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PubMed1997

Signaling in plants.

Higher plants are sessile organisms that perceive environmental cues such as light and chemical signals and respond by changing their morphologies. Signaling pathways utilize a complex network of interactions to orchestrate biochemical and physiological responses such as flowering, fruit ripening, germination, photosynthetic regulation, and shoot or root development. In this session, the mechanisms of signaling systems that trigger plant responses to light and to the gaseous hormone, ethylene, were discussed. These signals are first sensed by a receptor and transmitted to the nucleus by a complex network. A signal may be transmitted to the nucleus by any of several systems including GTP binding proteins (G proteins), which change activity upon GTP binding; protein kinase cascades, which sequentially phosphorylate and activate a series of proteins; and membrane ion channels, which change ionic characteristics of the cells. The signal is manifested in the nucleus as a change in the activity of DNA-binding proteins, which are transcription factors that specifically interact and modulate the regulatory regions of genes. Thus, detection of an environmental signal is transmitted through a transduction pathway, and changes in transcription factor activity may coordinate changes in the expression of a portfolio of genes to direct new developmental programs.

Arabidopsis↗
PubMed2003

Proteomic analysis of glycosylphosphatidylinositol-anchored membrane proteins.

Glycosylphosphatidylinositol-anchored proteins (GPI-APs) are a functionally and structurally diverse family of post-translationally modified membrane proteins found mostly in the outer leaflet of the plasma membrane in a variety of eukaryotic cells. Although the general role of GPI-APs remains unclear, they have attracted attention because they act as enzymes and receptors in cell adhesion, differentiation, and host-pathogen interactions. GPI-APs may represent potential diagnostic and therapeutic targets in humans and are interesting in plant biotechnology because of their key role in root development. We here present a general mass spectrometry-based proteomic "shave-and-conquer" strategy that specifically targets GPI-APs. Using a combination of biochemical methods, mass spectrometry, and computational sequence analysis we identified six GPI-APs in a Homo sapiens lipid raft-enriched fraction and 44 GPI-APs in an Arabidopsis thaliana membrane preparation, representing the largest experimental dataset of GPI-anchored proteins to date.

Amino Acid Sequence↗
PubMed1998

DNA binding and dimerisation determinants of Antirrhinum majus MADS-box transcription factors.

Members of the MADS-box family of transcription factors are found in eukaryotes ranging from yeast to humans. In plants, MADS-box proteins regulate several developmental processes including flower, fruit and root development. We have investigated the DNA-binding mechanisms used by four such proteins in Antirrhinum majus, SQUA, PLE, DEF and GLO. SQUA differs from the characterised mammalian and yeast MADS-box proteins as it can efficiently bind two different classes of DNA-binding site. SQUA induces bending of these binding sites and the sequence of the site plays a role in determining the magnitude of these bends. Similarly, PLE and DEF/GLO induce DNA bending although the direction of the resulting bends differ. Finally, we demonstrate that the MADS-box and I-domains are sufficient for homodimer formation by SQUA. However, the K-box in SQUA can also act as an oligomerisation motif and in the full-length protein, the K-box plays a different role in mediating dimerisation in the context of SQUA homodimers or heterodimers with PLE. Together these results contribute significantly to our understanding of the function of SQUA and other plant MADS-box proteins at the molecular level.

Binding Sites↗
PubMed2000

MADS-Box gene diversity in seed plants 300 million years ago.

MADS-box genes encode a family of transcription factors which control diverse developmental processes in flowering plants ranging from root development to flower and fruit development. Through phylogeny reconstructions, most of these genes can be subdivided into defined monophyletic gene clades whose members share similar expression patterns and functions. Therefore, the establishment of the diversity of gene clades was probably an important event in land plant evolution. In order to determine when these clades originated, we isolated cDNAs of 19 different MADS-box genes from Gnetum gnemon, a gymnosperm model species and thus a representative of the sister group of the angiosperms. Phylogeny reconstructions involving all published MADS-box genes were then used to identify gene clades containing putative orthologs from both angiosperm and gymnosperm lineages. Thus, the minimal number of MADS-box genes that were already present in the last common ancestor of extant gymnosperms and angiosperms was determined. Comparative expression studies involving pairs of putatively orthologous genes revealed a diversity of patterns that has been largely conserved since the time when the angiosperm and gymnosperm lineages separated. Taken together, our data suggest that there were already at least seven different MADS-box genes present at the base of extant seed plants about 300 MYA. These genes were probably already quite diverse in terms of both sequence and function. In addition, our data demonstrate that the MADS-box gene families of extant gymnosperms and angiosperms are of similar complexities.

