Patrick J. Gulick

Interaction network of proteins associated with abiotic stress response and development in wheat

Wheat is the most widely adapted crop to abiotic stresses and considered an excellent system to study stress tolerance in spite of its genetic complexity. Recent studies indicated that several hundred genes are either up- or down-regulated in response to stress treatment. To elucidate the function of some of these genes, an interactome of proteins associated with abiotic stress response and development in wheat was generated using the yeast two-hybrid GAL4 system and specific protein interaction assays. The interactome is comprised of 73 proteins, generating 97 interactions pairs. Twenty-one interactions were confirmed by bimolecular fluorescent complementation in Nicotiana benthamiana. A confidence-scoring system was elaborated to evaluate the significance of the interactions. The main feature of this interactome is that almost all bait proteins along with their interactors were interconnected, creating a spider web-like structure. The interactome revealed also the presence of a “cluster of proteins involved in flowering control” in three- and four-protein interaction loops.This network provides a novel insight into the complex relationships among transcription factors known to play central roles in vernalization, flower initiation and abscisic acid signaling, as well as associations that tie abiotic stress with other regulatory and signaling proteins. This analysis provides useful information in elucidating the molecular mechanism associated with abiotic stress response in plants.

Regulatory gene candidates and gene expression analysis of cold acclimation in winter and spring wheat

Freezing tolerance in plants develops through acclimation to cold by growth at low, above-freezing temperatures. Wheat is one of the most freezing-tolerant plants among major crop species and the wide range of freezing tolerance among wheat cultivars makes it an excellent model for investigation of the genetic basis of cold tolerance. Large numbers of genes are known to have altered levels of expression during the period of cold acclimation and there is keen interest in deciphering the signaling and regulatory pathways that control the changes in gene expression associated with acquired freezing tolerance. A 5740 feature cDNA amplicon microarray that was enriched for signal transduction and regulatory genes was constructed to compare changes in gene expression in a highly cold-tolerant winter wheat cultivar CDC Clair and a less tolerant spring cultivar, Quantum. Changes in gene expression over a time course of 14 days detected over 450 genes that were regulated by cold treatment and were differentially regulated between spring and winter cultivars, of these 130 are signaling or regulatory gene candidates, including: transcription factors, protein kinases, ubiquitin ligases and GTP, RNA and calcium binding proteins. Dynamic changes in transcript levels were seen at all periods of cold acclimation in both cultivars. There was an initial burst of gene activity detectable during the first day of CA, during which 90% of all genes with increases in transcript levels became clearly detectable and early expression differential between the two cultivars became more disparate with each successive period of cold acclimation.

Characterization of the Early Stages of Genetic Salt-Stress Responses in Salt-Tolerant Lophopyrum elongatum, Salt-Sensitive Wheat, and Their Amphiploid.

Eleven unique cDNA clones corresponding to genes showing enhanced mRNA accumulation in the early stages of salt stress (early salt stress induced, ESI) were previously isolated. The accumulation of these mRNAs in Lophopyrum elongatum (Host) A. Love, salt-sensitive wheat (Triticum aestivum L.), and their amphiploid is compared. The accumulation of ESI mRNAs was much greater in the L. elongatum roots than in the shoots. Additionally, mRNA accumulation in the roots of the three genotypes showed a biphasic response. The first phase occurred within a few hours after the onset of stress and had a large osmotic shock component, as indicated by induction of the accumulation of these mRNAs by a nonsaline osmoticum. The ion-specific component, however, also played a role. External Ca2+ reduced this response. The second phase was characterized by either constantly elevated mRNA levels or gradually increasing mRNA levels. The same biphasic response was elicited by exogenous abscisic acid (ABA). The response of all mRNAs to ABA closely approximated the response to 250 mM NaCl treatment in all three genotypes. The differences among the three genotypes in response to NaCl and ABA treatments were largely confined to the first phase of the response, in which mRNA levels were highest in L. elongatum and lowest in wheat. The levels of ESI mRNAs in the amphiploid closely approximated levels calculated on the basis of the doses of wheat and L. elongatum genomes in the amphiploid, which indicated an additive contribution of the genomes to early salt stress response in the amphiploid. The inducer of the ESI mRNA accumulation in response to NaCl and other osmotica is produced in the stressed roots and shows only minor, if any, translocation. A putative candidate for this inducer is root ABA.

Data mining for miRNAs and their targets in the Triticeae.

