Actinidia DRM1--an intrinsically disordered protein whose mRNA expression is inversely correlated with spring budbreak in kiwifruit

Intrinsically disordered proteins (IDPs) are a relatively recently defined class of proteins which, under native conditions, lack a unique tertiary structure whilst maintaining essential biological functions. Functional classification of IDPs have implicated such proteins as being involved in various physiological processes including transcription and translation regulation, signal transduction and protein modification. Actinidia DRM1 (Ade DORMANCY ASSOCIATED GENE 1), represents a robust dormancy marker whose mRNA transcript expression exhibits a strong inverse correlation with the onset of growth following periods of physiological dormancy. Bioinformatic analyses suggest that DRM1 is plant specific and highly conserved at both the nucleotide and protein levels. It is predicted to be an intrinsically disordered protein with two distinct highly conserved domains. Several Actinidia DRM1 homologues, which align into two distinct Actinidia-specific families, Type I and Type II, have been identified. No candidates for the Arabidopsis DRM1-Homologue (AtDRM2) an additional family member, has been identified in Actinidia.

Conservation and divergence of four kiwifruit SVP-like MADS-box genes suggest distinct roles in kiwifruit bud dormancy and flowering

MADS-box genes similar to Arabidopsis SHORT VEGETATIVE PHASE (SVP) have been implicated in the regulation of flowering in annual species and bud dormancy in perennial species. Kiwifruit (Actinidia spp.) are woody perennial vines where bud dormancy and out-growth affect flower development. To determine the role of SVP-like genes in dormancy and flowering of kiwifruit, four MADS-box genes with homology to Arabidopsis SVP, designated SVP1, SVP2, SVP3, and SVP4, have been identified and analysed in kiwifruit and functionally characterized in Arabidopsis. Phylogenetic analysis indicate that these genes fall into different sub-clades within the SVP-like gene group, suggesting distinct functions. Expression was generally confined to vegetative tissues, and increased transcript accumulation in shoot buds over the winter period suggests a role for these genes in bud dormancy. Down-regulation before flower differentiation indicate possible roles as floral repressors. Over-expression and complementation studies in Arabidopsis resulted in a range of floral reversion phenotypes arising from interactions with Arabidopsis MADS-box proteins, but only SVP1 and SVP3 were able to complement the svp mutant. These results suggest that the kiwifruit SVP-like genes may have distinct roles during bud dormancy and flowering.

An FTIR study of the induction and release of kiwifruit buds from dormancy

BACKGROUND

Many deciduous, perennial fruit crops require winter chilling for adequate budbreak and flowering. Recent research has shown that changes in sugar and amino acid profiles are associated with the release of buds from dormancy. This paper uses FTIR spectrometry to provide an alternative mechanism for tracking metabolic changes in the meristems of kiwifruit buds during winter dormancy. The results suggest that the application of multivariate analysis to FTIR spectra has the potential to be a reliable and fast method for detecting structural and compositional changes in fruit crops.

RESULTS

Ten wave numbers of the FTIR spectra are used to calculate a bud development function. This function has been validated using data from two seasons and four orchards, and by monitoring the effects of hydrogen cyanamide application, sugar concentrations and soil temperatures on this function. These wave numbers appear to be associated with carbohydrate, pectin and cellulose levels in the meristems.

CONCLUSION

It is expected that this FTIR signature can be used to advance our understanding of the influence of the various environmental and physiological factors on the breaking of bud dormancy and shoot outgrowth, including the optimum timing and concentrations of applications of budbreak regulators, such as hydrogen cyanamide.

A rapid transcriptional activation is induced by the dormancy-breaking chemical hydrogen cyanamide in kiwifruit (Actinidia deliciosa) buds

Budbreak in kiwifruit (Actinidia deliciosa) can be poor in locations that have warm winters with insufficient winter chilling. Kiwifruit vines are often treated with the dormancy-breaking chemical hydrogen cyanamide (HC) to increase and synchronize budbreak. This treatment also offers a tool to understand the processes involved in budbreak. A genomics approach is presented here to increase our understanding of budbreak in kiwifruit. Most genes identified following HC application appear to be associated with responses to stress, but a number of genes appear to be associated with the reactivation of growth. Three patterns of gene expression were identified: Profile 1, an HC-induced transient activation; Profile 2, an HC-induced transient activation followed by a growth-related activation; and Profile 3, HC- and growth-repressed. One group of genes that was rapidly up-regulated in response to HC was the glutathione S-transferase (GST) class of genes, which have been associated with stress and signalling. Previous budbreak studies, in three other species, also report up-regulated GST expression. Phylogenetic analysis of these GSTs showed that they clustered into two sub-clades, suggesting a strong correlation between their expression and budbreak across species.

