Expression profiling of the whole Arabidopsis shaggy-like kinase multigene family by real-time reverse transcriptase-polymerase chain reaction

Real-Time PCR: Revolutionizing Detection and Expression Analysis of Genes

Invention of polymerase chain reaction (PCR) technology by Kary Mullis in 1984 gave birth to real-time PCR. Real-time PCR - detection and expression analysis of gene(s) in real-time - has revolutionized the 21(st) century biological science due to its tremendous application in quantitative genotyping, genetic variation of inter and intra organisms, early diagnosis of disease, forensic, to name a few. We comprehensively review various aspects of real-time PCR, including technological refinement and application in all scientific fields ranging from medical to environmental issues, and to plant.

The Arabidopsis thaliana GSK3/Shaggy like kinase AtSK3-2 modulates floral cell expansion

The GSK3/Shaggy family of serine/threonine protein kinases is involved in a series of biological processes in animals, plants and yeast [Charrier et al. (2002) Plant Physiol 130:577-590; Jope and Johnson (2004) Trends Biochem Sci 29:95-102; Li and Nam (2002) Science 295:1299-1301; Piao et al. (2001) Plant J 27:305-314]. In Arabidopsis thaliana, out of the 10 members of the GSK3/Shaggy-like gene family (AtSKs), a biological function has been assigned to only 1 member (AtSK2-1) by mutation. In the present work, a study was undertaken to elucidate the function of AtSK3-2. We have generated mutated versions of the A. thaliana Shaggy-like kinase 3-2 (AtSK3-2), in which Lys(167) and Arg(178), respectively homologues to Lys(85) and Arg(96) of the mammal GSK3beta, were modified into Ala by site-directed mutagenesis. In vitro kinase activity assays of the mutated recombinant protein AtSK3-2-R178A showed that the "primed activity" of the mutated kinase was reduced by 90% while the "non-primed" activity was only 20% reduced compared to the wild-type protein kinase. However, the mutant protein AtSK3-2-K167A showed no activity. Arabidopsis transgenic lines over-expressing AtSK3-2-R178A displayed smaller floral organs, namely pedicels, sepals and petals. Conversely, over-expression of both the wild-type AtSK3-2 protein and the AtSK3-2-K167A mutated version, displayed no altered morphogenesis. Scanning electron microscopic analyses of the AtSK3-2-R178A transgenic plants clearly showed a reduced cell size in flower organs, in which quantitative RT-PCR expression analyses of cell wall expansion enzymes showed reduced transcript levels of three xyloglucan endotransglycosylases (XET), namely XTH22 (TCH4), XTH23 (XTR6) and XTH30 (XTR4). Our data show that AtSK3-2 plays an important role in the control of cell elongation in flower development.

A Proteasome-regulated Glycogen Synthase Kinase-3 Modulates Disease Response in Plants

Glycogen synthase kinase-3 (GSK-3) is a key player in various important signaling pathways in animals. The activity of GSK-3 is known to be modulated by protein phosphorylation and differential complex formation. However, little information is available regarding the function and regulation of plant GSK-3/shaggy-like kinases (GSKs). Analysis of the in vivo kinase activity of MsK1, a GSK from Medicago sativa, revealed that MsK1 is active in healthy plants and that MsK1 activity is down-regulated by the elicitor cellulase in a time- and dose-dependent manner. Surprisingly, cellulase treatment triggered the degradation of the MsK1 protein in a proteasome-dependent manner suggesting a novel mechanism of GSK-3 regulation. Inhibition of MsK1 kinase activity and degradation of the protein were two successive processes that could be uncoupled. In a transgenic approach, stimulus-induced inhibition of MsK1 was impeded by constant replenishment of MsK1 by a strong constitutive promoter. MsK1 overexpressing plants exhibited enhanced disease susceptibility to the virulent bacterial pathogen Pseudomonas syringae. MAP kinase activation in response to pathogen infection was compromised in plants with elevated MsK1 levels. These data strongly suggest that tight regulation of the plant GSK-3, MsK1, may be important for innate immunity to limit the severity of virulent bacterial infection.

Cross-species translocation of mRNA from host plants into the parasitic plant dodder

An intriguing new paradigm in plant biology is that systemically mobile mRNAs play a role in coordinating development. In this process, specific mRNAs are loaded into the phloem transport stream for translocation to distant tissues, where they may impact on developmental processes. However, despite its potential significance for plant growth regulation, mRNA trafficking remains poorly understood and challenging to study. Here, we show that phloem-mobile mRNAs can also traffic between widely divergent species from a host to the plant parasite lespedeza dodder (Cuscuta pentagona Engelm.). Reverse transcription-polymerase chain reaction and microarray analysis were used to detect specific tomato (Lycopersicon esculentum Mill.) transcripts in dodder grown on tomato that were not present in control dodder grown on other host species. Foreign transcripts included LeGAI, which has previously been shown to be translocated in the phloem, as well as nine other transcripts not reported to be mobile. Dodders are parasitic plants that obtain resources by drawing from the phloem of a host plant and have joint plasmodesmata with host cortical cells. Although viruses are known to move between dodder and its hosts, translocation of endogenous plant mRNA has not been reported. These results point to a potentially new level of interspecies communication, and raise questions about the ability of parasites to recognize, use, and respond to transcripts acquired from their hosts.

A novel drought-inducible gene, ATAF1, encodes a NAC family protein that negatively regulates the expression of stress-responsive genes in Arabidopsis

NAC proteins are plant-specific transcriptional regulators. ATAF1 was one of the first identified NAC proteins in Arabidopsis. In present study, we characterized the ATAF1 expression and biological function in response to water deficit stress. ATAF1 mRNA expression was strongly induced by dehydration and abscisic acid (ABA) treatment, but inhibited by water treatment, suggesting a general role in drought stress responses. Transient expression analysis in onion epidermal cells indicated the nuclear localization for the ATAF1::GFP fusion protein. Yeast transactivation analysis showed that ATAF1 had ability to activate reporter gene expression. Furthermore, domain deletion analysis revealed that the ATAF1 transactivation activity was conferred by its C-terminal domain. When ATAF1 gene was knocked out by T-DNA insertions, Arabidopsis ataf1-1 and ataf1-2 mutants displayed a recovery rate about seven times higher than wild-type plants in drought response test. This ataf1 phenotype was coincident with the enhanced expression of stress responsive marker genes, such as COR47, ERD10, KIN1, RD22 and RD29A under drought stress. Above evidences suggest that ATAF1, as a transcriptional regulator, negatively regulates the expression of stress responsive genes under drought stress in Arabidopsis.