MicroRNAs (miRNAs) and the mRNA targets of miRNAs were identified by sequence complementarity within a DNA sequence database for species of the Triticeae. Data screening identified 28 miRNA precursor sequences from 15 miRNA families that contained conserved mature miRNA sequences within predicted stem-loop structures. In addition, the identification of 337 target sequences among Triticeae genes provided further evidence of the existence of 26 miRNA families in the cereals. MicroRNA targets included genes that are homologous to known targets in diverse model species as well as novel targets. MicroRNA precursors and targets were identified in 10 related species, though the great majority of them were identified in bread wheat, Triticum aestivum, and barley, Hordeum vulgare, the two species with the largest EST data sets among the Triticeae.

Enzymatic prenylation of isoflavones in white lupin

Abstract Microsomal preparations of white lupin ( Lupinus albus ) radicles and cell suspension cultures catalyse the prenylation of positions 6, 8 and 3′ of the isoflavones genistein and 2′-hydroxygenistein. Both the substrates and the enzyme reaction products are natural constituents of lupin tissues. Enzymatic prenylation of isoflavones required dimethylallyl pyrophosphate (DMAPP) and 12 mM Mn 2+ with optimum activity at pH 7.5 in Tris-HCl buffer. The apparent K m values for DMAPP and the prenyl acceptors were 4 and 5 μM, respectively. Isopentenyl pyrophosphate was a competitive inhibitor of the prenylation reaction, with an apparent K i of 5 μM. The bulk of enzymatic activity was associated with the membrane fraction and could only be solubilized in the presence of a detergent. The differences observed in prenyltransferase activity ratios, in relation to the source of the enzyme and the type of detergent used, suggest that prenylation at positions 6, 8 and 3′ of isoflavones is catalysed by a number of distinct enzymes.

cDNA cloning and characterization of a 3′/5′-O-methyltransferase for partially methylated flavonols from Chrysosplenium americanum

Enzymatic O-methylation of plant secondary metabolites is an important mechanism for the inactivation of reactive hydroxyl groups and for the modification of their solubility. A cDNA clone (pFOMT3′) encoding the gene for the 3′/5′-O-methylation of partially methylated flavonols was isolated from Chrysosplenium americanum (Saxifragaceae). We used a PCR fragment obtained with degenerate oligonucleotides designed from conserved regions of various O-methyltransferases (OMTs). The pFOMT3′ cDNA sequence shows about 67–85% similarity to other plant OMT sequences. The recombinant protein expresses strict specificity for positions 3′/5′ (meta) of partially methylated flavonols, but does not accept quercetin or caffeic acid for further methylation. Southern blot analysis of the genomic DNA probed with an OMT sequence suggests the presence of a number of related genes in this species, consistent with the multiple enzymatic methylations involved in the biosynthesis of polymethylated flavonols in this plant.

Cloning and Regulation of Flavonol 3-Sulfotransferase in Cell-Suspension Cultures of Flaveria bidentis

Flaveria spp. accumulate flavonol sulfate esters whose biosynthesis is catalyzed by a number of position-specific flavonol sulfotransferases. Although the accumulation of sulfated flavonols appears to be tissue specific and developmentally regulated and to vary among related species, little is known about the mechanism of regulation controlling the synthesis of these metabolites. In the present work, we report the isolation of a cDNA clone from Flaveria bidentis (pBFST3) encoding flavonol 3-sulfotransferase (F3-ST), which catalyzes the first step in the biosynthesis of flavonol poly-sulfates. This clone (pBFST3) was expressed in Escherichia coli and produced an F3-ST with high affinity for the flavonol aglycones, quercetin, and its 7-methyl derivative, rhamnetin. In addition, the synthetic auxin 2,4-dichlorophenoxyacetic acid was shown to induce F3-ST enzyme activity and F3-ST mRNA transcript levels in cell cultures of F. bidentis. The F3-ST mRNA levels increased within the first 3 h, reaching a maximum after 24 h of treatment, and remained elevated for up to 48 h. Treatments with either quercetin 3-sulfate or quercetin 3,7,4[prime]-trisulfate reduced F3-ST enzyme activity in cell cultures but had no effect on the transcript levels. These results are discussed in relation to the putative role of flavonoid conjugates in the regulation of auxin transport.

Heterotrimeric Gα subunit from wheat (Triticum aestivum), GA3, interacts with the calcium-binding protein, Clo3, and the phosphoinositide-specific phospholipase C, PI-PLC1.