Analysis of expressed sequence tags from Actinidia: applications of a cross species EST database for gene discovery in the areas of flavor, health, color and ripening

Background

Kiwifruit (Actinidia spp.) are a relatively new, but economically important crop grown in many different parts of the world. Commercial success is driven by the development of new cultivars with novel consumer traits including flavor, appearance, healthful components and convenience. To increase our understanding of the genetic diversity and gene-based control of these key traits in Actinidia, we have produced a collection of 132,577 expressed sequence tags (ESTs).

Results

The ESTs were derived mainly from four Actinidia species (A. chinensis, A. deliciosa, A. arguta and A. eriantha) and fell into 41,858 non redundant clusters (18,070 tentative consensus sequences and 23,788 EST singletons). Analysis of flavor and fragrance-related gene families (acyltransferases and carboxylesterases) and pathways (terpenoid biosynthesis) is presented in comparison with a chemical analysis of the compounds present in Actinidia including esters, acids, alcohols and terpenes. ESTs are identified for most genes in color pathways controlling chlorophyll degradation and carotenoid biosynthesis. In the health area, data are presented on the ESTs involved in ascorbic acid and quinic acid biosynthesis showing not only that genes for many of the steps in these pathways are represented in the database, but that genes encoding some critical steps are absent. In the convenience area, genes related to different stages of fruit softening are identified.

Conclusion

This large EST resource will allow researchers to undertake the tremendous challenge of understanding the molecular basis of genetic diversity in the Actinidia genus as well as provide an EST resource for comparative fruit genomics. The various bioinformatics analyses we have undertaken demonstrates the extent of coverage of ESTs for genes encoding different biochemical pathways in Actinidia.

Protocol: a highly sensitive RT-PCR method for detection and quantification of microRNAs

MicroRNAs (miRNAs) are a class of small non-coding RNAs with a critical role in development and environmental responses. Efficient and reliable detection of miRNAs is an essential step towards understanding their roles in specific cells and tissues. However, gel-based assays currently used to detect miRNAs are very limited in terms of throughput, sensitivity and specificity. Here we provide protocols for detection and quantification of miRNAs by RT-PCR. We describe an end-point and real-time looped RT-PCR procedure and demonstrate detection of miRNAs from as little as 20 pg of plant tissue total RNA and from total RNA isolated from as little as 0.1 mul of phloem sap. In addition, we have developed an alternative real-time PCR assay that can further improve specificity when detecting low abundant miRNAs. Using this assay, we have demonstrated that miRNAs are differentially expressed in the phloem sap and the surrounding vascular tissue. This method enables fast, sensitive and specific miRNA expression profiling and is suitable for facilitation of high-throughput detection and quantification of miRNA expression.

Analyses of expressed sequence tags from apple

The domestic apple (Malus domestica; also known as Malus pumila Mill.) has become a model fruit crop in which to study commercial traits such as disease and pest resistance, grafting, and flavor and health compound biosynthesis. To speed the discovery of genes involved in these traits, develop markers to map genes, and breed new cultivars, we have produced a substantial expressed sequence tag collection from various tissues of apple, focusing on fruit tissues of the cultivar Royal Gala. Over 150,000 expressed sequence tags have been collected from 43 different cDNA libraries representing 34 different tissues and treatments. Clustering of these sequences results in a set of 42,938 nonredundant sequences comprising 17,460 tentative contigs and 25,478 singletons, together representing what we predict are approximately one-half the expressed genes from apple. Many potential molecular markers are abundant in the apple transcripts. Dinucleotide repeats are found in 4,018 nonredundant sequences, mainly in the 5'-untranslated region of the gene, with a bias toward one repeat type (containing AG, 88%) and against another (repeats containing CG, 0.1%). Trinucleotide repeats are most common in the predicted coding regions and do not show a similar degree of sequence bias in their representation. Bi-allelic single-nucleotide polymorphisms are highly abundant with one found, on average, every 706 bp of transcribed DNA. Predictions of the numbers of representatives from protein families indicate the presence of many genes involved in disease resistance and the biosynthesis of flavor and health-associated compounds. Comparisons of some of these gene families with Arabidopsis (Arabidopsis thaliana) suggest instances where there have been duplications in the lineages leading to apple of biosynthetic and regulatory genes that are expressed in fruit. This resource paves the way for a concerted functional genomics effort in this important temperate fruit crop.

