bluuebunny/crossref_metadata_2025_split huggingface dataset:
A custom microarray analysis of gene expression during programmed cell death in Arabidopsis thaliana
Authors: Swidzinski Jodi A. , Sweetlove Lee J. , Leaver Christopher J. 
Published: March 2003

SummaryProgrammed cell death (PCD) is a form of cellular suicide requiring active gene expression, and occurs in both animals and plants. While the cascade of events and the genes that control PCD have been extensively studied in animals, we remain largely ignorant about the similar process in plant cells. Many of the key proteins of animal cell death such as the Bcl‐2 family and the caspase family of proteases do not appear to be conserved in plants, suggesting that plants may employ unique mechanisms to execute PCD. To identify genetic elements of PCD in plants, we monitored changes in transcript levels of approximately 100 selected genes during cell death in an Arabidopsis cell suspension culture using a cDNA microarray. PCD was induced in the cell cultures by two independent means (heat treatment or by allowing the cultures to senesce) to allow the distinction to be drawn between changes in gene expression that are related to PCD and those that are specific to a particular treatment. We argue that genes whose expression is altered during PCD induced by two different means may be generally involved in all types of PCD. We show that certain oxidative stress‐related genes, including CSD1, CSD3, and GPX, in addition to cysteine proteinases, some transcription factors, and HR‐related genes may serve as markers of a core plant cell death programme. Additionally we observe a down‐regulation of the mitochondrial adenine nucleotide transporter and suggest that this may be an early event in the execution of plant PCD.
A knock‐out mutation in allene oxide synthase results in male sterility and defective wound signal transduction in Arabidopsis due to a block in jasmonic acid biosynthesis
Authors: Park Joon‐Hyun , Halitschke Rayko , Kim Ho Bang , Baldwin Ian T. , Feldmann Kenneth A. , Feyereisen René 
Published: March 2003

SummaryRecent studies on jasmonic acid (JA) biosynthetic mutants have shown that jasmonates play essential roles in pollen maturation and dehiscence and wound‐induced defence against biotic attacks. To better understand the biosynthetic mechanisms of this essential plant hormone, we isolated an Arabidopsis knock‐out mutant defective in the JA biosynthetic gene CYP74A (allene oxide synthase, AOS) using reverse genetics screening methods. This enzyme catalyses dehydration of the hydroperoxide to an unstable allene oxide in the JA biosynthetic pathway. Endogenous JA levels, which increase 100‐fold 1 h after wounding in wild‐type plants, do not increase after wounding in the aos mutant. In addition, the mutant showed severe male sterility due to defects in anther and pollen development. The male‐sterile phenotype was completely rescued by exogenous application of methyl jasomonate and by complementation with constitutive expression of the AOS gene. RT–PCR analysis showed that the induction of transcripts for vegetative storage protein and lipoxygenase genes, previously shown to be inducible by wound and jasmonate application in the wild‐type, was absent in the aos mutant. In transgenic plants constitutively expressing AOS, wound‐induced JA levels were 50–100% higher compared to wild‐type plants. Taken together with JA deficiency in the aos mutant, our results show that AOS is critical for the biosynthesis of all biologically active jasmonates. Our results also suggest that AOS expression is limiting JA levels in wounded plants, but that the AOS hydroperoxide substrate levels, controlled by upstream enzymes (lipoxygenase and phospholipase), determine JA levels in unwounded plants.
The broad‐spectrum potato cyst nematode resistance gene (Hero) from tomato is the only member of a large gene family of NBS‐LRR genes with an unusual amino acid repeat in the LRR region
Authors: Ernst Karin , Kumar Amar , Kriseleit Doris , Kloos Dorothee‐U. , Phillips Mark S. , Ganal Martin W. 
Published: March 2003

SummaryThe Hero gene of tomato is a broad spectrum resistance gene that confers a high level of resistance to all pathotypes of the potato cyst nematodes Globodera rostochiensis and partial resistance to G. pallida. The gene was identified by map‐based cloning, sequencing and complementation analysis of two susceptible tomato lines with an array of 13 overlapping cosmids spanning a total distance of 135 kb. Hero encodes a protein with a nucleotide‐binding site (NBS) and a leucine‐rich‐repeat (LRR) domain and is a member of a gene family of 14 highly homologous genes, which are clustered within a continuous 118‐kb region. The isolated Hero gene displayed resistance to various G. rostochiensis pathotypes and partial resistance to G. pallida pathotype Pa2/3 in transgenic tomato lines. None of the Hero homologues conferred resistance to G. rostochiensis pathotypes. Hero can be distinguished from its homologues by the length of a compound hexanucleotide microsatellite, which codes for a charged and repetitive amino acid domain within the LRR. We propose that the expansion of this microsatellite may be involved in the evolution of the Hero resistance gene.
The plasma membrane oxidase NtrbohD is responsible for AOS production in elicited tobacco cells
Authors: Simon‐Plas Françoise , Elmayan Taline , Blein Jean‐Pierre 
Published: March 2003