An optimized grapevine RNA isolation procedure and statistical determination of reference genes for real-time RT-PCR during berry development

BACKGROUND

Accuracy in quantitative real-time RT-PCR is dependent on high quality RNA, consistent cDNA synthesis, and validated stable reference genes for data normalization. Reference genes used for normalization impact the results generated from expression studies and, hence, should be evaluated prior to use across samples and treatments. Few statistically validated reference genes have been reported in grapevine. Moreover, success in isolating high quality RNA from grapevine tissues is typically limiting due to low pH, and high polyphenolic and polysaccharide contents.

RESULTS

We describe optimization of an RNA isolation procedure that compensates for the low pH found in grape berries and improves the ability of the RNA to precipitate. This procedure was tested on pericarp and seed developmental series, as well as steady-state leaf, root, and flower tissues. Additionally, the expression stability of actin, AP47 (clathrin-associated protein), cyclophilin, EF1-alpha (elongation factor 1-alpha), GAPDH (glyceraldehyde 3-phosphate dehydrogenase), MDH (malate dehydrogenase), PP2A (protein phosphatase), SAND, TIP41, alpha-tubulin, beta-tubulin, UBC (ubiquitin conjugating enzyme), UBQ-L40 (ubiquitin L40) and UBQ10 (polyubiquitin) were evaluated on Vitis vinifera cv. Cabernet Sauvignon pericarp using three different statistical approaches. Although several of the genes proved to be relatively stable, no single gene outperformed all other genes in each of the three evaluation methods tested. Furthermore, the effect of using one reference gene versus normalizing to the geometric mean of several genes is presented for the expression of an aquaporin and a sucrose transporter over a developmental series.

CONCLUSION

In order to quantify relative transcript abundances accurately using real-time RT-PCR, we recommend that combinations of several genes be used for normalization in grape berry development studies. Our data support GAPDH, actin, EF1-alpha and SAND as the most relevant reference genes for this purpose.

Regulation of the high-affinity NO3- uptake system by NRT1.1-mediated NO3- demand signaling in Arabidopsis

The NRT2.1 gene of Arabidopsis thaliana encodes a major component of the root high-affinity NO(3)(-) transport system (HATS) that plays a crucial role in NO(3)(-) uptake by the plant. Although NRT2.1 was known to be induced by NO(3)(-) and feedback repressed by reduced nitrogen (N) metabolites, NRT2.1 is surprisingly up-regulated when NO(3)(-) concentration decreases to a low level (<0.5 mm) in media containing a high concentration of NH(4)(+) or Gln (>or=1 mm). The NRT3.1 gene, encoding another key component of the HATS, displays the same response pattern. This revealed that both NRT2.1 and NRT3.1 are coordinately down-regulated by high external NO(3)(-) availability through a mechanism independent from that involving N metabolites. We show here that repression of both genes by high NO(3)(-) is specifically mediated by the NRT1.1 NO(3)(-) transporter. This mechanism warrants that either NRT1.1 or NRT2.1 is active in taking up NO(3)(-) in the presence of a reduced N source. Under low NO(3)(-)/high NH(4)(+) provision, NRT1.1-mediated repression of NRT2.1/NRT3.1 is relieved, which allows reactivation of the HATS. Analysis of atnrt2.1 mutants showed that this constitutes a crucial adaptive response against NH(4)(+) toxicity because NO(3)(-) taken up by the HATS in this situation prevents the detrimental effects of pure NH(4)(+) nutrition. It is thus hypothesized that NRT1.1-mediated regulation of NRT2.1/NRT3.1 is a mechanism aiming to satisfy a specific NO(3)(-) demand of the plant in relation to the various specific roles that NO(3)(-) plays, in addition to being a N source. A new model is proposed for regulation of the HATS, involving both feedback repression by N metabolites and NRT1.1-mediated repression by high NO(3)(-).

The protein kinase genes MAP3K epsilon 1 and MAP3K epsilon 2 are required for pollen viability in Arabidopsis thaliana

We have used reverse-genetic analysis to investigate the function of MAP3K epsilon 1 and MAP3K epsilon 2, a pair of closely related Arabidopsis thaliana genes that encode protein kinases. Plants homozygous for either map3k epsilon 1 or map3k epsilon 2 displayed no apparent mutant phenotype, whereas the double-mutant combination caused pollen lethality. Transmission of the double-mutant combination through the female gametophyte was normal. Tetrad analysis performed using the Arabidopsis quartet mutation demonstrated that the pollen-lethal phenotype segregated at meiosis with the map3k epsilon 1;map3k epsilon 2 genotype. We used transmission electron microscopy to determine that double-mutant pollen grains develop plasma membrane irregularities following pollen mitosis I. Analysis of the subcellular localization of a yellow fluorescent protein (YFP):MAP3Kepsilon1 fusion protein using confocal microscopy and biochemical fractionation indicated that a substantial portion of the MAP3Kepsilon1 present in Arabidopsis cells is localized to the plasma membrane. Taken together, our results suggest that MAP3Kepsilon1 is required for the normal functioning of the plasma membrane in developing Arabidopsis pollen.

Cross-talk between ethylene and drought signalling pathways is mediated by the sunflower Hahb-4 transcription factor

Hahb-4 is a member of the Helianthusannuus (sunflower) subfamily I of HD-Zip proteins that is transcriptionally regulated by water availability and abscisic acid. Transgenic Arabidopsis thaliana plants overexpressing this transcription factor (TF) exhibit a characteristic phenotype that includes a strong tolerance to water stress. Here we show that this TF is a new component of ethylene signalling pathways, and that it induces a marked delay in senescence. Plants overexpressing Hahb-4 are less sensitive to external ethylene, enter the senescence pathway later and do not show the typical triple response. Furthermore, transgenic plants expressing this gene under the control of its own inducible promoter showed an inverse correlation between ethylene sensitivity and Hahb-4 levels. Potential targets of Hahb-4 were identified by comparing the transcriptome of Hahb-4-transformed and wild-type plants using microarrays and quantitative RT-PCR. Expression of this TF has a major repressive effect on genes related to ethylene synthesis, such as ACO and SAM, and on genes related to ethylene signalling, such as ERF2 and ERF5. Expression studies in sunflower indicate that Hahb-4 transcript levels are elevated in mature/senescent leaves. Expression of Hahb-4 is induced by ethylene, concomitantly with several genes homologous to the targets identified in the transcriptome analysis (HA-ACOa and HA-ACOb). Transient transformation of sunflower leaves demonstrated the action of Hahb-4 in the regulation of ethylene-related genes. We propose that Hahb-4 is involved in a novel conserved mechanism related to ethylene-mediated senescence that functions to improve desiccation tolerance.

