slotreck/pickle huggingface dataset:
Auxin is one of the most important phytohormones and exerts pleiotropic effects on plant growth and development . Aux/IAA and auxin response factor ( ARF ) are two important protein families that are well recognized for their roles in auxin-mediated responses . Aux/IAA proteins are short-lived transcriptional regulators that mediate auxin responses through interaction with ARF transcription factors . Here , we systematically compared the genomic organization of the two families in rice . The expression profiles of both families were compared to show possible association of the two gene families at expression level , which would help reveal their synergistic relationships and functions . The expression profile analysis of Aux/IAA and ARF genes in 30 organs/tissues ( collected from an entire life cycle of rice ) suggested that Aux/IAA and ARF genes are expressed in very diverse patterns . In general , the genes showing similar expression patterns tended to be in the same phylogenetic subgroup even though their expression patterns were not always the same . Hierarchical cluster analysis revealed that there are eight pairs of IAA and ARF genes , with each pair showing highly correlated expression . The expression levels of the IAA gene family were also checked under various hormone treatments including abscisic acid , kinetin , gibberellin , jasmonic acid , auxin and brassinolide . The results indicated that most of the IAA genes respond to at least one of the treatments . Furthermore , DNA chip and real-time PCR results show that many genes in these families were responsive to various abiotic stresses , indicating an interaction between plant growth and abiotic stress . The effect of abiotic stress on plant growth and auxin distribution was further confirmed with the root growth of DR5-GUS transgenic rice under mannitol treatment , in which a close association between mannitol-induced changes of auxin distribution and root growth was observed .
Recent evidence suggests that oxidized lipid-derived molecules play significant roles in inducible plant defence responses against microbial pathogens , either by directly deterring parasite multiplication , or as signals involved in the induction of sets of defence genes . The synthesis of these oxylipins was hypothesized to be initiated by the phospholipase A2-mediated release of unsaturated fatty acids from membrane lipids . Here , we demonstrate that , in tobacco leaves reacting hypersensitively to tobacco mosaic virus , a strong increase in soluble phospholipase A2 ( PLA2 ) activity occurs at the onset of necrotic lesion appearance . This rapid PLA2 activation occurred before the accumulation of 12-oxophytodienoic and jasmonic acids , two fatty acid-derived defence signals . Three PLA2 isoforms were separated and the most active enzyme was partially purified , its N-terminal sequence displaying similarity with patatin , the major storage protein in potato tubers . Three related tobacco patatin-like cDNAs , called NtPat1 , NtPat2 and NtPat3 , were cloned , with NtPat2 encoding the PLA2 isolated from infected leaves . RT-PCR experiments showed a rapid transcriptional activation of the three NtPat genes in virus-infected leaves , preceding the increase in PLA2 activity . Recombinant NtPat1 and NtPat3 enzymes were active in an assay using labelled bacterial membranes , and also displayed high bona fide PLA2 activity on phosphatidylcholine substrate . These results point to a possible new role of patatin-like phospholipases in inducible plant defence responses . The induction kinetics together with the enzymatic activity data indicate that the NtPat proteins may provide precursors for oxylipin synthesis during the hypersensitive response to pathogens .
Azospirillum species are plant growth-promotive bacteria whose beneficial effects have been postulated to be partially due to production of phytohormones , including gibberellins ( GAs ) . In this work , Azospirillum brasilense strain Cd and Azospirillum lipoferum strain USA 5b promoted sheath elongation growth of two single gene GA-deficient dwarf rice ( Oryza sativa ) mutants , dy and dx , when the inoculated seedlings were supplied with [17,17 - 2H2]GA20-glucosyl ester or [ 17,17- 2H2]GA20-glucosyl ether . Results of capillary gas chromatography-mass spectrometry analysis show that this growth was due primarily to release of the aglycone [17,17 - 2H2]GA20 and its subsequent 3beta-hydroxylation to [17,17 - 2H2]GA1 by the microorganism for the dy mutant , and by both the rice plant and microorganism for the dx mutant .
