silver cation . These and additional immunoblot results suggest that ethylene signal antagonizes jasmonate signal in nicotine biosynthesis .
The volatile metabolite methyl jasmonate ( MeJA ) plays an important role in intra- and interplant communication and is involved in diverse biological processes . In this study , we report the cloning and functional characterization of a S-adenosyl-l-methionine : jasmonic acid carboxyl methyltransferase ( JMT ) from Fragaria vesca and Fragaria × ananassa . Biochemical assays and comprehensive transcript analyses showed that JMT has been erroneously annotated as gene fusion with a carboxyl methyltransferase ( CMT ) ( gene15184 ) in the first published genome sequence of F. vesca . Recombinant FvJMT catalyzed the formation of MeJA with KM value of 22.3μM while FvCMT and the fusion protein were almost inactive . Activity of JMT with benzoic acid and salicylic acid as substrates was less than 1.5 % of that with JA . Leucine at position 245 , an amino acid missing in other JMT sequences is essential for activity of FvJMT . In accordance with MeJA levels , JMT transcript levels decreased steadily during strawberry fruit ripening , as did the expression levels of JA biosynthesis and regulatory genes . It appears that CMT has originated by a recent duplication of JMT and lost its enzymatic activity toward JA . In the newest version of the strawberry genome sequence ( June 2014 ) CMT and JMT are annotated as separate genes in accordance with differential temporal and spatial expression patterns of both genes in Fragaria sp. In conclusion , MeJA , the inactive derivative of JA , is probably involved in early steps of fruit development by modulating the levels of the active plant hormone JA .
Protease inhibitors ( PIs ) function in the precise regulation of proteases , and are thus involved in diverse biological processes in many organisms . Here , we studied the functions of the Arabidopsis UNUSUAL SERINE PROTEASE INHIBITOR ( UPI ) gene , which encodes an 8.8   kDa protein of atypical sequence relative to other PIs . Plants harboring a loss-of-function UPI allele displayed enhanced susceptibility to the necrotrophic fungi Botrytis cinerea and Alternaria brassicicola as well as the generalist herbivore Trichoplusia ni . Further , ectopic expression conferred increased resistance to B.   cinerea and T.   ni . In contrast , the mutant has wild-type responses to virulent , avirulent and non-pathogenic strains of Pseudomonas syringae , thus limiting the defense function of UPI to necrotrophic fungal infection and insect herbivory . Expression of UPI is significantly induced by jasmonate , salicylic acid and abscisic acid , but is repressed by ethylene , indicating complex phytohormone regulation of UPI expression . The upi mutant also shows significantly delayed flowering , associated with decreased SOC1 expression and elevated levels of MAF1 , two regulators of floral transition . Recombinant UPI strongly inhibits the serine protease chymotrypsin but also weakly blocks the cysteine protease papain . Interestingly , jasmonate induces intra- and extracellular UPI accumulation , suggesting a possible role in intercellular or extracellular functions . Overall , our results show that UPI is a dual-specificity PI that functions in plant growth and defense , probably through the regulation of endogenous proteases and/or those of biotic invaders .
Plants subjected to drought and saline stress conditions suffer from tissue dehydration . Such dehydration is caused by the imbalance between root water uptake by roots and water loss by transpiration . Therefore , determination of root hydraulic properties is crucial to understand plant water balance . Root hydraulic conductivity ( L ) can be used to estimate root water transport capacity . L depends on root architecture ( length and diameter of the root and proliferation of secondary roots ) , radial water transport pathway ( root xylem vessels , plasmodesmata , apoplastic space , caspary bands ) , and on intrinsic membrane permeability to water ( aquaporins , water membrane protein channels ) . Different methods have been developed to measure L , such as Pressure Chamber , Free Exudation , High-Pressure Flowmeter ( HPFM ) , and Root Pressure Probe ( RPP ) . In this chapter , we will focus on Pressure Chamber , Free Exudation , and HPFM methods which have been used to determine the effect of jasmonates ( JA ) on root hydraulic conductivity .