NADK3, a novel cytoplasmic source of NADPH, is required under conditions of oxidative stress and modulates abscisic acid responses in Arabidopsis

In plants, excess reactive oxygen species are toxic molecules induced under environmental stresses, including pathogen invasions and abiotic stresses. Many anti-oxidant defense systems have been reported to require NADPH as an important reducing energy equivalent. However, the sources of NADPH and the molecular mechanisms of maintaining cytoplasmic redox balance are unclear. Here, we report the biological function of a putative cytoplasmic NADH kinase (NADK3) in several abiotic stress responses in Arabidopsis. We found that cytoplasmic NADPH is provided mostly by the product of the NADK3 gene in Arabidopsis. Expression of he NADK3 gene is responsive to abscisic acid (ABA) and abiotic stress conditions, including methyl violgen (MV), high salinity and osmotic shock. An NADK3 null mutant showed hypersensitivity to oxidative stress in both seed germination and seedling growth. Seed germination of the mutant plants also showed increased sensitivity to ABA, salt and mannitol. Furthermore, stress-related target genes were identified as upregulated in the mutant by mannitol and MV. Our study indicates that this cytoplasmic NADH kinase, a key source of the cellular reductant NADPH, is required for various abiotic stress responses.

Identification of genes of the plant-specific transcription-factor families cooperatively regulated by ethylene and jasmonate in Arabidopsis thaliana

The analysis of expression patterns of transcription-factor genes will be the basis for a better understanding of their biological functions in plants. In this study, we designed and developed an oligo-DNA macroarray consisting of gene-specific probes of 60-65 nucleotides for 288 transcription-factor genes, which cover COL, DOF, ERF, and NAC family genes. To investigate transcription-factor genes that are cooperatively regulated by jasmonate and ethylene in arabidopsis (Arabidopsis thaliana (L.) Heynh.) plants, we analyzed the expression profile of transcription-factor genes using the oligo-DNA macroarray technique in arabidopsis plants treated with methyl jasmonate and 1-aminocyclopropane-1-carboxylic acid. Then, transcript levels of candidate genes-which were selected based on the result of macroarray analysis-were evaluated by the quantitative real-time RT-PCR method. Finally, we identified an ERF family gene that is cooperatively regulated by both hormones, and designated as cooperatively regulated by ethylene and jasmonate 1 (CEJ1).

G-protein complex mutants are hypersensitive to abscisic acid regulation of germination and postgermination development

Abscisic acid (ABA) plays regulatory roles in a host of physiological processes throughout plant growth and development. Seed germination, early seedling development, stomatal guard cell functions, and acclimation to adverse environmental conditions are key processes regulated by ABA. Recent evidence suggests that signaling processes in both seeds and guard cells involve heterotrimeric G proteins. To assess new roles for the Arabidopsis (Arabidopsis thaliana) Galpha subunit (GPA1), the Gbeta subunit (AGB1), and the candidate G-protein-coupled receptor (GCR1) in ABA signaling during germination and early seedling development, we utilized knockout mutants lacking one or more of these components. Our data show that GPA1, AGB1, and GCR1 each negatively regulates ABA signaling in seed germination and early seedling development. Plants lacking AGB1 have greater ABA hypersensitivity than plants lacking GPA1, suggesting that AGB1 is the predominant regulator of ABA signaling and that GPA1 affects the efficacy of AGB1 execution. GCR1 acts upstream of GPA1 and AGB1 for ABA signaling pathways during germination and early seedling development: gcr1 gpa1 double mutants exhibit a gpa1 phenotype and agb1 gcr1 and agb1 gcr1 gpa1 mutants exhibit an agb1 phenotype. Contrary to the scenario in guard cells, where GCR1 and GPA1 have opposite effects on ABA signaling during stomatal opening, GCR1 acts in concert with GPA1 and AGB1 in ABA signaling during germination and early seedling development. Thus, cell- and tissue-specific functional interaction in response to a given signal such as ABA may determine the distinct pathways regulated by the individual members of the G-protein complex.

Slow dark deactivation of Arabidopsis chloroplast ATP synthase caused by a mutation in a nonplastidic SAC domain protein

Coupling factor slow recovery (cfs) is a recessive mutant of Arabidopsis with anomalous ATP synthase activation/deactivation characteristics as well as a distinct growth phenotype. The most significant feature of this mutant is that the dark-adapted deactivation of ATP synthase is a very slow relative to the wild type, indicating interference with ATP synthase regulation. Physical mapping of the mutation delimited it to a region in a pair of bacterial artificial chromosome clones. Examination of T-DNA insertion lines of all 34 putative genes located in this region identified two homozygous T-DNA insertion lines of the same gene, At3g59770, possessing phenotypes indistinguishable from the cfs mutant. At3g59770 had been previously identified as suppressor of actin 9 (SAC9), a protein with a SAC domain, a protein-protein interaction module containing two conserved tryptophans known as a WW domain, and an ATP/GTP-binding site motif A. Sequence analysis of cfs revealed a point mutation of G to A resulting in an amino acid substitution from tryptophan to STOP, thereby coding a truncated protein. Real-time-PCR amplification of the gene specific fragments showed that the T-DNA mutants did not have full-length transcripts whereas the cfs mutant transcribed a full-length mutated transcript. Further investigation of SAC9 RNA expression levels in different tissues of wild-type plants by RT-PCR revealed the highest expression in leaves. SAC 9 dysfunction interferes with ATP synthase deactivation, possibly by an alteration in phosphoinositide signaling inducing a stress mimicry response.

Primary metabolic pathways and signal transduction in sunflower (Helianthus annuus L.): comparison of transcriptional profiling in leaves and immature embryos using cDNA microarrays

The early stage of embryo development is a critical step in plant production. To identify genes with potential roles in the early sunflower seed development, a cDNA microarray approach was employed. We developed a thematic cDNA microarray containing clones representing high sequence similarities with known or predicted Arabidopsis genes implicated in different metabolic and signal transduction pathways. This 800-element cDNA array was used to compare the expression patterns in leaves and immature embryos (2 mm and 6 mm). Statistical analysis, using two-step ANOVA, revealed that 143 cDNA clones can be considered as differentially expressed. Of these, 62 clones were found to be up-regulated in leaves, 81 in embryos whereas only seven clones displayed increased level of mRNA in the 6 mm embryos when compared with 2 mm embryos. The differentially expressed clones are distributed among many metabolic and signal transduction pathways. For example, genes related to fatty acid metabolism and amino acid biosynthesis exhibited preferential expression patterns in immature embryos. Also, clones potentially encoding enzymes involved in the metabolism of ascorbate and aldarate, pyruvate, propanoate and inositol, and citrate cycle were found to be up-regulated in embryos. In contrast, cDNA clones putatively involved in energy metabolism were more abundant in leaves than embryos. Clones encoding potential signal transduction components including receptors, protein kinases, protein phosphatases, and transcription factors were also identified, with preferential expression profiles in immature embryos. The expression patterns derived from this study provide initial characterization of metabolic pathways and signalling transduction networks occurring in the early stage of sunflower seed development.