SummaryA cDNA encoding a protein, NtrbohD, located on the plasma membrane and homologue to the flavocytochrome of the neutrophil NADPH oxidase, was cloned in tobacco. The corresponding mRNA was accumulated when tobacco leaves and cells were treated with the fungal elicitor cryptogein. After elicitation with cryptogein, tobacco cells transformed with antisense constructs of NtrbohD showed the same extracellular alkalinization as the control, but no longer produced active oxygen species (AOS). This work represents the first demonstration of the function of a homologue of gp91–phox in AOS production in elicited tobacco cells.
STAIRS: a new genetic resource for functional genomic studies of Arabidopsis
Authors: Koumproglou Rachil , Wilkes Tim M. , Townson Paul , Wang Xiao Y , Beynon Jim , Pooni Harpal S. , Newbury H. John , Kearsey Mike J. 
Published: March 2003

SummaryMany biologically and economically important traits in plants and animals are quantitative/multifactorial, being controlled by several quantitative trait loci (QTL). QTL are difficult to locate accurately by conventional methods using molecular markers in segregating populations, particularly for traits of low heritability or for QTL with small effects. In order to resolve this, large (often unrealistically large) populations are required. In this paper we present an alternative approach using a specially developed resource of lines that facilitate QTL location first to a particular chromosome, then to successively smaller regions within a chromosome (≤ 0.5 cM) by means of simple comparisons among a few lines. This resource consists of ‘Stepped Aligned Inbred Recombinant Strains’ (STAIRS) plus single whole Chromosome Substitution Strains (CSSs). We explain the analytical power of STAIRS and illustrate their construction and use with Arabidopsis thaliana, although the principles could be applied to many organisms. We were able to locate flowering QTL at the top of chromosome 3 known to contain several potential candidate genes.
Opposite changes in membrane fluidity mimic cold and heat stress activation of distinct plant MAP kinase pathways
Authors: Sangwan Veena , Örvar Björn Lárus , Beyerly John , Hirt Heribert , Dhindsa Rajinder S. 
Published: March 2003

SummaryMitogen‐activated protein kinases (MAPKs) appear to be ubiquitously involved in signal transduction during eukaryotic responses to extracellular stimuli. In plants, no heat shock‐activated MAPK has so far been reported. Also, whereas cold activates specific plant MAPKs such as alfalfa SAMK, mechanisms of such activation are unknown. Here, we report a heat shock‐activated MAPK (HAMK) immunologically related to ERK (Extracellular signal‐Regulated Kinase) superfamily of protein kinases. Molecular mechanisms of heat‐activation of HAMK and cold‐activation of SAMK were investigated. We show that cold‐activation of SAMK requires membrane rigidification, whereas heat‐activation of HAMK occurs through membrane fluidization. The temperature stress‐ and membrane structure‐dependent activation of both SAMK and HAMK is mimicked at 25°C by destabilizers of microfilaments and microtubules, latrunculin B and oryzalin, respectively; but is blocked by jasplakinolide, a stabilizer of actin microfilaments. Activation of SAMK or HAMK by temperature, chemically modulated membrane fluidity, or by cytoskeleton destabilizers is inhibited by blocking the influx of extracellular calcium. Activation of SAMK or HAMK is also prevented by an antagonist of calcium‐dependent protein kinases (CDPKs). In summary, our data indicate that cold and heat are sensed by structural changes in the plasma membrane that translates the signal via cytoskeleton, Ca2+ fluxes and CDPKs into the activation of distinct MAPK cascades.
Environmental and auxin regulation of wood formation involves members of the Aux/IAA gene family in hybrid aspen
Authors: Moyle Richard , Schrader Jarmo , Stenberg Anneli , Olsson Olof , Saxena Sangeeta , Sandberg Göran , Bhalerao Rishikesh P 
Published: March 2003