Autophagy is an evolutionarily conserved intracellular process for vacuolar degradation of cytoplasmic components . In higher plants , autophagy defects result in early senescence and excessive immunity-related programmed cell death ( PCD ) irrespective of nutrient conditions ; however , the mechanisms by which cells die in the absence of autophagy have been unclear . Here , we demonstrate a conserved requirement for salicylic acid ( SA ) signaling for these phenomena in autophagy-defective mutants ( atg mutants ) . The atg mutant phenotypes of accelerated PCD in senescence and immunity are SA signaling dependent but do not require intact jasmonic acid or ethylene signaling pathways . Application of an SA agonist induces the senescence/cell death phenotype in SA-deficient atg mutants but not in atg npr1 plants , suggesting that the cell death phenotypes in the atg mutants are dependent on the SA signal transducer NONEXPRESSOR OF PATHOGENESIS-RELATED GENES1 . We also show that autophagy is induced by the SA agonist . These findings imply that plant autophagy operates a novel negative feedback loop modulating SA signaling to negatively regulate senescence and immunity-related PCD .
BACKGROUND AND AIMS : Rhizomes are underground stems with meristematic tissues capable of generating shoots and roots . However , mechanisms controlling rhizome formation and growth are yet to be completely understood . The objectives of this study were to investigate whether rhizome development could be regulated by cytokinins ( CKs ) and gibberellic acids ( GAs ) , and determine underlying mechanisms of regulation of rhizome formation and growth of tall fescue ( Festuca arundinacea ) by a CK or GA through proteomic and transcript analysis . METHODS : A rhizomatous genotype of tall fescue ( ' BR ' ) plants were treated with 6-benzylaminopurine ( BAP , a synthetic cytokinin ) or GA3 in hydroponic culture in growth chambers . Furthermore , comparative proteomic analysis of two-dimensional electrophoresis and mass spectrometry were performed to investigate proteins and associated metabolic pathways imparting increased rhizome number by BAP and rhizome elongation by GA3 KEY RESULTS : BAP stimulated rhizome formation while GA3 promoted rhizome elongation . Proteomic analysis identified 76 differentially expressed proteins ( DEPs ) due to BAP treatment and 37 DEPs due to GA3 treatment . Cytokinin-related genes and cell division-related genes were upregulated in the rhizome node by BAP and gibberellin-related and cell growth-related genes in the rhizome by GA3 CONCLUSIONS : Most of the BAP- or GA-responsive DEPs were involved in respiratory metabolism and amino acid metabolism . Transcription analysis demonstrated that genes involved in hormone metabolism , signalling pathways , cell division and cell-wall loosening were upregulated by BAP or GA3 The CK and GA promoted rhizome formation and growth , respectively , by activating metabolic pathways that supply energy and amino acids to support cell division and expansion during rhizome initiation and elongation in tall fescue .
Menthol mint ( Mentha arvensis L. ) cultivation is significantly affected by the heavy metals like cadmium ( Cd ) which also imposes severe health hazards . Two menthol mint cultivars namely Kosi and Kushal were evaluated under Cd stress conditions . Impact of plant growth regulators ( PGRs ) like salicylic acid ( SA ) , gibberellic acid ( GA(3 ) ) and triacontanol ( Tria ) on Cd stress tolerance was assessed . Reduced growth , photosynthetic parameters , mineral nutrient concentration , and increased oxidative stress biomarkers like electrolyte leakage , malondialdehyde , and hydrogen peroxide contents were observed under Cd stress . Differential upregulation of proline content and antioxidant activities under Cd stress was observed in both the cultivars . Interestingly , low electrolyte leakage , lipid peroxidation , hydrogen peroxide and Cd concentration in leaves were observed in Kushal compared to Kosi . Among all the PGRs tested , SA proved to be the   best in improving Cd-stress tolerance in both the cultivars but Kushal responded better than Kosi .
