slotreck/pickle huggingface dataset:
The effects of ethephon as a sugarcane ripener are attributed to ethylene . However , the role of this phytohormone at the molecular level is unknown . We performed a transcriptome analysis combined with the evaluation of sucrose metabolism and hormone profiling of sugarcane plants sprayed with ethephon or aminoethoxyvinylglycine ( AVG ) , an ethylene inhibitor , at the onset of ripening . The differential response between ethephon and AVG on sucrose level and sucrose synthase activity in internodes indicates ethylene as a potential regulator of sink strength . The correlation between hormone levels and transcriptional changes suggests ethylene as a trigger of multiple hormone signal cascades , with approximately 18 % of differentially expressed genes involved in hormone biosynthesis , metabolism , signalling , and response . A defence response elicited in leaves favoured salicylic acid over the ethylene/jasmonic acid pathway , while the upper internode was prone to respond to ethylene with strong stimuli on ethylene biosynthesis and signalling genes . Besides , ethylene acted synergistically with abscisic acid , another ripening factor , and antagonistically with gibberellin and auxin . We identified potential ethylene target genes and characterized the hormonal status during ripening , providing insights into the action of ethylene at the site of sucrose accumulation . A molecular model of ethylene interplay with other hormones is proposed .
Effects of α-ketol linolenic acid ( KODA ) application on endogenous abscisic acid ( ABA ) , jasmonic acid ( JA ) , and aromatic volatiles were investigated in ' Kyoho ' grapes ( Vitis labrusca × Vitis vinifera ) infected by a pathogen ( Glomerella cingulata ) . The expressions of 9-cis-epoxycarotenoid dioxygenase ( VvNCED1 ) , ABA 8'-hydroxylase ( VvCYP707A1 ) , lipoxygenase ( VvLOX ) , and allene oxide synthase ( VvAOS ) were also examined . The grape berries were dipped in 0.1mM KODA solution before inoculation with the pathogen and stored at 25 ° C for 12 days . The development of infection was significantly suppressed upon KODA treatment . Endogenous ABA , JA and phaseic acid ( PA ) were induced in inoculated berries . KODA application before inoculation increased endogenous ABA , PA and JA through the activation of VvNCED1 , VvCYP707A1 and VvAOS genes , respectively . In addition , terpenes , methyl salicylate ( Me-SA ) and C6-aldehydes such as (E)-2-hexenal and cis-3-hexenal associated with fungal resistance also increased in KODA-treated berries during storage . These results suggest that the synergistic effect of JA , ABA , and some aromatic volatiles induced by KODA application may provide resistance to pathogen infection in grape berries .
The induction of alpha-amylase triggered by gibberellic acid in barley embryos is repressed by sugars . We investigated the effects of glucose on the gibberellin signal transduction pathway to localize the site of interaction of the sugar/hormone signalling pathways . Our results indicate that glucose represses gibberellin signalling late along this hormone transduction pathway , downstream of transcription of the gibberellin-modulated transcriptional activator ( GAMYB ) needed for alpha-amylase induction . This result suggests either that glucose repression is transduced by a pathway independent of gibberellin signalling or that repression occurs at the level of GAMYB translation .
Seed germination is antagonistically controlled by the phytohormones gibberellic acid ( GA ) and abscisic acid ( ABA ) . GA promotes seed germination by enhancing the proteasome-mediated destruction of RGL2 ( for RGA-LIKE2 ) , a key DELLA factor repressing germination . By contrast , ABA blocks germination by inducing ABI5 ( for ABA-INSENSITIVE5 ) , a basic domain/leucine zipper transcription factor repressing germination . Decreased GA synthesis leads to an increase in endogenous ABA levels through a stabilized RGL2 , a process that may involve XERICO , a RING-H2 zinc finger factor promoting ABA synthesis . In turn , increased endogenous ABA synthesis is necessary to elevate not only ABI5 RNA and protein levels but also , critically , those of RGL2 . Increased ABI5 protein is ultimately responsible for preventing seed germination when GA levels are reduced . However , overexpression of ABI5 was not sufficient to repress germination , as ABI5 activity requires phosphorylation . The endogenous ABI5 phosphorylation and inhibition of germination could be recapitulated by the addition of a SnRK2 protein kinase to the ABI5 overexpression line . In sleepy1 mutant seeds , RGL2 overaccumulates ; germination of these seeds can occur under conditions that produce low ABI5 expression . These data support the notion that ABI5 acts as the final common repressor of germination in response to changes in ABA and GA levels .