SummaryIndole acetic acid (IAA/auxin) profoundly affects wood formation but the molecular mechanism of auxin action in this process remains poorly understood. We have cloned cDNAs for eight members of the Aux/IAA gene family from hybrid aspen (Populus tremula L. × Populus tremuloides Michx.) that encode potential mediators of the auxin signal transduction pathway. These genes designated as PttIAA1‐PttIAA8 are auxin inducible but differ in their requirement of de novo protein synthesis for auxin induction. The auxin induction of the PttIAA genes is also developmentally controlled as evidenced by the loss of their auxin inducibility during leaf maturation. The PttIAA genes are differentially expressed in the cell types of a developmental gradient comprising the wood‐forming tissues. Interestingly, the expression of the PttIAA genes is downregulated during transition of the active cambium into dormancy, a process in which meristematic cells of the cambium lose their sensitivity to auxin. Auxin‐regulated developmental reprogramming of wood formation during the induction of tension wood is accompanied by changes in the expression of PttIAA genes. The distinct tissue‐specific expression patterns of the auxin inducible PttIAA genes in the cambial region together with the change in expression during dormancy transition and tension wood formation suggest a role for these genes in mediating cambial responses to auxin and xylem development.
Complex transgene locus structures implicate multiple mechanisms for plant transgene rearrangement
Authors: Svitashev Sergei K. , Pawlowski Wojciech P. , Makarevitch Irina , Plank David W. , Somers David A. 
Published: March 2003

SummaryTo more fully characterize the internal structure of transgene loci and to gain further understanding of mechanisms of transgene locus formation, we sequenced more than 160 kb of complex transgene loci in two unrelated transgenic oat (Avena sativa L.) lines transformed using microprojectile bombardment. The transgene locus sequences from both lines exhibited extreme scrambling of non‐contiguous transgene and genomic fragments recombined via illegitimate recombination. A perfect direct repeat of the delivered DNA, and inverted and imperfect direct repeats were detected in the same transgene locus indicating that homologous recombination and synthesis‐dependent mechanism(s), respectively, were also involved in transgene locus rearrangement. The most unexpected result was the small size of the fragments of delivered and genomic DNA incorporated into the transgene loci via illegitimate recombination; 50 of the 82 delivered DNA fragments were shorter than 200 bp. Eleven transgene and genomic fragments were shorter than the DNA lengths required for Ku‐mediated non‐homologous end joining. Detection of these small fragments provided evidence that illegitimate recombination was most likely mediated by a synthesis‐dependent strand‐annealing mechanism that resulted in transgene scrambling. Taken together, these results indicate that transgene locus formation involves the concerted action of several DNA break‐repair mechanisms.
Ozone‐induced ethylene production is dependent on salicylic acid, and both salicylic acid and ethylene act in concert to regulate ozone‐induced cell death
Authors: Rao Mulpuri V. , Lee Hyung‐il , Davis Keith R. 
Published: March 2003

SummaryEthylene is known to influence plant defense responses including cell death in response to both biotic and abiotic stress factors. However, whether ethylene acts alone or in conjunction with other signaling pathways is not clearly understood. Ethylene overproducer mutants, eto1 and eto3, produced high levels of ethylene and developed necrotic lesions in response to an acute O3 exposure that does not induce lesions in O3‐tolerant wild‐type Col‐0 plants. Treatment of plants with ethylene inhibitors completely blocked O3‐induced ethylene production and partially attenuated O3‐induced cell death. Analyses of the responses of molecular markers of specific signaling pathways indicated a relationship between salicylic acid (SA)‐ and ethylene‐signaling pathways and O3 sensitivity. Both eto1 and eto3 plants constitutively accumulated threefold higher levels of total SA and exhibited a rapid increase in free SA and ethylene levels prior to lesion formation in response to O3 exposure. SA pre‐treatments increased O3 sensitivity of Col‐0, suggesting that constitutive high SA levels prime leaf tissue to exhibit increased magnitude of O3‐induced cell death. NahG and npr1 plants compromised in SA signaling failed to produce ethylene in response to O3 and other stress factors suggesting that SA is required for stress‐induced ethylene production. Furthermore, NahG expression in the dominant eto3 mutant attenuated ethylene‐dependent PR4 expression and rescued the O3‐induced HR (hypersensitive response) cell death phenotype exhibited by eto3 plants. Our results suggest that both SA and ethylene act in concert to influence cell death in O3‐sensitive genotypes, and that O3‐induced ethylene production is dependent on SA.
Both antisense and sense expression of biotin carboxyl carrier protein isoform 2 inactivates the plastid acetyl‐coenzyme A carboxylase in Arabidopsis thaliana
Authors: Thelen Jay J. , Ohlrogge John B. 
Published: March 2003