Amino Acid Sequence↗
PubMed1995

Purification and characterization of phospholipase D (PLD) from rice (Oryza sativa L.) and cloning of cDNA for PLD from rice and maize (Zea mays L.).

Phospholipase D (PLD) was purified to high homogeneity from rice bran (Oryza sativa L.). Two peaks of PLD activity were resolved by Mono Q anion-exchange chromatography. The molecular mass of PLD in both peaks was 82 kDa on SDS-PAGE and 78 kDa in gel filtration. Antibodies raised against the protein in one of the peaks precipitated the enzyme activities in both peaks. Enzymatic characteristics of PLD in the two peaks were identical except for a difference of 0.1 in the isoelectric points. Sequence analysis covering more than 10% of the amino acids of the proteins and peptide mapping did not detect any difference in the primary structure of the proteins. A cDNA for PLD was isolated from rice and it encoded a protein of 812 residues. The N-terminal sequences of purified PLDs matched the deduced amino acid sequence starting from residue 47. A Northern blot showed this gene was expressed in leaves, roots, developing seeds and cultured cells, and a Southern blot detected a single band of rice genomic DNA hybridizing to the cDNA. A cDNA for PLD was also isolated from maize. The similarity of the deduced amino acid sequences of PLD was 90% between rice and maize, 73% between the cereals and castor bean.

Amino Acid Sequence↗
PubMed2002

Isolation of MADS-box genes from sweet potato (Ipomoea batatas (L.) Lam.) expressed specifically in vegetative tissues.

New MADS-domain genes, IbMADS3 and IbMADS4, were isolated from pigmented and tuber-forming root tissue in sweet potato (Ipomoea batatas L.). Both genes were expressed preferentially in vegetative tissues, especially root tissues; white fibrous roots, pigmented roots, and developing tuberous roots. On sequence alignment, these genes fell into the STMADS group composed of SVP, STMADS11, STMADS16 and AGL24, which share high sequence similarity, similar expression patterns and similar function. Transcripts of these two genes in roots were found in the vascular cambium region. This particular expression pattern of these genes may lead to a higher proliferative potential of vegetative tissues, and may facilitate tuber initiation in sweet potato. These genes may lead to important information on the morphogenesis of vegetative structures.

Amino Acid Sequence↗
PubMed2004

Arabidopsis response regulator, ARR22, ectopic expression of which results in phenotypes similar to the wol cytokinin-receptor mutant.

Arabidopsis thaliana has a number of response regulators (ARRs) implicated in the histidine (His)-->aspartate (Asp) phosphorelay signal transduction. According to the current consistent model, both the type-A and type-B ARR family members play crucial roles in the cytokinin signaling circuitry. However, this higher plant has a few extra ARRs, on which no attention has been paid so far. Characterization of these extra ARRs might provide us with new insight into the His-->Asp phosphorelay signal transduction in plants. For this reason, in this study we extensively examined the natures of such a representative (named ARR22). Transcripts of ARR22 were expressed predominantly in reproductive organs, and a GFP::ARR22 fusion protein was localized in the cytoplasmic space in onion epidermal cells. The purified ARR22 protein had the ability to undergo phosphorylation in vitro, when incubated with phospho-AHP5, indicating that ARR22 has the fundamental ability to participate into a His-Asp phosphorelay pathway in its own right. In plants, transgenic lines overexpressing ARR22 were characterized (referred to as ARR22-ox), which showed the characteristic dwarf phenotypes with poorly developed root systems. The results of Northern blot hybridization with selected sets of hormone-responsive genes suggested that cytokinin responses are selectively attenuated in ARR22-ox, while other hormone responses (auxin, ABA and ethylene) occur normally. The results of microarray analyses with cytokinin-treated wild-type and ARR22-ox plants further supported the view that cytokinin responses are globally attenuated in ARR22-ox, at least, at the level of gene regulation. Finally, we demonstrated that the dwarf phenotypes of ARR22-ox are very similar to those of the wooden leg (wol) mutant, which has a severe lesion in the AHK4/CRE1 cytokinin-receptor of histidine protein kinase. These results suggested that ARR22 might also be implicated, directly or indirectly, in the cytokinin-responsive His-->Asp phophorelay signal transduction.