A novel isoform of ATPase c subunit from pearl millet that is differentially regulated in response to salinity and calcium

Vacuolar ATPases help in maintaining the pH of the vacuoles and thereby play a crucial role in the functioning of vacuolar sodium-proton antiporter. Though the various subunits that make V(1) and V(0) sector have been reported in plants their regulation is not understood completely. We have cloned three different isoforms of vacuolar ATPase subunit c (VHA-c) from Pennisetum glaucum with homologies among themselves varying from 38% to approximately 73% at the nucleic acid level. Using real-time PCR approach we have shown that the three isoforms are regulated in a tissue-specific manner under salinity stress. While isoform III is constitutively expressed in roots and shoots and does not respond to stress, isoform I is upregulated under stress. Isoform II is expressed mainly in roots; however, under salinity stress its expression is downregulated in roots and upregulated in shoots. Tissue specific expression under salinity stress of isoform II was also seen after exogenous application of calcium. This study for the first time shows the presence of three isoforms of PgVHA-c and their differential regulation during plant development, and also under abiotic stress.

Phylogenetic diversification of glycogen synthase kinase 3/SHAGGY-like kinase genes in plants

BACKGROUND

The glycogen synthase kinase 3 (GSK3)/SHAGGY-like kinases (GSKs) are non-receptor serine/threonine protein kinases that are involved in a variety of biological processes. In contrast to the two members of the GSK3 family in mammals, plants appear to have a much larger set of divergent GSK genes. Plant GSKs are encoded by a multigene family; analysis of the Arabidopsis genome revealed the existence of 10 GSK genes that fall into four major groups. Here we characterized the structure of Arabidopsis and rice GSK genes and conducted the first broad phylogenetic analysis of the plant GSK gene family, covering a taxonomically diverse array of algal and land plant sequences.

RESULTS

We found that the structure of GSK genes is generally conserved in Arabidopsis and rice, although we documented examples of exon expansion and intron loss. Our phylogenetic analyses of 139 sequences revealed four major clades of GSK genes that correspond to the four subgroups initially recognized in Arabidopsis. ESTs from basal angiosperms were represented in all four major clades; GSK homologs from the basal angiosperm Persea americana (avocado) appeared in all four clades. Gymnosperm sequences occurred in clades I, III, and IV, and a sequence of the red alga Porphyra was sister to all green plant sequences.

CONCLUSION

Our results indicate that (1) the plant-specific GSK gene lineage was established early in the history of green plants, (2) plant GSKs began to diversify prior to the origin of extant seed plants, (3) three of the four major clades of GSKs present in Arabidopsis and rice were established early in the evolutionary history of extant seed plants, and (4) diversification into four major clades (as initially reported in Arabidopsis) occurred either just prior to the origin of the angiosperms or very early in angiosperm history.

Analysis of organ-specific, expressed genes in Oncidium orchid by subtractive expressed sequence tags library

The pseudobulb of Oncidium orchid plays a key role in water, carbohydrate, and other nutrition support during floral development, yet a large scale of gene expression analysis involved in the metabolisms have not been evaluated. By subtracting RsaI-digested cDNAs of leaf from those of psuedobulb, an efficient subtractive cDNA library was developed. In total, 1080 subtractive expressed sequence tags (ESTs) were obtained. Analysis revealed approximately 636 unique gene parts, 120 clusters and 516 singles. Of these sequences, 74.8% were annotated on the database of NCBI GenBank. Peroxidase, sodium/dicarboxylate cotransporter, and mannose-binding lectin were highly expressed. Some gene profiles were identified as related to carbohydrate metabolism involved in mannan, pectin, starch and sucrose biosynthesis. A large fraction of the ESTs (35%) were classified into transportation, stress-related, cell cycle, or regulatory functions. Most genes that were differentially expressed are important in early flowering development, carbohydrate metabolism and stress-response physiology. This efficient organ-specific EST library represented an explicit transcriptome profile of Oncidium pseudobulb.

Expression profiling of the Arabidopsis annexin gene family during germination, de-etiolation and abiotic stress

Annexins are a multigene family in most plant species and are suggested to play a role in a wide variety of essential cellular processes. In Arabidopsis thaliana there are eight different annexins (AnnAt1-8), which range from 29% to 83% in deduced amino acid sequence identity. As a first step toward clarifying the individual functions of these annexins, in this study we have used quantitative real time reverse transcription PCR to assess their differential expression in different tissues or after different stimuli. We determined which annexins are expressed during germination and early seedling growth by assaying annexin expression levels in dry and germinating seeds and in 7-day-old light-grown seedlings. Our results indicate that transcripts for all eight annexins are present in germinating seeds and that transcript levels for all the annexins increase by 7 days of normal growth. We assayed transcript levels in dark grown roots, cotyledons, and hypocotyls and found that the relative abundance of each annexin varied in these dark-grown tissues. We also examined the effects of red and far red light treatments on annexin expression in 5.5-day-old etiolated seedlings. Light treatments significantly altered transcript levels in hypocotyls and cotyledons for only two members of the gene family. Finally, we monitored annexin expression changes in response to a variety of abiotic stresses. We found that the expression of most of the Arabidopsis annexin genes is differentially regulated by exposure to salt, drought, and high- and low-temperature conditions, indicating a likely role for members of this gene family in stress responses.

MGOUN3: evidence for chromatin-mediated regulation of FLC expression

The MGOUN3(MGO3)/BRUSHY1(BRU1)/TONSOKU(TSK) gene of Arabidopsis thaliana encodes a nuclear leucine-glycine-asparagine (LGN) domain protein that may be implicated in chromatin dynamics and genome maintenance. Mutants with defects in MGO3 display a fasciated stem and disorganized meristem structures. The transition to flowering was examined in mgo3 mutants and it was found that, under short days, the mutants flowered significantly earlier than the wild-type plants. Study of flowering-time associated gene expression showed that the floral transition inhibitor gene FLC was under-expressed in the mutant background. Ectopic expression of the flower-specific genes AGAMOUS (AG), PISTILLATA (PI), and SEPALLATA3 (SEP3) in mgo3 vegetative organs was also detected. Western blot and chromatin immunoprecipitation experiments suggested that histone H3 acetylation may be altered in the mgo3 background. Together, these data suggest that MGO3 is required for the correct transition to flowering and that this may be mediated by histone acetylation and associated changes in FLC expression.