BACKGROUND : Rare data are available on the molecular responses of higher plants to low pH. Seedlings of ' Sour pummelo ' ( Citrus grandis ) and ' Xuegan ' ( Citrus sinensis ) were treated daily with nutrient solution at a pH of 2.5 , 3 , or 6 ( control ) for nine months . Thereafter , we first used 2-dimensional electrophoresis ( 2-DE ) to investigate low pH-responsive proteins in Citrus leaves . Meanwhile , we examined low pH-effects on leaf gas exchange , carbohydrates , ascorbate , dehydroascorbate and malondialdehyde . The objectives were to understand the adaptive mechanisms of Citrus to low pH and to identify the possible candidate proteins for low pH-tolerance . RESULTS : Our results demonstrated that Citrus were tolerant to low pH , with a slightly higher low pH-tolerance in the C. sinensis than in the C. grandis . Using 2-DE , we identified more pH   2.5-responsive proteins than pH   3-responsive proteins in leaves . This paper discussed mainly on the pH   2.5-responsive proteins . pH   2.5 decreased the abundances of proteins involved in ribulose bisphosphate carboxylase/oxygenase activation , Calvin cycle , carbon fixation , chlorophyll biosynthesis and electron transport , hence lowering chlorophyll level , electron transport rate and photosynthesis . The higher oxidative damage in the pH   2.5-treated C. grandis leaves might be due to a combination of factors including higher production of reactive oxygen species , more proteins decreased in abundance involved in antioxidation and detoxification , and lower ascorbate level . Protein and amino acid metabolisms were less affected in the C. sinensis leaves than those in the C. grandis leaves when exposed to pH   2.5 . The abundances of proteins related to jasmonic acid biosynthesis and signal transduction were increased and decreased in the pH   2.5-treated C. sinensis and C. grandis leaves , respectively . CONCLUSIONS : This is the first report on low pH-responsive proteins in higher plants . Thus , our results provide some novel information on low pH-toxicity and -tolerance in higher plants .
Nonspecific lipid transfer proteins ( nsLTPs ) are small , basic cystein-rich proteins believed to be involved in plant defense mechanisms . Three cDNAs coding nsLTPs from grape ( Vitis vinifera sp. ) were cloned by reverse-transcriptase-polymerase chain reaction ( RT-PCR ) and PCR . The expression of nsLTP genes was investigated in 41B-rootstock grape cell suspension , in response to various defense-related signal molecules . Ergosterol ( a fungi-specific sterol ) and a proteinaceous elicitor purified from Botrytis cinerea strongly and rapidly induced the accumulation of nsLTP mRNAs . Jasmonic acid , cholesterol , and sitosterol also promoted nsLTPs mRNA accumulation , although to a lesser extent , whereas salicylic acid had no effect . High performance liquid chromatography analysis indicated that the amounts of three LTP isoforms ( previously named P1 , P2 , and P4 ) were increased by ergosterol . None of the four isoforms displayed any significant antifungal properties , with the exception of the P4 isoform , which reduced Botrytis mycelium growth in vitro , but only in calcium-free medium . The results are discussed in the context of plant-pathogen interactions .
We analyzed expression of marker genes for three defense pathways during infection by Cauliflower mosaic virus ( CaMV ) , a compatible pathogen of Arabidopsis ( Arabidopsis thaliana ) , using luciferase reporter transgenes and directly by measuring transcript abundance . Expression of PR-1 , a marker for salicylic acid signaling , was very low until 8 d postinoculation and then rose sharply , coinciding with the rise in virus levels . In contrast , as early as 2 h postinoculation , transcriptional up-regulation of GST1-a marker for reactive oxygen species-and PDF1.2-a marker for jasmonic acid/ethylene defense signaling-was detectable in the virus-inoculated leaf and systemically . In parallel with the activation of GST1 , H(2)O(2 ) accumulated locally and systemically in virus- but not mock-inoculated plants . However , in plants inoculated with infectious CaMV DNA rather than virus particles , the onset of systemic luciferase activity was delayed by 24 to 48 h , suggesting that virion structural proteins act as the elicitor . This phenomenon , which we term the rapid systemic response , preceded virus movement from the inoculated leaf ; therefore , the systemic signal is not viral . Systemic , but not local , H(2)O(2 ) accumulation was abolished in rbohDF double mutants and in etr1 - 1 and ein2 - 1 mutants , implicating NADPH oxidase and ethylene signaling in the generation and transduction of the response . Ethylene , but not rbohDF mutants , also showed reduced susceptibility to CaMV , whereas in NahG transgenics , virus levels were similar to wild type . These findings implicate reactive oxygen species and ethylene in signaling in response to CaMV infection , but suggest that salicylic acid does not play an effective role .