Amino Acid Sequence↗
PubMed1986

Dormancy of micropropagated sour cherry plantlets.

Micropropagation of fruit trees results in the early onset of dormancy in the young plantlets. Prechilling of shoot cultures of sour cherry cvs Schattenmorelle and North Star at 4 degrees C for 6-8 weeks prolonged shoot extension of the plantlets but longer cold treatments adversely affected shoot growth and survival. Chilling of cultures had no affect on rhizogenesis. No significant influence of ABA, GA(3) or ABA + GA(3) was observed on root development. Gibberellic acid A(3) did not stimulate extension of the shoots, but when supplied together with ABA, it significantly decreased both shoot extension and the number of actively growing apices of plantlets of cv Schattenmorelle. The combined hormonal treatment had no effect on plantlets of the North Star cv.

Journal Article↗
PubMed2003

Photosynthesis-nitrogen relationships: interpretation of different patterns between Pseudotsuga menziesii and Populus x euroamericana in a mini-stand experiment.

We compared photosynthesis-nitrogen relationships of one broad-leaved (poplar; Populus x euroamericana (Dole) Guinier) and one conifer (Douglas-fir; Pseudotsuga menziesii (Mirb.) Franco) species. Plants were grown in large pots to allow free root development and were kept well watered. We determined effects of low, intermediate and high nitrogen supply rates on area-based leaf nitrogen (Na) and chlorophyll concentrations, leaf mass per area (LMA), light-saturated photosynthesis (Amax), maximum carboxylation (Vcmax) and electron transport rate (Jmax), photosynthetic nitrogen-use efficiency (PNUE), and proportions of leaf N in active Rubisco (PR), bioenergetic pools (PB) and the light-harvesting complex (PLH). Nitrogen supply significantly affected leaf Na. Leaf mass per area did not differ between species and was unaffected by the N treatments. In both species, there was a positive correlation between leaf Na and chlorophyll concentration, and between leaf Na and the photosynthetic parameters Amax, Jmax and Vcmax. At comparable leaf Na, however, poplar showed twofold higher PNUE and a threefold steeper slope of the Amax- nitrogen relationship than Douglas-fir. Leaf Na was negatively correlated with PNUE in Douglas-fir but not in poplar. Leaf Na was also negatively correlated with PR, PB and PLH in Douglas-fir, whereas in poplar, a negative correlation was found only for PLH. Parameter PR was significantly higher in poplar than in Douglas-fir. The ratio of CO2 concentration in the intercellular space to that in ambient air was higher in poplar than in Douglas-fir. Overall, our data suggest that differences in the photosynthesis-nitrogen relationship and PNUE between Douglas-fir and poplar primarily reflect a different investment of N to active Rubisco, and possibly a different constraint to CO2 diffusion.

Carbon Dioxide↗
PubMed2006

Determination of genetic stability in long-term somatic embryogenic cultures and derived plantlets of cork oak using microsatellite markers.

Microsatellites were used to test genetic stability in somatic embryos (SE) of Quercus suber L. The SE were obtained by a simple somatic embryogenesis protocol: leaf explants from two adult plants (QsG0, QsG5) and from two juvenile plants (QsGM1, QsGM2) were inoculated on Murashige and Skoog (MS) medium with 2,4-dichlorophenoxyacetic acid and zeatin. Calluses with primary embryogenic structures were transferred to MSWH (MS medium without growth regulators) and SE proliferated by secondary somatic embryogenesis. High morphological heterogeneity was found among cotyledonary SE. However, converted plants looked morphologically normal with well-developed rooting systems and shoots. The genetic stability of the plant material during the somatic embryogenesis process was evaluated by using six to eight nuclear microsatellites transferred from Q. myrsinifolia Blume, Q. petraea (Matts.) Liebl. and Q. robur L. Five of eight microsatellites distinguished among the genotypes analyzed, and for QsG0, QsGM1 and QsGM2, uniform microsatellite patterns were generally observed within and between SE and the respective donor genotypes. For genotype QsG5, the same pattern was observed in all samples analyzed except one, where the mutation percentage was 2.5%. We conclude that microsatellite markers can be used to assess genetic stability of clonal materials and to determine genetic stability throughout the process of somatic embryogenesis. The simple somatic embryogenesis protocol described has potential for the commercial propagation of Q. suber because it results in a low percentage of mutations.