BACKGROUND : Breeding for genes controlling key agronomic traits is an important goal of rice genetic improvement . To gain insight into genes controlling grain morphology , we screened M(3 ) plants derived from 1,000 whole-genome sequenced ( WGS ) M(2 ) Kitaake mutants to identify lines with altered grain size . RESULTS : In this study , we isolated a mutant , named fast-neutron ( FN ) 60 - 4 , which exhibits a significant reduction in grain size . We crossed FN60 - 4 with the parental line Kitaake and analyzed the resulting backcross population . Segregation analysis of 113 lines from the BC(2)F(2 ) population revealed that the mutant phenotype is controlled by a single semi-dominant locus . Mutant FN60 - 4 is reduced 20 % in plant height and 8.8 % in 1000-grain weight compared with Kitaake . FN60 - 4 also exhibits an 8 % reduction in cell number and a 9 % reduction in cell length along the vertical axis of the glume . We carried out whole-genome sequencing of DNA pools extracted from segregants with long grains or short grains , and revealed that one gene , LOC_Os09g02650 , cosegregated with the grain size phenotype in the BC(1)F(2 ) and BC(2)F(2 ) populations . This mutant allele was named grain shape 9 - 1 ( gs9 - 1 ) . gs9 - 1 carries a 3-bp deletion that affects two amino acids . This locus is a new allele of the BC12/GDD1/MTD1 gene that encodes a kinesin-like protein involved in cell-cycle progression , cellulose microfibril deposition and gibberellic acid ( GA ) biosynthesis . The GA biosynthesis-related gene KO2 is down-regulated in gs9 - 1 . The dwarf phenotype of gs9 - 1 can be rescued by adding exogenous GA(3 ) . In contrast to the phenotypes for the other alleles , the gs9 - 1 is less severe , consistent with the nature of the mutation , which does not disrupt the open reading frame as observed for the other alleles . CONCLUSIONS : In this study , we isolated a mutant , which exhibits altered grain shape and identified the mutated gene , gs9 - 1 . Our study reveals that gs9 - 1 is a semi-dominant gene that carries a two-amino acid mutation . gs9 - 1 is allelic to the BC12/GDD1/MTD1 gene involved in GA biosynthesis . These results demonstrate the efficiency and convenience of cloning genes from the whole-genome sequenced Kitaake mutant population to advance investigations into genes controlling key agronomic traits in rice .
Germination is a process of seed sprouting that facilitates embryo growth . The breakdown of reserved starch in the endosperm into simple sugars is essential for seed germination and subsequent seedling growth . At the early stage of germination , gibberellic acid ( GA ) activates transcription factor GAMYB to promote de novo synthesis of isoforms of α-amylase in the aleurone layer and scutellar epithelium of the embryo . Here , we demonstrate that wheat germination is regulated by plant target of rapamycin ( TOR ) signaling . TOR is a central component of the essential-nutrient-dependent pathway controlling cell growth in all eukaryotes . It is known that rapamycin , a highly specific allosteric inhibitor of TOR , is effective in yeast and animal cells but ineffective in most of higher plants likely owing to structural differences in ubiquitous rapamycin receptor FKBP12 . The action of rapamycin on wheat growth has not been studied . Our data show that rapamycin inhibits germination of wheat seeds and of their isolated embryos in a dose-dependent manner . The involvement of Triticum aestivum TOR ( TaTOR ) in wheat germination was consistent with the suppression of wheat embryo growth by specific inhibitors of the TOR kinase : pp242 or torin1 . Rapamycin or torin1 interfered with GA function in germination because of a potent inhibitory effect on α-amylase and GAMYB gene expression . The TOR inhibitors selectively targeted the GA-dependent gene expression , whereas expression of the abscisic acid-dependent ABI5 gene was not affected by either rapamycin or torin1 . To determine whether the TaTOR kinase activation takes place during wheat germination , we examined phosphorylation of a ribosomal protein , T. aestivum S6 kinase 1 ( TaS6K1 ; a substrate of TOR ) . The phosphorylation of serine 467 ( S467 ) in a hydrophobic motif on TaS6K1 was induced in a process of germination triggered by GA . Moreover , the germination-induced phosphorylation of TaS6K1 on S467 was dependent on TaTOR and was inhibited by rapamycin or torin1 . Besides , a gibberellin biosynthesis inhibitor ( paclobutrazol ; PBZ ) blocked not only α-amylase gene expression but also TaS6K1 phosphorylation in wheat embryos . Thus , a hormonal action of GA turns on the synthesis of α-amylase in wheat germination via activation of the TaTOR-S6K1 signaling pathway .