The present study was aimed to investigate the effects of subacute and subchronic treatment of some plant growth regulators ( PGRs ) , such as abscisic acid ( ABA ) and gibberellic acid ( GA3 ) , on neurological and immunological biomarkers in various tissues of rats . The activities of acetylcholinesterase ( AChE ) and butrylcholinesterase ( BChE ) were selected as biomarkers for neurotoxic biomarkers . Adenosine deaminase ( ADA ) and myeloperoxidase ( MPO ) were measured as indicators for immunotoxic investigation purpose . Wistar albino rats were orally administered with 25 and 50 ppm of PGRs ad libitum for 25 - 50 days continuously with drinking water . The treatment of PGRs caused different effects on the activities of enzymes . Results showed that the administrations of ABA and GA3 increased AChE and BChE activities in some tissues of rats treated with both the dosages and periods of ABA and GA3 . With regard to the immunotoxic effects , ADA activity fluctuated , while MPO activity increased after subacute and subchronic exposure of treated rat tissues to both dosages when compared with the controls . The observations presented led us to conclude that the administrations of PGRs at subacute and subchronic exposure increased AChE , BChE , and MPO activities , while fluctuating the ADA activity in various tissues of rats . This may reflect the potential role of these parameters as useful biomarkers for toxicity of PGRs .
Jasmonates control defense gene expression and male fertility in the model plant Arabidopsis thaliana . In both cases , the involvement of the jasmonate pathway is complex , involving large-scale transcriptional reprogramming . Additionally , jasmonate signaling is hard-wired into the auxin , ethylene , and salicylate signal networks , all of which are under intense investigation in Arabidopsis . In male fertility , jasmonic acid ( JA ) is the essential signal intervening both at the level of anther elongation and in pollen dehiscense . A number of genes potentially involved in jasmonate-dependent anther elongation have recently been discovered . In the case of defense , at least two jasmonates , JA and its precursor 12-oxo-phytodienoic acid ( OPDA ) , are necessary for the fine-tuning of defense gene expression in response to various microbial pathogens and arthropod herbivores . However , only OPDA is required for full resistance to some insects and fungi . Other jasmonates probably affect yet more physiological responses . A series of breakthroughs have identified the SKP/CULLIN/F-BOX ( SCF ) , CORONATINE INSENSITIVE ( COI1 ) complex , acting together with the CONSTITUTIVE PHOTOMORPHOGENIC 9 ( COP9 ) signalosome , as central regulatory components of jasmonate signaling in Arabidopsis . The studies , mostly involving mutational approaches , have paved the way for suppressor screens that are expected to further extend our knowledge of jasmonate signaling . When these and other new mutants affecting jasmonate signaling are characterized , new nodes will be added to the Arabidopsis Jasmonate Signaling Pathway Connections Map , and the lists of target genes regulated by jasmonates in Arabidopsis will be expanded .
The large WRKY transcription factor family is mainly involved in regulating plant immune responses . Arabidopsis WRKY33 is a key transcriptional regulator of hormonal and metabolic processes towards Botrytis cinerea strain 2100 infection and is essential for resistance . In contrast to B. cinerea strain 2100 , the strain B05.10 is virulent on wild-type ( WT ) Col-0 Arabidopsis plants highlighting the genetic diversity within this pathogen species . We analysed how early WRKY33-dependent responses are affected upon infection with strain B05.10 and found that most of these responses were strongly dampened during this interaction . Ectopic expression of WRKY33 resulted in complete resistance towards this strain indicating that virulence of B05.10 , at least partly , depends on suppressing WRKY33 expression/protein accumulation . As a consequence , the expression levels of direct WRKY33 target genes , including those involved in the biosynthesis of camalexin , were also reduced upon infection . Concomitantly , elevated levels of the phytohormone abscisic acid ( ABA ) were observed . Molecular and genetic studies revealed that ABA negatively influences defence to B05.10 and effects jasmonic acid/ethylene ( JA/ET ) and salicylic acid ( SA ) levels . Susceptibility/resistance was determined by the antagonistic effect of ABA on JA , and this crosstalk required suppressing WRKY33 functions at early infection stages . This indicates that B. cinerea B05.10 promotes disease by suppressing WRKY33-mediated host defences .