Alleles↗
PubMed1988

Drought tolerance, growth partitioning and vigor in eucalypt seedlings and rooted cuttings.

To clarify the physiological basis of productivity differences among rooted cuttings and seedlings of eucalypt species, relationships between morphology and water relations were examined in 4-month-old seedlings of Eucalyptus grandis W. Hill ex Maiden, E. urophylla S.T. Blake and E. cloeziana F. Muell. and in 4-month-old rooted cuttings of three E. grandis cultivars. Four-month-old seedlings had greater dry weights, lower leaf area/root dry weight (LA/RDW) ratios and lower shoot/root dry weight (S/R) ratios than 4-month-old rooted cuttings. For all cultivars of E. grandis, tall rooted cuttings, as defined by height at age 4 weeks, had greater dry weights by age 4 months and lower LA/RDW and S/R ratios than short rooted cuttings. There were differences in height growth, dry matter productivity and relative shoot and root development among cuttings of different E. grandis cultivars, but these differences were not as great as the differences between short and tall grades of the same cultivar and between seedlings and cuttings. Consistent with the differences in LA/RDW and S/R ratios, seedlings had higher daytime water potentials (Psi(x)) than cuttings, and tall cuttings had higher daytime values of Psi(x) than short cuttings. Differences in Psi(x) were also related to stomatal conductance (g(wv)), which was up to 300% greater in short cuttings than in tall cuttings. Among seedlings, those of E. cloeziana, which had the smallest dry weight at age 4 months, had the highest g(wv), whereas those of E. grandis, which had the greatest dry weight at age 4 months, had the lowest g(wv). Unlike seedlings and the tall cuttings, short cuttings lost turgor when subjected to drought. The differences observed in susceptibility to water stress may account in part for the associated differences in dry matter production. Xylem pressure potential and relative water deficit at zero turgor did not differ significantly among the types of plants studied, which suggests that differences in growth rates were not the result of differences in dehydration tolerance.

Journal Article↗
PubMed2006

Direct uptake of soil nitrogen by mosses.

Mosses are one of the most diverse and widespread groups of plants and often form the dominant vegetation in montane, boreal and arctic ecosystems. However, unlike higher plants, mosses lack developed root and vascular systems, which is thought to limit their access to soil nutrients. Here, we test the ability of two physiologically and taxonomically distinct moss species to take up soil- and wet deposition-derived nitrogen (N) in natural intact turfs using stable isotopic techniques (15N). Both species exhibited increased concentrations of shoot 15N when exposed to either soil- or wet deposition-derived 15N, demonstrating conclusively and for the first time, that mosses derive N from the soil. Given the broad physiological and taxonomic differences between these moss species, we suggest soil N uptake may be common among mosses, although further studies are required to test this prediction. Soil N uptake by moss species may allow them to compete for soil N in a wide range of ecosystems. Moreover, since many terrestrial ecosystems are N limited, soil N uptake by mosses may have implications for plant community structure and nutrient cycling. Finally, soil N uptake may place some moss species at greater risk from N pollution than previously appreciated.

Bryophyta↗
PubMed1993

Group 3 Late Embryogenesis Abundant Proteins in Desiccation-Tolerant Seedlings of Wheat (Triticum aestivum L.).