Effects of ethylene , gibberellins , and kinetin on the germination of two lots of Chenopodium album L. seeds , collected from the field in 1982 and 1983 , were studied in relation to the availability of nitrate . The experiments were conducted in darkness and at temperatures ranging from 12 to 32 degrees C. Ethylene induced over 75 % germination in the 1983 seed but had little effect on the 1982 seed . Nitrate was only slightly promotive in either of the two seed lots . A combination of ethylene and nitrate , however , acted synergistically on 1982 seed , resulting in as much germination as that induced in 1983 seed by ethylene alone . In 1983 seed , a combination of ethylene and nitrate was only marginally more effective than ethylene . A similar relationship was observed in the effects of gibberellic acid(4 + 7 ) ( GA(4 + 7 ) ) and nitrate on seeds from the two lots . The 1982 seed , which responded synergistically to combinations of nitrate with ethylene or GA(4 + 7 ) was found to contain an extremely low endogenous level of nitrate as compared to 1983 seed . Thus , high levels of either endogenous or applied nitrate appeared to enhance the germination response to ethylene or GA(4 + 7).Kinetin had no effect on 1982 seed and only a small promotive effect on 1983 seed . There was no synergism between kinetin and nitrate in either of the seed lots .
Herbivore attacks induce leaves to emit a specific blend of volatiles . Here we show that exposure to Tetranychus urticae-induced volatiles , as well as T. urticae infestation and artificial wounding , activates the transcription of the genes involved in the biosynthesis of ethylene [ S-adenosylmethionine ( SAM ) synthetase and 1-aminocyclopropane-1-carboxylic acid oxidase ] and a gene involved in the biosynthesis of polyamines from SAM ( SAM decarboxylase ) in lima bean leaves . Moreover , exposure of leaves to any one of the seven major chemical components of T. urticae-induced volatiles also induces expression of these genes . Furthermore , we found that , when lima bean plants were exposed to T. urticae-induced volatiles , they emitted ethylene . Lima bean plants infested by T. urticae and artificially wounded plants also emitted ethylene . Endogenous polyamine levels were not increased in the exposed leaves or the infested leaves , suggesting that polyamine production from SAM was only slightly promoted at the metabolic levels present in the leaves . We found that jasmonate ( JA ) accumulated in leaves exposed to T. urticae-induced volatiles , and that both JA and salicylate ( SA ) accumulated in leaves infested by T. urticae . These findings , as well as results of pharmacological analyses , suggest that , in leaves exposed to T. urticae-induced volatiles , ethylene biosynthesis might be regulated by pathways involving JA and the ethylene positive feedback loop . They also suggest that ethylene biosynthesis might be regulated by signaling pathways involving JA , SA and ethylene in T. urticae-infested leaves .
A highly sensitive and accurate multiplex gas chromatography-mass spectrometry (GC-MS/MS)-technique is reported for the quantitative analysis of acidic phytohormones in Arabidopsis thaliana and other plant species . The optimized setup allows the routine processing and analysis of between 20 mg and 5 g of tissue . The protocol was designed and the equipment used was chosen to facilitate implementation of the method into other laboratories and to provide access to state-of-the-art analytical tools for the acidic phytohormones and related signaling molecules .
A wheat ethylene receptor homologue ( W-er1 ) was isolated from a wheat stem cDNA library using the Arabidopsis ETR1 cDNA as a probe . The predicted amino acid sequence of W-er1 is over 70 % similar to ERS1 from Arabidopsis and exhibits homology to bacterial two-component response regulators within the histidine kinase domain . Northern hybridization demonstrated that W-er1 was expressed in stem , leaf and root tissues . Treatments known to induce senescence of detached leaves including jasmonate , abscisic acid and wounding , increased the accumulation of W-er1 mRNA , while benzyladenine treatment did not . These data suggest that W-er1 may play a role in the process of leaf senescence .