Pathogen-responsive expression of glycosyltransferase genes UGT73B3 and UGT73B5 is necessary for resistance to Pseudomonas syringae pv tomato in Arabidopsis

The genome sequencing of Arabidopsis (Arabidopsis thaliana) has revealed that secondary metabolism plant glycosyltransferases (UGTs) are encoded by an unexpectedly large multigenic family of 120 members. Very little is known about their actual function in planta, in particular during plant pathogen interactions. Among them, members of the group D are of particular interest since they are related to UGTs involved in stress-inducible responses in other plant species. We provide here a detailed analysis of the expression profiles of this group of Arabidopsis UGTs following infection with Pseudomonas syringae pv tomato or after treatment with salicylic acid, methyljasmonate, and hydrogen peroxide. Members of the group D displayed distinct induction profiles, indicating potential roles in stress or defense responses notably for UGT73B3 and UGT73B5. Analysis of UGT expression in Arabidopsis defense-signaling mutants further revealed that their induction is methyljasmonate independent, but partially salicylic acid dependent. T-DNA tagged mutants (ugt73b3 and ugt73b5) exhibited decreased resistance to P. syringae pv tomato-AvrRpm1, indicating that expression of the corresponding UGT genes is necessary during the hypersensitive response. These results emphasize the importance of plant secondary metabolite UGTs in plant-pathogen interactions and provide foundation for future understanding of the exact role of UGTs during the hypersensitive response.

Evaluation of control transcripts in real-time RT-PCR expression analysis during maritime pine embryogenesis

In order to determine the suitability of reference or housekeeping genes as internal controls in real-time reverse transcriptase PCR (RT-PCR) assays for quantification of target mRNAs, we studied the levels of expression of four candidate reference genes in maritime pine by real-time RT-PCR. The expression levels obtained for glyceraldehyde-3-phosphate-dehydrogenase, 18S ribosomal RNA, eukaryotic translation initiation factor eIF4AII and ubiquitin in nine stages of embryo development revealed that none of the genes tested proved to be suitable as an internal control. Copy number quantification of the four transcripts showed an average relative variation of seven fold. We propose that the combination of a precise method for RNA quantification, internal controls for monitoring RT reaction and PCR efficiency and a robust external standard curve can guarantee a reliable absolute quantification of mRNA transcripts in real time RT-PCR. This approach may avoid the controversy in the use of housekeeping genes and may assume special significance in tissues undergoing developmental changes.

Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis

Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future.

Genome-wide identification and testing of superior reference genes for transcript normalization in Arabidopsis

Gene transcripts with invariant abundance during development and in the face of environmental stimuli are essential reference points for accurate gene expression analyses, such as RNA gel-blot analysis or quantitative reverse transcription-polymerase chain reaction (PCR). An exceptionally large set of data from Affymetrix ATH1 whole-genome GeneChip studies provided the means to identify a new generation of reference genes with very stable expression levels in the model plant species Arabidopsis (Arabidopsis thaliana). Hundreds of Arabidopsis genes were found that outperform traditional reference genes in terms of expression stability throughout development and under a range of environmental conditions. Most of these were expressed at much lower levels than traditional reference genes, making them very suitable for normalization of gene expression over a wide range of transcript levels. Specific and efficient primers were developed for 22 genes and tested on a diverse set of 20 cDNA samples. Quantitative reverse transcription-PCR confirmed superior expression stability and lower absolute expression levels for many of these genes, including genes encoding a protein phosphatase 2A subunit, a coatomer subunit, and an ubiquitin-conjugating enzyme. The developed PCR primers or hybridization probes for the novel reference genes will enable better normalization and quantification of transcript levels in Arabidopsis in the future.

Organization and Expression of the GSK3/Shaggy Kinase Gene Family in the Moss Physcomitrella patens Suggest Early Gene Multiplication in Land Plants and an Ancestral Response to Osmotic Stress

GSK3/Shaggy kinases are involved in a wide range of fundamental processes in animal development and metabolism. In angiosperm plants, these kinases are encoded by moderate-sized gene families, which appear to have a complex set of functions. Here, we present the characterization of five members of the GSK3/Shaggy gene family in the bryophyte Physcomitrella patens. The P. patens GSK3/Shaggy kinases (PpSK) are organized in a group of closely related paralogues with respect to their gene sequence and structure. Indeed, a phylogenetic analysis of the GSK3/Shaggy kinase sequences from plants and animals showed that the five PpSK proteins are monophyletic, and closer to subgroups I and IV described in angiosperms. Expression analyses performed by quantitative real-time RT-PCR on a wide range of growing conditions showed that PpSK genes responded only to either desiccation, PEG or sorbitol. As demonstrated by both inductions of marker genes and protonemal cell plasmolyses, these treatments resulted in a hyperosmotic stress. Altogether, these data suggest that (1) GSK3/Shaggy kinase gene multiplication occurred early in plant evolution, before the separation between bryophytes and vascular plants, and (2) both gene loss and duplication occurred in the ancestor of P. patens along with functional gene diversification in angiosperms. However, conservation of the transcriptional responses between Physcomitrella and Arabidopsis suggests the identification of an ancestral response of the GSK3/Shaggy kinases genes to osmotic stress.

Functional analysis of the BIN 2 genes of cotton

Brassinosteroids (BR) promote the elongation of cotton fibers and may be a factor in determining their final length. To begin to understand the role of BR-mediated responses in the development of cotton fibers we have characterized the BIN 2 genes of cotton. BIN 2 is a member of the shaggy-like protein kinase family that has been identified as a negative regulator of BR signaling in Arabidopsis. Sequence analyses indicate that the tetraploid cotton genome includes four genes with strong sequence similarity to BIN 2. These genes fall into two distinct subclasses based on sequence and expression patterns. Sequence comparisons with corresponding genes from cotton species that have the diploid A and D genomes, respectively, shows that each pair of genes comprises homeologs derived from the A and D sub-genomes. Transgenic Arabidopsis plants that express these cotton BIN 2 cDNAs show reduced growth and similar phenotypes to the semi-dominant bin 2 mutant plants. These results indicate that the cotton BIN 2 genes encode functional BIN 2 isoforms that can inhibit BR signaling. Further analyses of the function of BIN 2 genes and their possible roles in determining fiber yield and quality are underway.