Dormant seeds and young seedlings of wheat (Triticum aestivum L.) tolerate desiccation. A transcript expressed in this desiccation-tolerant tissue has been cloned and sequenced (J. Curry, C.F. Morris, M.K. Walker-Simmons [1991] Plant Mol Biol 16: 1073-1076). This wheat cDNA clone encodes a protein that is homologous to other group 3 late embryogenesis abundant (LEA) proteins. In this report, we describe the production of polyclonal antibodies to the protein product of the cDNA clone and assess group 3 LEA protein levels in desiccation-tolerant tissue. The group 3 LEA antibodies detected four major proteins in wheat with molecular masses from 27 to 30.5 kD. The genes for these proteins mapped to wheat chromosomes 1A, 1B, and 1D. The group 3 LEA proteins were present in mature seed embryos and were maintained when growth-arrested, dormant seeds were hydrated for 111 h. However, in germinating seeds the group 3 LEA proteins declined and were no longer detectable by 111 h. We severely dehydrated seedlings (more than 90% water loss) to assess group 3 LEA transcript and protein accumulation in tissues of these desiccation-tolerant plants. In response to dehydration, abscisic acid (ABA) levels increased dramatically and group 3 LEA mRNAs were induced in root, shoot, and scutellar tissue. However, group 3 LEA proteins were detected only in shoot and scutellar tissue and not in root tissue. Treatment of nonstressed seedlings with 20 [mu]M ABA resulted in low levels of group 3 LEA proteins in the roots, whereas higher levels were found in the shoot and scutellar tissue. When dehydrated seedlings were rehydrated, shoot and scutellar tissue resumed growth. The roots did not resume growth and subsequently died. New roots developed later from the scutellar tissue. Thus, in severely dehydrated wheat seedlings, the accumulation of high levels of group 3 LEA proteins is correlated with tissue dehydration tolerance.

Journal Article↗
PubMed2003

Identification of glycosylphosphatidylinositol-anchored proteins in Arabidopsis. A proteomic and genomic analysis.

In a recent bioinformatic analysis, we predicted the presence of multiple families of cell surface glycosylphosphatidylinositol (GPI)-anchored proteins (GAPs) in Arabidopsis (G.H.H. Borner, D.J. Sherrier, T.J. Stevens, I.T. Arkin, P. Dupree [2002] Plant Physiol 129: 486-499). A number of publications have since demonstrated the importance of predicted GAPs in diverse physiological processes including root development, cell wall integrity, and adhesion. However, direct experimental evidence for their GPI anchoring is mostly lacking. Here, we present the first, to our knowledge, large-scale proteomic identification of plant GAPs. Triton X-114 phase partitioning and sensitivity to phosphatidylinositol-specific phospholipase C were used to prepare GAP-rich fractions from Arabidopsis callus cells. Two-dimensional fluorescence difference gel electrophoresis and one-dimensional sodium dodecyl sulfate-polyacrylamide gel electrophoresis demonstrated the existence of a large number of phospholipase C-sensitive Arabidopsis proteins. Using liquid chromatography-tandem mass spectrometry, 30 GAPs were identified, including six beta-1,3 glucanases, five phytocyanins, four fasciclin-like arabinogalactan proteins, four receptor-like proteins, two Hedgehog-interacting-like proteins, two putative glycerophosphodiesterases, a lipid transfer-like protein, a COBRA-like protein, SKU5, and SKS1. These results validate our previous bioinformatic analysis of the Arabidopsis protein database. Using the confirmed GAPs from the proteomic analysis to train the search algorithm, as well as improved genomic annotation, an updated in silico screen yielded 64 new candidates, raising the total to 248 predicted GAPs in Arabidopsis.

Arabidopsis↗
PubMed2005

A mutation in the anticodon of a single tRNAala is sufficient to confer auxin resistance in Arabidopsis.

Auxin-resistant mutants have been useful for dissecting the mechanisms that underlie auxin-mediated biological processes. Here we report the isolation and molecular characterization of a novel auxin-resistant mutant in Arabidopsis (Arabidopsis thaliana). Like known mutated AUX/IAA transcription factors, the mutant described here displayed dominant resistance to exogenously supplied auxins (sirtinol, 2,4-dichlorophenoxyacetic acid, indole-3-acetic acid) and a host of pleiotropic phenotypes, including apical hook deformation, defects in lateral root development, reduced stature, and homozygous lethality. This mutant showed the same sensitivity to the ethylene precursor 1-aminocyclopropane carboxylic acid as wild-type plants, and retained the ability to induce IAA19 expression in response to exogenously supplied indole-3-acetic acid. To our surprise, these phenotypes were not caused by a mutation in an AUX/IAA gene, but rather a mutation in a tRNA(ala) gene in which the anticodon was found changed from CGC to CAC. Such a change results in a tRNA that is charged with alanine but recognizes the second most highly used valine codon in Arabidopsis. Therefore, the observed phenotypes are likely the composite of stochastic mutations of many proteins, including downstream effectors.