Bimodal patterns of floral gene expression over the two seasons that kiwifruit flowers develop

Polymerase chain reaction fragments with homology to the Arabidopsis floral meristem identity genes LEAFY and APETALA1 have been isolated from kiwifruit (Actinidia deliciosa [A. Chev.] C. F. Liang and A. R. Ferguson) and have been named ALF and AAP1, respectively. Northern hybridisation analyses have shown that ALF and AAP1 have bimodal patterns of annual expression in developing first-order axillary buds and their subsequent shoots. This pattern of expression is consistent with the 2-year cycle of axillary bud, flower and fruit development observed in kiwifruit. The first period of expression was early in first-order bud development (late spring of the first growing season), when second-order meristems are initiated, and the second, approximately 10 months later, when those meristems differentiate flowers (late spring of the second growing season). In situ hybridisation analyses on axillary buds collected during late spring of the first growing season have shown ALF expression throughout the developing first-order buds and AAP1 expression was localised in developing second-order axillary meristems. During the spring of the second growing season, transcript accumulation for both ALF and AAP1 is localised in differentiating flowers. Our results show that important developmental events are occurring very early in kiwifruit first-order axillary bud development (spring of the first growing season) and it is likely that this includes floral commitment (evocation).

S-alk(en)yl-L-cysteine sulfoxides, alliinase and aroma in Leucocoryne

Levels of S-alk(en)yl-L-cysteine sulfoxides, alliinase and enzymatically generated pyruvic acid were determined in the bulb, leaf and scape of five species and a natural hybrid of Leucocoryne (Liliaceae), a genus of ornamental geophytes indigenous to Chile. (+)-S-Methyl-L-cysteine sulfoxide (MCSO) was present in all plant parts of all species at levels between 0.09 and 1.41 mg g(-1) fr. wt. Trans-(+)-S-(1-propenyl)-L-cysteine sulfoxide (PRENCSO) was present in plant parts of three species only (L. angustipetala, L. oadorata and L. purpurea) at levels between 0.12 and 1.82 mg g(-1) fr. wt. No other S-alk(en)yl-L-cysteine sulfoxides were detected. Alliinase (EC 4.4.1.4) was detected in the leaf, bulb and scape of L. angustipetala and L. purpurea, only in the leaves of L. coquimbensis and L. purpurea x L. coquimbensis, and only in the bulb of L. odorata. Enzymatically generated pyruvic acid was detected in all plant parts of all species at levels between trace amounts and 5.33 micromol g(-1) fr. wt. As PRENCSO is produced only in Leucocoryne species exhibiting a strong and unpleasant onion-like aroma, it is probable that the enzymatic degradation of PRENCSO is the main cause of that aroma. Consequently, Leucocoryne cultivars should be selected in species and hybrids that lack the ability to synthesise PRENCSO.

Stable production of human gastric lipase by chromosomal integration in the fission yeast Schizosaccharomyces pombe

Strains of the fission yeast Schizosaccharomyces pombe have been constructed containing single or multiple chromosomally integrated copies of an expression cassette for production of human gastric lipase. Integrant strains of S. pombe secrete active lipase and are stable for lipase production over a minimum of 50 generations in non-selective media. Lipase activity levels for integrant strains containing up to three tandem copies of the expression cassette are strongly correlated with copy number of the cassette in both complete and minimal media. Lipase activity is higher in complete medium than in minimal medium. Strains carrying three chromosomally integrated expression cassette copies can be grown without selection in complete medium and are capable of significantly higher lipase activities than strains containing the expression cassette on a multicopy plasmid.