Arabidopsis ADC genes involved in polyamine biosynthesis are essential for seed development

Arginine decarboxylase (ADC) is a rate-limiting enzyme that catalyzes the first step of polyamine (PA) biosynthesis in Arabidopsis thaliana. We generated a double mutant deficient in Arabidopsis two ADC genes (ADC1-/- ADC2-/-) and examined their roles in seed development. None of the F2 seedlings from crosses of adc1-1 and adc2-2 had the ADC1-/- ADC2-/- genotype. In addition, some abnormal seeds were observed among the ADC1+/- ADC2-/- and ADC1-/- ADC2+/- siliques. Viable offspring with the ADC1-/- ADC2-/- genotype could not be obtained from the ADC1+/- ADC2-/- and ADC1-/- ADC2+/- plants. These results indicate that AtADC genes are required for production of polyamines that are essential for normal seed development in Arabidopsis.

Differential expression profiles of growth-related genes in the elongation zone of maize primary roots

Growth in the apical elongation zone of plant roots is central to the development of functional root systems. Rates of root segmental elongation change from accelerating to decelerating as cell development proceeds from newly formed to fully elongated status. One of the primary variables regulating these changes in elongation rates is the extensibility of the elongating cell walls. To help decipher the complex molecular mechanisms involved in spatially variable root growth, we performed a gene identification study along primary root tips of maize (Zea mays) seedlings using suppression subtractive hybridization (SSH) and candidate gene approaches. Using SSH we isolated 150 non-redundant cDNA clones representing root growth-related genes (RGGs) that were preferentially expressed in the elongation zone. Differential expression patterns were revealed by Northern blot analysis for 41 of the identified genes and several candidate genes. Many of the genes have not been previously reported to be involved in root growth processes in maize. Genes were classified into groups based on the predicted function of the encoded proteins: cell wall metabolism, cytoskeleton, general metabolism, signaling and unknown. In-situ hybridization performed for two selected genes, confirmed the spatial distribution of expression shown by Northern blots and revealed subtle differences in tissue localization. Interestingly, spatial profiles of expression for some cell wall related genes appeared to correlate with the profile of accelerating root elongation and changed appropriately under growth-inhibitory water deficit.

DEAD-box RNA helicases in Arabidopsis thaliana: establishing a link between quantitative expression, gene structure and evolution of a family of genes

The model genome of Arabidopsis thaliana contains a DEAD-box RNA helicase family (RH) of 58 members, i.e. almost twice as many as in the animal or yeast genomes. Transcript profiling using real-time quantitative polymerase chain reaction (PCR) has been obtained for 20 AtRHs from nine different organs. Two AtRHs exhibited plant-specific profiles associated with photosynthetic and sink organs. The other 18 AtRHs had the same transcript profile, and the levels of transcription of these 'housekeeping'AtRHs were under strict quantitative control over a large range of values. Transcript levels may be very different between the most recently duplicated genes. The master regulatory element in the definition of the transcript level is the simultaneous presence of a TATA-box and an intron in the 5' untranslated region (UTR). There is a positive and highly significant correlation between the size of the 5' UTR intron and the transcription level, as long as a characteristic TATA-box is present. Our work on the housekeeping AtRHs suggests a scenario for the evolution of duplicated genes, leading to both highly and poorly transcribed genes in the same terminal branch of the phylogenetic tree. The general evolutionary drive of the AtRH family, after duplication of a highly transcribed ancestral AtRH, was towards an alteration of the transcriptional activity of the divergent duplicates through successive events of suppression of the TATA-box and/or the 5' UTR intron.

Validating internal controls for quantitative plant gene expression studies

BACKGROUND

Real-time reverse transcription PCR (RT-PCR) has greatly improved the ease and sensitivity of quantitative gene expression studies. However, accurate measurement of gene expression with this method relies on the choice of a valid reference for data normalization. Studies rarely verify that gene expression levels for reference genes are adequately consistent among the samples used, nor compare alternative genes to assess which are most reliable for the experimental conditions analyzed.

RESULTS

Using real-time RT-PCR to study the expression of 10 poplar (genus Populus) housekeeping genes, we demonstrate a simple method for determining the degree of stability of gene expression over a set of experimental conditions. Based on a traditional method for analyzing the stability of varieties in plant breeding, it defines measures of gene expression stability from analysis of variance (ANOVA) and linear regression. We found that the potential internal control genes differed widely in their expression stability over the different tissues, developmental stages and environmental conditions studied.

CONCLUSION

Our results support that quantitative comparisons of candidate reference genes are an important part of real-time RT-PCR studies that seek to precisely evaluate variation in gene expression. The method we demonstrated facilitates statistical and graphical evaluation of gene expression stability. Selection of the best reference gene for a given set of experimental conditions should enable detection of biologically significant changes in gene expression that are too small to be revealed by less precise methods, or when highly variable reference genes are unknowingly used in real-time RT-PCR experiments.

AtSGP1, AtSGP2 and MAP4Kα are nucleolar plant proteins that can complement fission yeast mutants lacking a functional SIN pathway

In the fission yeast Schizosaccharomyces pombe, the onset of septum formation is signalled via the septation initiation network (SIN) involving several protein kinases and a GTPase. Arabidopsis thaliana and Brassica napus proteins homologous to fission yeast spg1p (AtSGP1, AtSGP2), cdc7p (AtMAP3Kϵ1, AtMAP3Kϵ2, BnMAP3Kϵ1) and sid1p (AtMAP4Kα1, AtMAP4Kα2, BnMAP4Kα2) exhibit a significant similarity. The plant proteins AtSGP1/2 and BnMAP4Kα2 are able to complement the S. pombe mutant proteins spg1-B8 and sid1-239, respectively and to induce mutisepta when overexpressed in wild-type yeast. Yeast two-hybrid assays demonstrated interactions both between plant proteins and between plant and yeast proteins of the SIN pathway. However, the primary structure of the proteins as well as the partial complementation of yeast mutants indicates that plant homologous proteins and their yeast counterparts have diverged during evolution. Real-time RT-PCR studies demonstrated plant SIN-related gene expression in all organs tested and a co-expression pattern during the cell cycle, with a higher accumulation at G2-M. During interphase, the plant SIN-related proteins were found to co-localise predominantly in the nucleolus of the plant cells, as shown by fusions to green fluorescent protein. These data suggest the existence of a plant SIN-related pathway.