Anticodon↗
PubMed2000

Auxin metabolism in the root apical meristem.

Within the root meristem of flowering plants is a group of mitotically inactive cells designated the quiescent center (QC). Recent work links the quiescent state to high levels of the growth regulator auxin that accumulates in the QC via polar transport. This in turn results in elevated levels of the enzyme ascorbic acid oxidase (AAO), resulting in a reduction of ascorbic acid (AA) within the QC and mitotic quiescence. We present evidence for additional interactions between auxin, AAO, and AA, and report that, in vitro, AAO oxidatively decarboxylates auxin, suggesting a mechanism for regulating auxin levels within the QC. We also report that oxidative decarboxylation occurs at the root tip and that an intact root cap must be present for this metabolic event to occur. Finally, we consider how interaction between auxin and AAO may influence root development by regulating the formation of the QC.

Ascorbate Oxidase↗
PubMed2001

Quantitative trait loci for component physiological traits determining salt tolerance in rice.

Rice (Oryza sativa) is sensitive to salinity, which affects one-fifth of irrigated land worldwide. Reducing sodium and chloride uptake into rice while maintaining potassium uptake are characteristics that would aid growth under saline conditions. We describe genetic determinants of the net quantity of ions transported to the shoot, clearly distinguishing between quantitative trait loci (QTL) for the quantity of ions in a shoot and for those that affect the concentration of an ion in the shoot. The latter coincide with QTL for vegetative growth (vigor) and their interpretation is therefore ambiguous. We distinguished those QTL that are independent of vigor and thus directly indicate quantitative variation in the underlying mechanisms of ion uptake. These QTL independently govern sodium uptake, potassium uptake, and sodium:potassium selectivity. The QTL for sodium and potassium uptake are on different linkage groups (chromosomes). This is consistent with the independent inheritance of sodium and potassium uptake in the mapping population and with the mechanistically different uptake pathways for sodium and potassium in rice under saline conditions (apoplastic leakage and membrane transport, respectively). We report the chromosomal location of ion transport and selectivity traits that are compatible with agronomic needs and we indicate markers to assist selection in a breeding program. Based upon knowledge of the underlying mechanisms of ion uptake in rice, we argue that QTL for sodium transport are likely to act through the control of root development, whereas QTL for potassium uptake are likely to act through the structure or regulation of membrane-sited transport components.

Analysis of Variance↗
PubMed2016

Characterization of Class III Peroxidases from Switchgrass.

Class III peroxidases (CIIIPRX) catalyze the oxidation of monolignols, generate radicals, and ultimately lead to the formation of lignin. In general, CIIIPRX genes encode a large number of isozymes with ranges of in vitro substrate specificities. In order to elucidate the mode of substrate specificity of these enzymes, we characterized one of the CIIIPRXs (PviPRX9) from switchgrass (Panicum virgatum), a strategic plant for second-generation biofuels. The crystal structure, kinetic experiments, molecular docking, as well as expression patterns of PviPRX9 across multiple tissues and treatments, along with its levels of coexpression with the majority of genes in the monolignol biosynthesis pathway, revealed the function of PviPRX9 in lignification. Significantly, our study suggested that PviPRX9 has the ability to oxidize a broad range of phenylpropanoids with rather similar efficiencies, which reflects its role in the fortification of cell walls during normal growth and root development and in response to insect feeding. Based on the observed interactions of phenylpropanoids in the active site and analysis of kinetics, a catalytic mechanism involving two water molecules and residues histidine-42, arginine-38, and serine-71 was proposed. In addition, proline-138 and gluntamine-140 at the 137P-X-P-X140 motif, leucine-66, proline-67, and asparagine-176 may account for the broad substrate specificity of PviPRX9. Taken together, these observations shed new light on the function and catalysis of PviPRX9 and potentially benefit efforts to improve biomass conservation properties in bioenergy and forage crops.

Amino Acid Sequence↗