SummaryTo further characterize the role of biotin carboxyl carrier protein isoform 2 (BCCP2) in acetyl‐coenzyme A carboxylase (ACCase) function and fatty acid biosynthesis, plants with reduced or increased expression of this protein were characterized. Analysis of 38 independent Arabidopsis lines expressing antisense BCCP2 transcript behind a constitutive promoter showed no significant phenotype, though antisense transcript was highly expressed. In developing seed, BCCP2 protein was reduced by an average of 38% resulting in a 9% average decrease in fatty acid content in mature seed. Over‐expression of BCCP2 behind a seed‐specific napin promoter increased the amount of holo‐BCCP2 in developing seed by an average of twofold, as determined with anti‐biotin antibodies. Surprisingly, the average fatty acid content of T2 seed from over‐expression lines was 23% lower than wild‐type seed. These plants also exhibited reduced seed setting in 18 of 20 T1 lines which was coincident with increased individual seed mass. Quantification of total BCCP2 in developing siliques using anti‐BCCP2 antibodies indicated that as much as 60% of total plastidial BCCP2 was in the non‐biotinylated form (apo‐BCCP2). Although apo‐BCCP2 was highly over‐expressed in developing seed, accumulation of other ACCase subunits was unaffected. The specific activity of ACCase was up to 65% lower in developing seed of over‐expression lines versus wild type. This was attributed to the assembly of biologically inactive (non‐biotinylated) ACCase complexes. Consistent with ACCase exerting control over de novo fatty acid synthesis, reduced activity in developing seed resulted in lower oil content, altered fatty acid composition and reduced seed setting.
The impact of oxidative stress on Arabidopsis mitochondria
Authors: Sweetlove L.J. , Heazlewood J.L. , Herald V. , Holtzapffel R. , Day D.A. , Leaver C.J. , Millar A.H. 
Published: March 2003

SummaryTreatment of Arabidopsis cell culture for 16 h with H2O2, menadione or antimycin A induced an oxidative stress decreasing growth rate and increasing DCF fluorescence and lipid peroxidation products. Treated cells remained viable and maintained significant respiratory rates. Mitochondrial integrity was maintained, but accumulation of alternative oxidase and decreased abundance of lipoic acid‐containing components during several of the treatments indicated oxidative stress. Analysis of the treatments was undertaken by IEF/SDS‐PAGE, comparison of protein spot abundances and tandem mass spectrometry. A set of 25 protein spots increased >3‐fold in H2O2/menadione treatments, a subset of these increased in antimycin A‐treated samples. A set of 10 protein spots decreased significantly during stress treatments. A specific set of mitochondrial proteins were degraded by stress treatments. These damaged components included subunits of ATP synthase, complex I, succinyl CoA ligase, aconitase, and pyruvate and 2‐oxoglutarate dehydrogenase complexes. Nine increased proteins represented products of different genes not found in control mitochondria. One is directly involved in antioxidant defense, a mitochondrial thioredoxin‐dependent peroxidase, while another, a thioredoxin reductase‐dependent protein disulphide isomerase, is required for protein disulfide redox homeostasis. Several others are generally considered to be extramitochondrial but are clearly present in a highly purified mitochondrial fraction used in this study and are known to play roles in stress response. Using H2O2 as a model stress, further work revealed that this treatment induced a protease activity in isolated mitochondria, putatively responsible for the degradation of oxidatively damaged mitochondrial proteins and that O2 consumption by mitochondria was significantly decreased by H2O2 treatment.
Molecular analysis of the stylar‐expressed Solanum chacoense small asparagine‐rich protein family related to the HT modifier of gametophytic self‐incompatibility in Nicotiana
Authors: O'Brien M. , Kapfer C. , Major G. , Laurin M. , Bertrand C. , Kondo K. , Kowyama Y. , Matton D. P. 
Published: March 2003