Expression of fungal pectin methylesterase in transgenic tobacco leads to alteration in cell wall metabolism and a dwarf phenotype

A transgenic tobacco plant (Nicotiana tabacum L.) expressing a fungal pectin methylesterase (PME; EC 3.1.1.11) gene derived from a black filamentous fungus, Aspergillus niger was created. Fungal PME should have a wider range of adaptability to substrate pectin compared with plant PME. As expected, the proportion of methyl esters in pectin was reduced in the transgenic tobacco. Consequently, the transgenic plant showed short internodes, small leaves and a dwarf phenotype. At a cellular level, the longitudinal lengths of stem epidermal cells were shorter than those of control plants. This is the first report that fungal PME promotes dwarfism in plants. It is worth noting that in the PME-expressing dwarf plant, the expression levels of cell wall metabolism related genes that included endo-1,4-beta-glucanase, cellulose synthase, endo-xyloglucan transferase and expansin gene were decreased. These results suggest that the expression of fungal PME in plants affects the cell wall metabolism.

Identification of nine sucrose nonfermenting 1-related protein kinases 2 activated by hyperosmotic and saline stresses in Arabidopsis thaliana

Several calcium-independent protein kinases were activated by hyperosmotic and saline stresses in Arabidopsis cell suspension. Similar activation profiles were also observed in seedlings exposed to hyperosmotic stress. One of them was identified to AtMPK6 but the others remained to be identified. They were assumed to belong to the SNF1 (sucrose nonfermenting 1)-related protein kinase 2 (SnRK2) family, which constitutes a plant-specific kinase group. The 10 Arabidopsis SnRK2 were expressed both in cells and seedlings, making the whole SnRK2 family a suitable candidate. Using a family-specific antibody raised against the 10 SnRK2, we demonstrated that these non-MAPK protein kinases activated by hyperosmolarity in cell suspension were SnRK2 proteins. Then, the molecular identification of the involved SnRK2 was investigated by transient expression assays. Nine of the 10 SnRK2 were activated by hyperosmolarity induced by mannitol, as well as NaCl, indicating an important role of the SnRK2 family in osmotic signaling. In contrast, none of the SnRK2 were activated by cold treatment, whereas abscisic acid only activated five of the nine SnRK2. The probable involvement of the different Arabidopsis SnRK2 in several abiotic transduction pathways is discussed.

Real-time PCR: what relevance to plant studies?

The appearance of genetically modified organisms on the food market a few years ago, and the demand for more precise and reliable techniques to detect foreign (transgenic or pathogenic) DNA in edible plants, have been the driving force for the introduction of real-time PCR techniques in plant research. This was followed by numerous fundamental research applications aiming to study the expression profiles of endogenous genes and multigene families. Since then, the interest in this technique in the plant scientist community has increased exponentially. This review describes the technical features of quantitative real-time PCR that are especially relevant to plant research, and summarizes its present and future applications.

The Arabidopsis putative G protein-coupled receptor GCR1 interacts with the G protein alpha subunit GPA1 and regulates abscisic acid signaling

Heterotrimeric G proteins composed of alpha, beta, and gamma subunits link ligand perception by G protein-coupled receptors (GPCRs) with downstream effectors, providing a ubiquitous signaling mechanism in eukaryotes. The Arabidopsis thaliana genome encodes single prototypical Galpha (GPA1) and Gbeta (AGB1) subunits, and two probable Ggamma subunits (AGG1 and AGG2). One Arabidopsis gene, GCR1, encodes a protein with significant sequence similarity to nonplant GPCRs and a predicted 7-transmembrane domain structure characteristic of GPCRs. However, whether GCR1 actually interacts with GPA1 was unknown. We demonstrate by in vitro pull-down assays, by yeast split-ubiquitin assays, and by coimmunoprecipitation from plant tissue that GCR1 and GPA1 are indeed physically coupled. GCR1-GPA1 interaction depends on intracellular domains of GCR1. gcr1 T-DNA insertional mutants exhibit hypersensitivity to abscisic acid (ABA) in assays of root growth, gene regulation, and stomatal response. gcr1 guard cells are also hypersensitive to the lipid metabolite, sphingosine-1-phosphate (S1P), which is a transducer of the ABA signal upstream of GPA1. Because gpa1 mutants exhibit insensitivity in aspects of guard cell ABA and S1P responses, whereas gcr1 mutants exhibit hypersensitivity, GCR1 may act as a negative regulator of GPA1-mediated ABA responses in guard cells.

Real-time PCR monitoring of fungal development in Arabidopsis thaliana infected by Alternaria brassicicola and Botrytis cinerea

Reliable methods for disease severity assessment are of crucial importance in the study of plant pathogen interactions, either for disease diagnostic on the field or to assess phenotypical differences in plants or pathogen strains. Currently, most of the assays used in fungal disease diagnostic rely on visual assessment of the symptoms, lesion diameter measurement or spore counting. However, these tests are tedious and often cannot discriminate between slightly different levels of resistance. Besides, they are not well suited to assess fungal development in the early phases of the infection, before macroscopical symptoms are visible or before sporulation. We describe here a pathogenicity assay based on the relative quantification of fungal and plant DNA in infected Arabidopsis thaliana leaves by means of real-time quantitative PCR. We show that it allows to monitor quantitatively the growth of the fungi Alternaria brassicicola and Botrytis cinerea in a sensitive and reliable way. Although highly sensitive, this test also exhibits a high robustness, which is crucial to significantly discriminate between lines displaying slightly different levels of resistance. Therefore, it allows to assess fungal development from the very first stages of infection and provides a fast and very practical alternative to currently described assays for phenotyping either plant mutant lines or fungal strains.

Regulation of flower development in Arabidopsis by SCF complexes

SCF complexes are the largest and best studied family of E3 ubiquitin protein ligases that facilitate the ubiquitylation of proteins targeted for degradation. The SCF core components Skp1, Cul1, and Rbx1 serve in multiple SCF complexes involving different substrate-specific F-box proteins that are involved in diverse processes including cell cycle and development. In Arabidopsis, mutations in the F-box gene UNUSUAL FLORAL ORGANS (UFO) result in a number of defects in flower development. However, functions of the core components Cul1 and Rbx1 in flower development are poorly understood. In this study we analyzed floral phenotypes caused by altering function of Cul1 or Rbx1, as well as the effects of mutations in ASK1 and ASK2. Plants homozygous for a point mutation in the AtCUL1 gene showed reduced floral organ number and several defects in each of the four whorls. Similarly, plants with reduced AtRbx1 expression due to RNA interference also exhibited floral morphological defects. In addition, compared to the ask1 mutant, plants homozygous for ask1 and heterozygous for ask2 displayed enhanced reduction of B function, as well as other novel defects of flower development, including carpelloid sepals and an inhibition of petal development. Genetic analyses demonstrate that AGAMOUS (AG) is required for the novel phenotypes observed in the first and second whorls. Furthermore, the genetic interaction between UFO and AtCUL1 supports the idea that UFO regulates multiple aspects of flower development as a part of SCF complexes. These results suggest that SCF complexes regulate several aspects of floral development in Arabidopsis.