The patatin-related phospholipase A ( pPLA ) hydrolyzes membrane glycerolipids to produce monoacyl compounds and free fatty acids . Phospholipids are cleaved by pPLAIIα at the sn-1 and sn-2 positions , and galactolipids , including those containing oxophytodienoic acids , can also serve as substrates . Ablation of pPLAIIα decreased lysophosphatidylcholine and lysophosphatidylethanolamine levels , but increased free linolenic acid . pPLAIIα-deficient plants displayed a higher level of jasmonic acid and methyl jasmonate , as well as the oxylipin-biosynthetic intermediates 13-hydroperoxylinolenic acid and 12-oxophytodienoic acid than wild-type ( WT ) plants . The expression of genes involved in oxylipin production was also higher in the pPLAIIα-deficient mutant than in WT plants . The mutant plants lost water more quickly than WT plants . The stomata of WT and mutant plants responded similarly to abscisic acid . In response to desiccation , the mutant and WT leaves produced abscisic acid at the same rate , but , after 4   h of desiccation , the jasmonic acid level was much higher in mutant than WT leaves . These results indicate that pPLAIIα negatively regulates oxylipin production and suggest a role in the removal of oxidatively modified fatty acids from membranes .
GP-1 , a novel glycoprotein from Streptomyces sp. ZX01 has a plant immunity-inducing effect . GP-1-treated plants exhibited enhanced systemic resistance with a significant reduction in TMV lesions on tobacco leaves , but its antiviral mechanism remains unclear . In this study , early plant defense-related responses , such as Ca(2 + ) influx , callose apposition , oxidative burst , hypersensitive response , programmed cell death , increase in nitric oxide ( NO ) , and stomatal closure , were investigated under GP-1 treatment , and the mechanism of how GP-1 induces viral resistance in Nicotiana benthamiana was studied . Results showed that GP-1 induced [Ca(2+)](cyt ) rapidly in tobacco leaves and suspended cells , followed by reactive oxygen species ( ROS ) and NO elevation . Transcriptome analysis showed significant differences in expression levels between the GP-1-treated N. benthamiana and the control and showed significantly upregulated and enriched pathways including defense and immune reaction . Similar to typical pathogen-associated molecular patterns , GP-1 induced callose deposition and stomatal closure to form defense barriers against pathogen invasion . The expression of defense-related genes further confirmed the above conclusions . By analyzing transcriptome in N. benthamiana and the contents of salicylic acid ( SA ) and jasmonic acid ( JA ) , GP-1 enhanced viral resistance of tobacco by improving the SA and JA contents , strengthening plant secondary metabolites activities , promoting systemic accumulation of pathogenesis-related proteins in TMV- inoculated tobacco there by producing antiviral activity .
Infection by necrotrophs is a complex process that starts with the breakdown of the cell wall ( CW ) matrix initiated by CW-degrading enzymes and results in an extensive tissue maceration . Plants exploit induced defense mechanisms based on biochemical modification of the CW components to protect themselves from enzymatic degradation . The pectin matrix is the main CW target of Botrytis cinerea , and pectin methylesterification status is strongly altered in response to infection . The methylesterification of pectin is controlled mainly by pectin methylesterases ( PMEs ) , whose activity is posttranscriptionally regulated by endogenous protein inhibitors ( PMEIs ) . Here , AtPMEI10 , AtPMEI11 , and AtPMEI12 are identified as functional PMEIs induced in Arabidopsis ( Arabidopsis thaliana ) during B. cinerea infection . AtPMEI expression is strictly regulated by jasmonic acid and ethylene signaling , while only AtPMEI11 expression is controlled by PME-related damage-associated molecular patterns , such as oligogalacturonides and methanol . The decrease of pectin methylesterification during infection is higher and the immunity to B. cinerea is compromised in pmei10 , pmei11 , and pmei12 mutants with respect to the control plants . A higher stimulation of the fungal oxalic acid biosynthetic pathway also can contribute to the higher susceptibility of pmei mutants . The lack of PMEI expression does not affect hemicellulose strengthening , callose deposition , and the synthesis of structural defense proteins , proposed as CW-remodeling mechanisms exploited by Arabidopsis to resist CW degradation upon B. cinerea infection . We show that PME activity and pectin methylesterification are dynamically modulated by PMEIs during B. cinerea infection . Our findings point to AtPMEI10 , AtPMEI11 , and AtPMEI12 as mediators of CW integrity maintenance in plant immunity .