SummaryGametophytic self‐incompatibility (GSI) systems involving the expression of stylar ribonucleases have been described and extensively studied in many plant families including the Solanaceae, Rosaceae and Scrophulariaceae. Pollen recognition and rejection is governed in the style by specific ribonucleases called S‐RNases, but in many self‐incompatibility (SI) systems, modifier loci that can modulate the SI response have been described at the genetic level. Here, we present at the molecular level, the isolation and characterization of two Solanum chacoense homologues of the Nicotiana HT modifier that had been previously shown to be necessary for the SI reaction to occur in N. alata (McClure et al., 1999). HT homologues from other solanaceous species have also been isolated and a phylogenetic analysis reveals that the HT genes fall into two groups. In S. chacoense, these small proteins named ScHT‐A and ScHT‐B are expressed in the style and are developmentally regulated during anthesis identically to the S‐RNases as well as following compatible and incompatible pollination. To elucidate the precise role of each HT isoform, antisense ScHT‐A and RNAi ScHT‐B lines were generated. Conversion from SI to self‐compatibility (SC) was only observed in RNAi ScHT‐B lines with reduced levels of ScHT‐B mRNA. These results confirm the role of the HT modifier in solanaceous SI and indicate that only the HT‐B isoform is directly involved in SI.
A natural recessive resistance gene against potato virus Y in pepper corresponds to the eukaryotic initiation factor 4E (eIF4E)
Authors: Ruffel Sandrine , Dussault Marie‐Hélène , Palloix Alain , Moury Benoît , Bendahmane Abdelhafid , Robaglia Christophe , Caranta Carole 
Published: March 2003

SummaryWe show here that the pvr2 locus in pepper, conferring recessive resistance against strains of potato virus Y (PVY), corresponds to a eukaryotic initiation factor 4E (eIF4E) gene. RFLP analysis on the PVY‐susceptible and resistant pepper cultivars, using an eIF4E cDNA from tobacco as probe, revealed perfect map co‐segregation between a polymorphism in the eIF4E gene and the pvr2 alleles, pvr21 (resistant to PVY‐0) and pvr22 (resistant to PVY‐0 and 1). The cloned pepper eIF4E cDNA encoded a 228 amino acid polypeptide with 70–86% nucleotide sequence identity with other plant eIF4Es. The sequences of eIF4E protein from two PVY‐susceptible cultivars were identical and differed from the eIF4E sequences of the two PVY‐resistant cultivars Yolo Y (YY) (pvr21) and FloridaVR2 (F) (pvr22) at two amino acids, a mutation common to both resistant genotypes and a second mutation specific to each. Complementation experiments were used to show that the eIF4E gene corresponds to pvr2. Thus, potato virus X‐mediated transient expression of eIF4E from susceptible cultivar Yolo Wonder (YW) in the resistant genotype YY resulted in loss of resistance to subsequent PVY‐0 inoculation and transient expression of eIF4E from YY (resistant to PVY‐0; susceptible to PVY‐1) rendered genotype F susceptible to PVY‐1. Several lines of evidence indicate that interaction between the potyvirus genome‐linked protein (VPg) and eIF4E are important for virus infectivity, suggesting that the recessive resistance could be due to incompatibility between the VPg and eIF4E in the resistant genotype.
The circadian clock regulated RNA‐binding protein AtGRP7 autoregulates its expression by influencing alternative splicing of its own pre‐mRNA
Authors: Staiger Dorothee , Zecca Laura , Kirk Dominika A. Wieczorek , Apel Klaus , Eckstein Luca 
Published: March 2003

SummaryThe clock‐regulated RNA‐binding protein AtGRP7 is part of a negative feedback circuit through which the protein influences circadian oscillations of its own transcript. Constitutive overexpression of AtGRP7 in transgenic plants leads to the appearance of a low amount of an alternatively spliced Atgrp7 transcript with a premature stop codon. It is generated by the use of a 5′ cryptic splice site in the middle of the intron at the expense of the fully spliced mRNA, indicating a role for AtGRP7 in splice site selection. Accelerated decay of this transcript accounts for its low steady state abundance. This implicates a mechanism for the AtGRP7 feedback loop: Atgrp7 expression is downregulated, as AtGRP7 protein accumulates over the circadian cycle, partly by the generation of an alternate transcript that due to its instability does not accumulate to high levels and does not produce a functional protein. Recombinant AtGRP7 protein specifically interacts with the 3′ untranslated region and the intron of its transcript, suggesting that the shift in splice site selection and downregulation involves binding of AtGRP7 to its pre‐mRNA. AtGRP7 also influences the choice of splice sites in the Atgrp8 transcript encoding a related RNA‐binding protein, favoring the production of an alternatively spliced, unstable Atgrp8 transcript. This conservation points to the importance of this regulatory mechanism to control the level of the clock‐regulated glycine‐rich RNA‐binding proteins and shows how AtGRP7 can control abundance of target transcripts.