Bowman-Birk inhibitor ( BBI ) genes encode serine protease inhibitors well known for their anticarcinogenic properties and roles in plant defense against insects and pathogens . Here we investigated the expression of a BBI gene in response to water deficit , recovery and phytohormones . A full length cDNA encoding a novel BBI ( AhBBI ) was isolated from peanut ( Arachis hypogaea L. ) leaves . The deduced protein is a polypeptide of 11.5kDa containing a signal peptide of 20 amino acids which is missing from peanut seed full-length BBI . Sequence analysis showed that AhBBI presents the characteristic features of BBIs but its first inhibitory loop is unique among the Fabaceae species . Real-time PCR analyses indicated that in peanut leaves , AhBBI is upregulated by water deficit and exogenous jasmonic acid ( JA ) but repressed by abscissic acid ( ABA ) after 24h of treatment . The transcripts accumulation patterns during water deficit differed between two cultivars studied in relation to their tolerance levels to drought . AhBBI transcripts accumulated earlier and stronger in the tolerant cultivar ( cv . Fleur11 ) compared to the susceptible one ( cv . 73 - 30 ) suggesting that BBI genes are involved in drought stress tolerance . Subsequent rehydration reversed the accumulation of AhBBI transcripts in both cultivars but at different levels . The overall role of BBI in abiotic stress tolerance and the possible mechanisms of action are discussed .
Apoplast , the diffusional space between plant cell plasma membranes , is an important medium for signaling within and between the cells . Apoplastic reactive oxygen species ( ROS ) are crucial signaling molecules in various biological processes . ROS signaling is interconnected with the response to several hormones , including jasmonic acid ( JA ) , salicylic acid ( SA ) and ethylene . Using ozone ( O3 ) to activate apoplastic ROS signaling , we performed global and targeted analysis of transcriptional changes and cell death assays to dissect the contribution of hormone signaling and various transcription factors ( TFs ) in the regulation of gene expression and cell death . The contributions of SA , JA , and ethylene were assessed through analysis of single , double , and triple mutants deficient in biosynthesis or signaling for all three hormones . Even in the triple mutant , the global gene expression responses to O3 were mostly similar to the wild-type . Cell death in the JA receptor mutant coi1 - 16 was suppressed by impairment of the NADPH oxidase RBOHF , suggesting a role for a ROS signal in limiting the spread of cell death . In response to apoplastic ROS , there is not a single signaling pathway that regulates gene expression or cell death . Instead , several pathways regulate the apoplastic ROS response via combinatorial or overlapping mechanisms .
BACKGROUND : Salt stress is a devastating environmental stress that causes plant growth inhibition and yield reduction . OBJECTIVE : The identification of salt-tolerant genes brings hope for the generation of salinity-tolerant crop plants through molecular breeding . METHODS : In this study , one salt-sensitive and one salt-tolerant maize inbred line were screened from 242 maize inbred lines . Reactive oxygen species (ROS)-related enzyme activities were detected and salt-responsive comparative transcriptome analysis was performed for control and 220 mM NaCl treated maize leaves . RESULTS : Salt-tolerant maize inbred line ( L87 ) showed higher ROS-related enzyme ( SOD , POD , APX and CAT ) activities and accumulated relatively lower levels of ROS under salt stress . Of the total DEGs , 1856 upregulated DEGs were specific to L87 , including stress tolerance-related members of the 70kDa family of heat shock proteins ( Hsp70s ) and aquaporins . The DEGs involved in the abscisic acid ( ABA ) , ethylene , jasmonic acid ( JA ) and salicylic acid ( SA ) signal transduction pathways may determine the difference in salt tolerance between the two varieties , especially one central component SnRK2 , that positively regulates ABA signaling and was only upregulated in L87 . Analysis of DEGs related to ROS scavenging showed that some peroxidase ( POD ) , glutathione S-transferase ( GST ) , catalase ( CAT ) and superoxide dismutase ( SOD ) genes specific to L87 probably enhanced its salt tolerance . The analysis of differentially expressed transcription factors ( TFs ) suggested that WRKY TFs could contribute to the difference in salt tolerance between the two maize lines . CONCLUSION : Compared with Salt-sensitive maize inbred line ( L29 ) , L87 exhibits specific regulatory mechanisms related to salt tolerance , including plant hormone interactions , ROS scavenging and the regulation of TFs . Our study identifies new candidate genes that may regulate maize tolerance to salt stress and provides useful information for breeding maize with high salt resistance .