The canonical Gα subunit of the heterotrimeric G protein complex from wheat (Triticum aestivum), GA3, and the calcium-binding protein, Clo3, were revealed to interact both in vivo and in vitro and Clo3 was shown to enhance the GTPase activity of GA3. Clo3 is a member of the caleosin gene family in wheat with a single EF-hand domain and is induced during cold acclimation. Bimolecular Fluorescent Complementation (BiFC) was used to localize the interaction between Clo3 and GA3 to the plasma membrane (PM). Even though heterotrimeric G-protein signaling and Ca2+ signaling have both been shown to play a role in the response to environmental stresses in plants, little is known about the interaction between calcium-binding proteins and Gα. The GAP activity of Clo3 towards GA3 suggests it may play a role in the inactivation of GA3 as part of the stress response in plants. GA3 was also shown to interact with the phosphoinositide-specific phospholipase C, PI-PLC1, not only in the PM but also in the endoplasmic reticulum (ER). Surprisingly, Clo3 was also shown to interact with PI-PLC1 in the PM and ER. In vitro analysis of the protein–protein interaction showed that the interaction of Clo3 with GA3 and PI-PLC1 is enhanced by high Ca2+ levels. Three-way affinity characterizations with GA3, Clo3 and PI-PLC1 showed the interaction with Clo3 to be competitive, which suggests that Clo3 may play a role in the Ca2+-triggered feedback regulation of both GA3 and PI-PLC1. This hypothesis was further supported by the demonstration that Clo3 has GAP activity with GA3.

Identification and characterization of rye genes not expressed in allohexaploid triticale

BackgroundOne of the most important evolutionary processes in plants is polyploidization. The combination of two or more genomes in one organism often initially leads to changes in gene expression and extensive genomic reorganization, compared to the parental species. Hexaploid triticale (x Triticosecale) is a synthetic hybrid crop species generated by crosses between T. turgidum and Secale cereale. Because triticale is a recent synthetic polyploid it is an important model for studying genome evolution following polyploidization. Molecular studies have demonstrated that genomic sequence changes, consisting of sequence elimination or loss of expression of genes from the rye genome, are common in triticale. High-throughput DNA sequencing allows a large number of genes to be surveyed, and transcripts from the different homeologous copies of the genes that have high sequence similarity can be better distinguished than hybridization methods previously employed.ResultsThe expression levels of 23,503 rye cDNA reference contigs were analyzed in 454-cDNA libraries obtained from anther, root and stem from both triticale and rye, as well as in five 454-cDNA data sets created from triticale seedling shoot, ovary, stigma, pollen and seed tissues to identify the classes of rye genes silenced or absent in the recent synthetic hexaploid triticale. Comparisons between diploid rye and hexaploid triticale detected 112 rye cDNA contigs (~0.5%) that were totally undetected by expression analysis in all triticale tissues, although their expression was relatively high in rye tissues. Non-expressed rye genes were found to be strikingly less similar to their closest BLASTN matches in the wheat genome or in the other Triticum genomes than a test set of 200 random rye genes. Genes that were not detected in the RNA-seq data were further characterized by testing for their presence in the triticale genome by PCR using genomic DNA as a template.ConclusionGenes with low similarity between rye sequences and their closest matches in the Triticum genome have a higher probability to be repressed or absent in the allopolyploid genome.

Characterization of the caleosin gene family in the Triticeae

BackgroundThe caleosin genes encode proteins with a single conserved EF hand calcium-binding domain and comprise small gene families found in a wide range of plant species. Some members of the gene family have been shown to be upregulated by environmental stresses including low water availability and high salinity. Caleosin 3 from wheat has been shown to interact with the α-subunit of the heterotrimeric G proteins, and to act as a GTPase activating protein (GAP). This study characterizes the size and diversity of the gene family in wheat and related species and characterizes the differential tissue-specific expression of members of the gene family.ResultsA total of 34 gene family members that belong to eleven paralogous groups of caleosins were identified in the hexaploid bread wheat, T. aestivum. Each group was represented by three homeologous copies of the gene located on corresponding homeologous chromosomes, except the caleosin 10, which has four gene copies. Ten gene family members were identified in diploid barley, Hordeum vulgare, and in rye, Secale cereale, seven in Brachypodium distachyon, and six in rice, Oryza sativa. The analysis of gene expression was assayed in triticale and rye by RNA-Seq analysis of 454 sequence sets and members of the gene family were found to have diverse patterns of gene expression in the different tissues that were sampled in rye and in triticale, the hybrid hexaploid species derived from wheat and rye. Expression of the gene family in wheat and barley was also previously determined by microarray analysis, and changes in expression during development and in response to environmental stresses are presented.ConclusionsThe caleosin gene family had a greater degree of expansion in the Triticeae than in the other monocot species, Brachypodium and rice. The prior implication of one member of the gene family in the stress response and heterotrimeric G protein signaling, points to the potential importance of the caleosin gene family. The complexity of the family and differential expression in various tissues and under conditions of abiotic stress suggests the possibility that caleosin family members may play diverse roles in signaling and development that warrants further investigation.