The mitogen-activated protein kinase ( MAPK ) signaling cascade is critical for regulating plant defense systems against various kinds of pathogen and environmental stresses . One component of this cascade , the MAP kinase kinases ( MAPKK ) , has not yet been shown to be induced in plants following biotic attacks , such as those by insects and fungi . We describe here a gene coding for a blast ( Magnaporthe grisea)- and insect ( Nilaparvata lugens)-responsive putative MAPK kinase , OmMKK1 ( Oryza minuta MAPKK 1 ) , which was identified in a library of O. minuta expressed sequence tags ( ESTs ) . Two copies of OmMKK1 are present in the O. minuta genome . They encode a predicted protein with molecular mass 39 kDa and pI of 6.2 . Transcript patterns following imbibition of plant hormones such as methyl jasmonic acid ( MeJA ) , ethephone , salicylic acid ( SA ) and abscisic acid ( ABA ) , as well as exposure to methyl viologen ( MV ) , revealed that the expression of OmMKK1 is related to defense response signaling pathways . A comparative analysis of OmMKK1 and its O. sativa ortholog OsMKK1 showed that both were induced by stress-related hormones and biotic stresses , but that the kinetics of their responses differed despite their high amino acid sequence identity ( 96 % ) .
Salinity is a major environmental factor that constrains soybean yield and grain quality . Given our past observations using the salt-sensitive soybean ( Glycine max [ L. ] Merr . ) accession C08 on its early responses to salinity and salt-induced transcriptomic modifications , the aim of this study was to assess the lipid profile changes in this cultivar before and after short-term salt stress , and to explore the adaptive mechanisms underpinning lipid homeostasis . To this end , lipid profiling and proteomic analyses were performed on the leaves of soybean seedlings subjected to salt treatment for 0 , 0.5 , 1 , and 2 h. Our results revealed that short-term salt stress caused dynamic lipid alterations resulting in recycling for both galactolipids and phospholipids . A comprehensive understanding of membrane lipid adaption following salt treatment was achieved by combining time-dependent lipidomic and proteomic data . Proteins involved in phosphoinositide synthesis and turnover were upregulated at the onset of salt treatment . Salinity-induced lipid recycling was shown to enhance jasmonic acid and phosphatidylinositol biosyntheses . Our study demonstrated that salt stress resulted in a remodeling of membrane lipid composition and an alteration in membrane lipids associated with lipid signaling and metabolism in C08 leaves .
Glomus mosseae , a representative species of Endogonaceae ( Phycomycetes ) able to form vesicular-arbuscular mycorrhiza , was investigated for phytohormone production . Spores of G. mosseae were axenically germinated in water , and the resultant mycelial growth was assayed by standard procedures for extracting plant hormones from microbial cultures . Paper partition chromatography and specific bioassays were used to separate and identify plant growth-regulating substances . The microorganism synthesized at least two gibberellin-like substances , one with R(f ) corresponding in position to authentic gibberellic acid , and four substances with the properties of cytokinins .
BACKGROUND : Seed dormancy is controlled by the physiological or structural properties of a seed and the external conditions . It is induced as part of the genetic program of seed development and maturation . Seeds with deep physiological embryo dormancy can be stimulated to germinate by a variety of treatments including cold stratification . Hormonal imbalance between germination inhibitors ( e.g. abscisic acid ) and growth promoters ( e.g. gibberellins ) is the main cause of seed dormancy breaking . Differences in the status of hormones would affect expression of genes required for germination . Proteomics offers the opportunity to examine simultaneous changes and to classify temporal patterns of protein accumulation occurring during seed dormancy breaking and germination . Analysis of the functions of the identified proteins and the related metabolic pathways , in conjunction with the plant hormones implicated in seed dormancy breaking , would expand our knowledge about this process . RESULTS : A proteomic approach was used to analyse the mechanism of dormancy breaking in Norway maple seeds caused by cold stratification , and the participation of the abscisic ( ABA ) and gibberellic ( GA ) acids . Forty-four proteins showing significant changes were identified by mass spectrometry . Of these , eight spots were identified as water-responsive , 18 spots were ABA- and nine GA-responsive and nine spots were regulated by both hormones . The classification of proteins showed that most of the proteins associated with dormancy breaking in water were involved in protein destination . Most of the ABA- and GA-responsive proteins were involved in protein destination and energy metabolism . CONCLUSION : In this study , ABA was found to mostly down-regulate proteins whereas GA up-regulated proteins abundance . Most of the changes were observed at the end of stratification in the germinated seeds . This is the most active period of dormancy breaking when seeds pass from the quiescent state to germination . Seed dormancy breaking involves proteins of various processes but the proteasome proteins , S-adenosylmethionine synthetase , glycine-rich RNA binding protein , ABI3-interacting protein 1 , EF-2 and adenosylhomocysteinase are of particular importance . The effect of exogenously applied hormones was not a determining factor for total inhibition ( ABA ) or stimulation ( GA ) of Norway maple seed dormancy breaking and germination but proteomic data has proven these hormones play a role .