Brca2 is involved in meiosis in Arabidopsis thaliana as suggested by its interaction with Dmc1

Two BRCA2-like sequences are present in the Arabidopsis genome. Both genes are expressed in flower buds and encode nearly identical proteins, which contain four BRC motifs. In a yeast two-hybrid assay, the Arabidopsis Brca2 proteins interact with Rad51 and Dmc1. RNAi constructs aimed at silencing the BRCA2 genes at meiosis triggered a reproducible sterility phenotype, which was associated with dramatic meiosis alterations. We obtained the same phenotype upon introduction of RNAi constructs aimed at silencing the RAD51 gene at meiosis in dmc1 mutant plants. The meiotic figures we observed strongly suggest that homologous recombination is highly disturbed in these meiotic cells, leaving aberrant recombination events to repair the meiotic double-strand breaks. The 'brca2' meiotic phenotype was eliminated in spo11 mutant plants. Our experiments point to an essential role of Brca2 at meiosis in Arabidopsis. We also propose a role for Rad51 in the dmc1 context.

Nuclear protein phosphatases with Kelch-repeat domains modulate the response to brassinosteroids in Arabidopsis

Perception of the plant steroid hormone brassinolide (BL) by the membrane-associated receptor kinase BRI1 triggers the dephosphorylation and accumulation in the nucleus of the transcriptional modulators BES1 and BZR1. We identified bsu1-1D as a dominant suppressor of bri1 in A abidopsis. BSU1 encodes a nuclear-localized serine-threonine protein phosphatase with an N-terminal Kelch-repeat domain, and is preferentially expressed in elongating cells. BSU1 is able to modulate the phosphorylation state of BES1, counter acting the action of the glycogen synthase kinase-3 BIN2, and leading to inc eased steady-state levels of dephosphorylated BES1. BSU1 belongs to a small gene family; loss-of-function analyses unravel the extent of functional overlap among members of the family and confirm the role of these phosphatases in the control of cell elongation by BL. Our data indicate that BES1 is subject to antagonistic phosphorylation and dephosphorylation reactions in the nucleus, which fine-tune the amplitude of the response to BL.

Structure and expression profile of the sucrose synthase multigene family in Arabidopsis

The release of the complete genome sequence of Arabidopsis enabled the largest sucrose synthase family described to date, comprising six distinct members, for which expression profiles were not yet available, to be identified. Aimed at understanding the precise function of each AtSUS member among the family, a comparative study of protein structure was performed, together with an expression profiling of the whole gene family using the technique of real-time quantitative reverse transcriptase-polymerase chain reaction. Transcript levels were analysed in several plant organs, including both developing and germinating seeds. A series of treatments such as oxygen deprivation, dehydration, cold treatment, or various sugar feedings were then carried out to characterize the members of the family further. The AtSUS genes exhibit distinct but partially redundant expression profiles. Under anaerobic conditions, for instance, both AtSUS1 and AtSUS4 mRNA levels increase, but in a distinct manner. AtSUS2 is specifically and highly induced in seeds at 12 d after flowering and appears as a marker of seed maturation. AtSUS3 seems to be induced in various organs under dehydration conditions including leaves deprived of water or submitted to osmotic stress as well as late-maturing seeds. AtSUS5 and AtSUS6 are expressed in nearly all plant organs and do not exhibit any transcriptional response to stresses. These results add new insights on the expression of SUS genes and are discussed in relation to distinct functions for each member of the AtSUS family.

Pathogen-responsive expression of a putative ATP-binding cassette transporter gene conferring resistance to the diterpenoid sclareol is regulated by multiple defense signaling pathways in Arabidopsis

The ATP-binding cassette (ABC) transporters are encoded by large gene families in plants. Although these proteins are potentially involved in a number of diverse plant processes, currently, very little is known about their actual functions. In this paper, through a cDNA microarray screening of anonymous cDNA clones from a subtractive library, we identified an Arabidopsis gene (AtPDR12) putatively encoding a member of the pleiotropic drug resistance (PDR) subfamily of ABC transporters. AtPDR12 displayed distinct induction profiles after inoculation of plants with compatible and incompatible fungal pathogens and treatments with salicylic acid, ethylene, or methyl jasmonate. Analysis of AtPDR12 expression in a number of Arabidopsis defense signaling mutants further revealed that salicylic acid accumulation, NPR1 function, and sensitivity to jasmonates and ethylene were all required for pathogen-responsive expression of AtPDR12. Germination assays using seeds from an AtPDR12 insertion line in the presence of sclareol resulted in lower germination rates and much stronger inhibition of root elongation in the AtPDR12 insertion line than in wild-type plants. These results suggest that AtPDR12 may be functionally related to the previously identified ABC transporters SpTUR2 and NpABC1, which transport sclareol. Our data also point to a potential role for terpenoids in the Arabidopsis defensive armory.

A role for the GCC-box in jasmonate-mediated activation of the PDF1.2 gene of Arabidopsis

The PDF1.2 gene of Arabidopsis encoding a plant defensin is commonly used as a marker for characterization of the jasmonate-dependent defense responses. Here, using PDF1.2 promoter-deletion lines linked to the beta-glucoronidase-reporter gene, we examined putative promoter elements associated with jasmonate-responsive expression of this gene. Using stably transformed plants, we first characterized the extended promoter region that positively regulates basal expression from the PDF1.2 promoter. Second, using promoter deletion constructs including one from which the GCC-box region was deleted, we observed a substantially lower response to jasmonate than lines carrying this motif. In addition, point mutations introduced into the core GCC-box sequence substantially reduced jasmonate responsiveness, whereas addition of a 20-nucleotide-long promoter element carrying the core GCC-box and flanking nucleotides provided jasmonate responsiveness to a 35S minimal promoter. Taken together, these results indicated that the GCC-box plays a key role in conferring jasmonate responsiveness to the PDF1.2 promoter. However, deletion or specific mutations introduced into the core GCC-box did not completely abolish the jasmonate responsiveness of the promoter, suggesting that the other promoter elements lying downstream from the GCC-box region may also contribute to jasmonate responsiveness. In other experiments, we identified a jasmonate- and pathogen-responsive ethylene response factor transcription factor, AtERF2, which when overexpressed in transgenic Arabidopsis plants activated transcription from the PDF1.2, Thi2.1, and PR4 (basic chitinase) genes, all of which contain a GCC-box sequence in their promoters. Our results suggest that in addition to their roles in regulating ethylene-mediated gene expression, ethylene response factors also appear to play important roles in regulating jasmonate-responsive gene expression, possibly via interaction with the GCC-box.