The secretion of active recombinant human gastric lipase by Saccharomyces cerevisiae

The expression of the complete human gastric lipase (HGL) gene in Saceharomyces cerevisiae grown in defined medium resulted in the secretion of active recombinant HGL (rec.HGL) to levels of up to approximately 11 mg/liter. Of the total measurable HGL activity, 90% was detected by assaying intact cells, suggesting that the majority of rec.HGL produced was secreted but stayed attached to the cell wall. The remaining 10% was present in the growth medium and from this source active rec.HGL was purified 300-fold by a combination of hydrophobic interaction and ion-exchange chromatography. Rec.HGL migrated on reduced SDS-PAGE as three bands with estimated molecular masses of 47,45, and 43 kDa. All three forms cross-reacted with an antibody raised to natural HGL and their treatment with Endo H showed them to be N-linked glycosylation variants of a single polypeptide. The 47-kDa species was isolated using lentil lectin Sepharose 4B and shown to possess a specific activity comparable to that of the natural enzyme. Rec.HGL had an acid pH activity optimum using either tributyrin or olive oil as substrate and did not lose activity if incubated in the presence of pepsin at pH 2.0. These results demonstrate that HGL secreted by Saccharomyces cerevisiae retained those properties of the natural enzyme required for its use in the treatment of pancreatic insufficiency.

Production of human gastric lipase in the fission yeast Schizosaccharomyces pombe

A cDNA encoding human gastric lipase (hGL) has been expressed on multicopy plasmids in the fission yeast Schizosaccharomyces pombe (Sp). Active lipase is secreted from transformants containing the hGL cDNA under the control of either the Sp adh1 promoter (Padh1) or the plant cauliflower mosaic virus (CaMV) 35S promoter. Cell-wall-associated lipase activities are greatest in the early logarithmic growth phase and with Padh1. Western blot analysis indicates that a protein of identical molecular mass to natural hGL is secreted by Sp, although the major secreted product is of a higher molecular mass than either native hGL or recombinant hGL produced in the budding yeast Saccharomyces cerevisiae (Sc). Several distinct hGL are present within cells at all growth phases. Treatment of these proteins with endoglycosidase H gives rise to a single species equivalent in size to deglycosylated natural hGL, indicating that most of these are glycosylation intermediates. An hGL of similar molecular mass accumulates intracellularly in Sp when a modified version of cDNA is used which lacks the sequence encoding the natural secretory signal peptide. Production of hGL markedly slows the growth rate of Sp. The average copy number per cell of the plasmid expressing the hGL cDNA from the recombinant Padh1 is 2-3, as compared with 11-12 for the control plasmid.

Effect of Hydrogen Cyanamide on Amino Acid Profiles in Kiwifruit Buds during Budbreak

Buds, and resultant shoots, were collected from kiwifruit (Actinidia deliciosa [A. Chev.] CF Liang et AR Ferguson var deliciosa cv Hayward) vines from late autumn until late spring with and without hydrogen cyanamide treatment. Those samples were weighed and analyzed for total nitrogen and free amino acids. By 7 days after hydrogen cyanamide treatment, the amount of proline had risen to nearly one-quarter of the total amino acid pool in the treated buds and that proportion was maintained for at least 14 days before it declined. The maximum concentration detected in treated buds was 25.8 micromoles per gram dry weight, 6.6 times that detected in untreated buds. By 95 days after treatment, the relative amounts of proline were not significantly different.

Carbohydrate requirements of peach fruit growth and respiration

Data on the seasonal patterns of fruit growth and dark respiration of two peach (Prunus persica (L.) Batsch) cultivars were combined with temperature data to calculate the carbohydrate requirements of an "average" peach fruit from bloom to harvest. The two peach cultivars used were June Lady (an early maturing (mid-June) cultivar) and O'Henry (a late maturing (early-August) cultivar). At harvest, the mean dry weight of the June Lady fruit was 17.8 g (139.7 g fresh weight) and of O'Henry fruits was 30.9 g (213.9 g fresh weight), and the times from full bloom to harvest were 107 and 154 days, respectively. The total calculated fruit respiration requirements were 132 and 300 mmol CO(2) fruit(-1) season(-1) for June Lady and O'Henry fruits, respectively. Total calculated carbohydrate requirements for fruit growth and respiration are 23.9 and 43.8 g CH(2)O fruit(-1) season(-1) for June Lady and O'Henry fruits, respectively. Fruit respiration accounted for 16.3% of the total carbohydrate requirements of June Lady fruits and 0.5% of the total carbohydrate requirements of O'Henry fruits.

Effect of growth temperature upon heat sensitivity in Saccharomyces cerevisiae

The resistance of exponentially growing yeast cells to killing by exposure to 52 degrees C increase markedly as the growth temperature was increased. Identical killing curves were obtained for cells suspended in growth medium or in 0.9% saline. Cells resistant to killing at 52 degrees C were quite sensitive to killing at slightly higher temperatures. These results suggest a primary role for membrane damage in the mechanism of heat killing.