BACKGROUND : Drought is a severe environmental stress . It is estimated that about 50 % of the world rice production is affected mainly by drought . Apart from conventional breeding strategies to develop drought-tolerant crops , innovative computational approaches may provide insights into the underlying molecular mechanisms of stress response and identify drought-responsive markers . Here we propose a network-based computational approach involving a meta-analytic study of seven drought-tolerant rice genotypes under drought stress . RESULTS : Co-expression networks enable large-scale analysis of gene-pair associations and tightly coupled clusters that may represent coordinated biological processes . Considering differentially expressed genes in the co-expressed modules and supplementing external information such as resistance/tolerance QTLs , transcription factors , network-based topological measures , we identify and prioritize drought-adaptive co-expressed gene modules and potential candidate genes . Using the candidate genes that are well-represented across the datasets as ' seed ' genes , two drought-specific protein-protein interaction networks ( PPINs ) are constructed with up- and down-regulated genes . Cluster analysis of the up-regulated PPIN revealed ABA signalling pathway as a central process in drought response with a probable crosstalk with energy metabolic processes . Tightly coupled gene clusters representing up-regulation of core cellular respiratory processes and enhanced degradation of branched chain amino acids and cell wall metabolism are identified . Cluster analysis of down-regulated PPIN provides a snapshot of major processes associated with photosynthesis , growth , development and protein synthesis , most of which are shut down during drought . Differential regulation of phytohormones , e.g. , jasmonic acid , cell wall metabolism , signalling and posttranslational modifications associated with biotic stress are elucidated . Functional characterization of topologically important , drought-responsive uncharacterized genes that may play a role in important processes such as ABA signalling , calcium signalling , photosynthesis and cell wall metabolism is discussed . Further transgenic studies on these genes may help in elucidating their biological role under stress conditions . CONCLUSION : Currently , a large number of resources for rice functional genomics exist which are mostly underutilized by the scientific community . In this study , a computational approach integrating information from various resources such as gene co-expression networks , protein-protein interactions and pathway-level information is proposed to provide a systems-level view of complex drought-responsive processes across the drought-tolerant genotypes .
BACKGROUND : Plant genes that provide a different response to a similar dehydration stress illustrate the concept of transcriptional ' dehydration stress memory ' . Pre-exposing a plant to a biotic stress or a stress-signaling hormone may increase transcription from response genes in a future stress , a phenomenon known as ' gene priming ' . Although known that primed transcription is preceded by accumulation of H3K4me3 marks at primed genes , what mechanism provides for their appearance before the transcription was unclear . How augmented transcription is achieved , whether/how the two memory phenomena are connected at the transcriptional level , and whether similar molecular and/or epigenetic mechanisms regulate them are fundamental questions about the molecular mechanisms regulating gene expression . RESULTS : Although the stress hormone jasmonic acid ( JA ) was unable to induce transcription of tested dehydration stress response genes , it strongly potentiated transcription from specific ABA-dependent ' memory ' genes . We elucidate the molecular mechanism causing their priming , demonstrate that stalled RNA polymerase II and H3K4me3 accumulate as epigenetic marks at the JA-primed ABA-dependent genes before actual transcription , and describe how these events occur mechanistically . The transcription factor MYC2 binds to the genes in response to both dehydration stress and to JA and determines the specificity of the priming . The MEDIATOR subunit MED25 links JA-priming with dehydration stress response pathways at the transcriptional level . Possible biological relevance of primed enhanced transcription from the specific memory genes is discussed . CONCLUSIONS : The biotic stress hormone JA potentiated transcription from a specific subset of ABA-response genes , revealing a novel aspect of the JA- and ABA-signaling pathways ' interactions . H3K4me3 functions as an epigenetic mark at JA-primed dehydration stress response genes before transcription . We emphasize that histone and epigenetic marks are not synonymous and argue that distinguishing between them is important for understanding the role of chromatin marks in genes ' transcriptional performance . JA-priming , specifically of dehydration stress memory genes encoding cell/membrane protective functions , suggests it is an adaptational response to two different environmental stresses .