Lettuce ( Lactuca sativa L. ) endosperm cell walls isolated prior to radicle emergence underwent autohydrolysis , the rate of which was correlated with whether radicle emergence would subsequently occur . Extraction of endosperm cell walls with 6 M LiCl suppressed autohydrolysis , and the desalted extract possessed activity that was capable of hydrolyzing purified locust bean galactomannan but not arabinogalactan , carboxymethylcellulose , glucomannan , polygalacturonic acid , tomato galactomannan , or native lettuce endosperm cell walls . Some hydrolytic activity was detected on endosperm cell walls if they were modified by partial trifluoroacetic acid hydrolysis or pretreatment with guanidinium thiocyanate . In extended incubations the cell wall enzyme extract released only large molecular mass fragments from locust bean galactomannan , indicating primarily endo-activity . Galactomannan-hydrolyzing activity in the cell wall extract increased as a function of imbibition time and was greatest just prior to radicle emergence . Thermoinhibition ( imbibition at 32[deg]C ) or treatment with abscisic acid at a temperature optimal for germination ( 25[deg]C ) suppressed both germination and endosperm cell wall mannanase activity , whereas alleviation of thermoinhibition with gibberellic acid was accompanied by significant enhancement of mannanase activity . We conclude that a cell wall-bound endo-[beta]-mannanase is expressed in lettuce endosperm prior to radicle emergence and is regulated by the same conditions that govern germination .
Leaf angle is an important agronomic trait in cereals and shares a close relationship with crop architecture and grain yield . Although it has been previously reported that ZmCLA4 can influence leaf angle , the underlying mechanism remains unclear . In this study , we used the Gal4-LexA/UAS system and transactivation analysis to demonstrate in maize ( Zea mays ) that ZmCLA4 is a transcriptional repressor that regulates leaf angle . DNA affinity purification sequencing ( DAP-Seq ) analysis revealed that ZmCLA4 mainly binds to promoters containing the EAR motif ( CACCGGAC ) as well as to two other motifs ( CCGARGS and CDTCNTC ) to inhibit the expression of its target genes . Further analysis of ZmCLA4 target genes indicated that ZmCLA4 functions as a hub of multiple plant hormone signaling pathways : ZmCLA4 was found to directly bind to the promoters of multiple genes including ZmARF22 and ZmIAA26 in the auxin transport pathway , ZmBZR3 in the brassinosteroid signaling pathway , two ZmWRKY genes involved in abscisic acid metabolism , ZmCYP genes ( ZmCYP75B1 , ZmCYP93D1 ) related to jasmonic acid metabolism , and ZmABI3 involved in the ethylene response pathway . Overall , our work provides deep insights into the ZmCLA4 regulatory network in controlling leaf angle in maize .
In order to characterize a specific extracellular 21-kDa calmodulin-binding protein ( named : ECBP21 ) from Angelica dahurica L. suspension-cultured cells , the cDNA coding for the protein has been cloned . Here , Southern blot analysis shows that there are at least two copies of ECBP21 gene in Angelica genome . Using truncated versions of ECBP21 and synthetic peptide in CaM binding assays , we mapped the calmodulin-binding domain to a 16-amino acid stretch ( residues 200 - 215 ) at the C-terminal region . The ECBP21 was localized in the cell wall area by the immunogold electron microscopy and by GFP labeling method . These results define ECBP21 as a kind of an extracellular calmodulin-binding protein ( CaMBP ) . Furthermore , using Northern blot analysis , we examined the expression dynamics of ecbp21 during the incubation of Angelica suspension-cultured cells and the treatments with some growth regulators . The above studies further provide the molecular evidence for the existence of the gene coding for extracellular CaMBPs and imply a possible role for ECBP21 .
Abscisic acid ( ABA ) inhibits the production of ethylene induced by water stress in excised wheat leaves and counteracts the stimulatory effect of 6-benzyladenine ( BA ) on this process . The stimulatory effect of BA and the inhibitory effect of ABA were equally pronounced whether external or endogenous ethylene levels were determined . When leaves were sprayed or floated on solutions of BA , indole-3-acetic acid ( IAA ) , gibberellic acid ( GA3 ) , or ABA , the relative activities of these growth regulators on stress-induced ethylene at 10(-4 ) mol l(-1 ) were BA > IAA > GA3>controls > ABA . In non-stressed leaves , however , where the levels of ethylene produced were 2 - 20 times smaller , the relative activities were IAA > BA > GA3>controls > ABA . The effects of BA and ABA spray treatment on water stress induced ethylene were closely similar whether the solutions were applied 2 or 18 h prior to the initiation of water stress . The relationships between the levels of endogenous growth regulators in the plant and ethylene release induced by water stress are discussed .