The oxidative deamination of N-methylputrescine is an essential step in both pyridine and tropane alkaloid biosynthesis . Reverse genetic approaches have not resulted in the cloning of a methylputrescine oxidase gene ( MPO ) . However , we have used a homology-based approach to clone a full-length tobacco MPO1 cDNA . The MPO1 gene is part of a small multigene family comprised of approximately six members . MPO1-like transcript levels increased in roots that were either deprived of auxin or treated with methyl jasmonic acid . Similar to other known nicotine biosynthetic genes in domesticated tobacco , MPO1-like mRNA levels were lower in roots with the mutant a and b alleles . The MPO1 protein was expressed in bacteria as a recombinant Thioredoxin-His(6)-MPO1 fusion protein . The recombinant MPO1 protein utilized N-methylputrescine more efficiently than other diamines . Therefore , the kinetic properties of the MPO1 enzyme may play an important role in determining the pyridine alkaloid profiles observed in tobacco roots .
How plants perceive insect attacks is an area of active research . Numerous studies have shown that regurgitant from feeding insects elicits a defense response in plants , which is often assumed to be distinct from a wound response . We have characterized the inducible defense response in hybrid poplar and found it to be qualitatively similar between wounding and application of regurgitant from forest tent caterpillar . We suggest that this is likely attributable to our wounding treatment which is much more intense compared to most other studies . These overlapping responses appear to be activated via jasmonic acid signaling , and we speculate that they are both triggered by elicitors of plant origin . Wounding would release such elicitor molecules when leaf cells are disrupted , and regurgitant may contain them in a modified or processed form . This hypothesis could explain why some other necrosis-inducing stresses also induce herbivore defense genes .
BACKGROUND : Sugarcane smut caused by Sporisorium scitamineum is one of the most severe fungal diseases in the sugarcane industry . Using a molecular biological technique to mine sugarcane resistance genes can provide gene resources for further genetic engineering of sugarcane disease-resistant breeding . Jasmonate ZIM ( zinc-finger inflorescence meristem ) domain ( JAZ ) proteins , which involved in the responses to plant pathogens and abiotic stresses , are important signaling molecules of the jasmonic acid ( JA ) pathway . RESULTS : Seven differentially expressed sugarcane JAZ genes , ScJAZ1-ScJAZ7 , were mined from the transcriptome of sugarcane after inoculation with S. scitamineum . Bioinformatic analyses revealed that these seven ScJAZ genes encoded basic proteins that contain the TIFY and CCT_2 domains . Quantitative reverse transcription polymerase chain reaction ( qRT-PCR ) analysis demonstrated that the ScJAZ1-ScJAZ7 genes were tissue specific and differentially expressed under adverse stress . During S. scitamineum infection , the transcripts of ScJAZ4 and ScJAZ5 were both upregulated in the susceptible genotype ROC22 and the resistant genotype Yacheng05 - 179 ; ScJAZ1 , ScJAZ2 , ScJAZ3 , and ScJAZ7 were downregulated in Yacheng05 - 179 and upregulated in ROC22 ; and the expression of ScJAZ6 did not change in ROC22 , but was upregulated in Yacheng05 - 179 . The transcripts of the seven ScJAZ genes were increased by the stimuli of salicylic acid and abscisic acid , particularly methyl jasmonate . The expression of the genes ScJAZ1-ScJAZ7 was immediately upregulated by the stressors hydrogen peroxide , sodium chloride , and copper chloride , whereas slightly induced after treatment with calcium chloride and polyethylene glycol . In addition , the expression of ScJAZ6 , as well as seven tobacco immunity-associated marker genes were upregulated , and antimicrobial activity against Pseudomonas solanacearum and Fusarium solani var . coeruleum was observed during the transient overexpression of ScJAZ6 in Nicotiana benthamiana , suggesting that the ScJAZ6 gene is associated with plant immunity . CONCLUSIONS : The different expression profiles of the ScJAZ1-ScJAZ7 genes during S. scitamineum infection , the positive response of ScJAZ1-ScJAZ7 to hormones and abiotic treatments , and the function analysis of the ScJAZ6 gene revealed their involvement in the defense against biotic and abiotic stresses . The findings of the present study facilitate further research on the ScJAZ gene family especially their regulatory mechanism in sugarcane .
Global warming frequently leads to extreme temperatures , which pose a serious threat to the growth , development , and yield formation of crops such as maize . This study aimed to deeply explore the molecular mechanisms of young ear development under heat stress . We selected the heat-tolerant maize variety Zhengdan 958 ( T ) and heat-sensitive maize variety Xianyu 335 ( S ) , and subjected them to heat stress in the V9 ( 9th leaf ) , V12 ( 12th leaf ) , and VT ( tasseling ) growth stages . We combined analysis of the maize phenotype with omics technology and physiological indicators to compare the differences in young ear morphology , total number of florets , floret fertilization rate , grain abortion rate , number of grains , and main metabolic pathways between plants subjected to heat stress and those left to develop normally . The results showed that after heat stress , the length and diameter of young ears , total number of florets , floret fertilization rate , and number of grains all decreased significantly , whereas the length of the undeveloped part at the top of the ear and grain abortion rate increased significantly . In addition , the differentially expressed genes ( DEGs ) in young ears were significantly enriched in the hormone signaling pathways . The endogenous hormone content in young ears exhibited different changes : zeatin ( ZT ) and zeatin riboside ( ZR ) decreased significantly , but gibberellin acid(3 ) ( GA(3 ) ) , gibberellin acid(4 ) ( GA(4 ) ) , and abscisic acid ( ABA ) increased significantly , in ears subjected to heat stress . In the heat-tolerant maize variety , the salicylic acid ( SA ) , and jasmonic acid ( JA ) content in the vegetative growth stage also increased in ears subjected to heat stress , whereas the opposite effect was observed for the heat-sensitive variety . The changes in endogenous hormone content of young ears that were subjected to heat stress significantly affected ear development , resulting in a reduction in the number of differentiated florets , fertilized florets and grains , which ultimately reduced the maize yield .
Salicylic acid ( SA ) , jasmonic acid ( JA ) , ethylene ( ET ) , and their interactions mediate plant responses to pathogen and herbivore attack . JA-SA and JA-ET cross-signaling are well studied , but little is known about SA-ET cross-signaling in plant-herbivore interactions . When the specialist herbivore tobacco hornworm ( Manduca sexta ) attacks Nicotiana attenuata , rapid and transient JA and ET bursts are elicited without significantly altering wound-induced SA levels . In contrast , attack from the generalist beet armyworm ( Spodoptera exigua ) results in comparatively lower JA and ET bursts , but amplified SA bursts . These phytohormone responses are mimicked when the species ' larval oral secretions ( OS(Se ) and OS(Ms ) ) are added to puncture wounds . Fatty acid-amino acid conjugates elicit the JA and ET bursts , but not the SA burst . OS(Se ) had enhanced glucose oxidase activity ( but not beta-glucosidase activity ) , which was sufficient to elicit the SA burst and attenuate the JA and ET levels . It is known that SA antagonizes JA ; glucose oxidase activity and associated hydrogen peroxide also antagonizes the ET burst . We examined the OS(Ms)-elicited SA burst in plants impaired in their ability to elicit JA ( antisense [as]-lox3 ) and ET ( inverted repeat [ir]-aco ) bursts and perceive ET ( 35s-etr1b ) after fatty acid-amino acid conjugate elicitation , which revealed that both ET and JA bursts antagonize the SA burst . Treating wild-type plants with ethephone and 1-methylcyclopropane confirmed these results and demonstrated the central role of the ET burst in suppressing the OS(Ms)-elicited SA burst . By suppressing the SA burst , the ET burst likely facilitates unfettered JA-mediated defense activation in response to herbivores that otherwise would elicit SA .