Auxin: regulation, action, and interaction.

Jasmonates: biosynthesis, perception, signal transduction and action in plant stress response, growth and development. An update to the 2007 review in Annals of Botany

Epigenetic phenomena in animals and plants are mediated by DNA methylation and stable chromatin modifications. There has been considerable interest in whether environmental factors modulate the establishment and maintenance of epigenetic modifications, and could thereby influence gene expression and phenotype. Chemical pollutants, dietary components, temperature changes and other external stresses can indeed have long-lasting effects on development, metabolism and health, sometimes even in subsequent generations. Although the underlying mechanisms remain largely unknown, particularly in humans, mechanistic insights are emerging from experimental model systems. These have implications for structuring future research and understanding disease and development.

Epigenetics and the environment: emerging patterns and implications.

EVidenceModeler (EVM) is presented as an automated eukaryotic gene structure annotation tool that reports eukaryotic gene structures as a weighted consensus of all available evidence. EVM, when combined with the Program to Assemble Spliced Alignments (PASA), yields a comprehensive, configurable annotation system that predicts protein-coding genes and alternatively spliced isoforms. Our experiments on both rice and human genome sequences demonstrate that EVM produces automated gene structure annotation approaching the quality of manual curation.

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Automated Eukaryotic Gene Structure Annotation Using EVidenceModeler and the Program to Assemble Spliced Alignments

■ Abstract Cytokinins are structurally diverse and biologically versatile. The chemistry and physiology of cytokinin have been studied extensively, but the regulation of cytokinin biosynthesis, metabolism, and signal transduction is still largely undefined. Recent advances in cloning metabolic genes and identifying putative receptors portend more rapid progress based on molecular techniques. This review centers on cytokinin metabolism with connecting discussions on biosynthesis and signal transduction. Important findings are summarized with emphasis on metabolic enzymes and genes. Based on the information generated to date, implications and future research directions are presented.

Cytokinin metabolism and action

Dormancy of buds is a critical developmental process that allows perennial plants to survive extreme seasonal variations in climate. Dormancy transitions in underground crown buds of the model herbaceous perennial weed leafy spurge were investigated using a 23 K element cDNA microarray. These data represent the first large-scale transcriptome analysis of dormancy in underground buds of an herbaceous perennial species. Crown buds collected monthly from August through December, over a five year period, were used to monitor the changes in the transcriptome during dormancy transitions. Nearly 1,000 genes were differentially-expressed through seasonal dormancy transitions. Expected patterns of gene expression were observed for previously characterized genes and physiological processes indicated that resolution in our analysis was sufficient for identifying shifts in global gene expression. Gene ontology of differentially-expressed genes suggests dormancy transitions require specific alterations in transport functions (including induction of a series of mitochondrial substrate carriers, and sugar transporters), ethylene, jasmonic acid, auxin, gibberellic acid, and abscisic acid responses, and responses to stress (primarily oxidative and cold/drought). Comparison to other dormancy microarray studies indicated that nearly half of the genes identified in our study were also differentially expressed in at least two other plant species during dormancy transitions. This comparison allowed us to identify a particular MADS-box transcription factor related to the DORMANCY ASSOCIATED MADS-BOX genes from peach and hypothesize that it may play a direct role in dormancy induction and maintenance through regulation of FLOWERING LOCUS T.

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Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.)

At harvest, potato (Solanum tuberosum L.) tubers are dormant and will not sprout. As the period of postharvest storage is extended, tuber dormancy is broken and sprout growth commences. The loss of tuber dormancy and onset of sprout growth is accompanied by numerous biochemical changes, many of which are detrimental to the nutritional and processing qualities of potatoes. Endogenous hormones have been proposed to play a significant role in tuber dormancy regulation. The involvement of all major classes of endogenous hormones in tuber dormancy is reviewed. Based on available evidence, it is concluded that both ABA and ethylene are required for dormancy induction, but only ABA is needed to maintain bud dormancy. An increase in cytokinin sensitivity and content appear to be the principal factors leading to the loss of dormancy. Changes in endogenous IAA and GA content appear to be more closely related to the regulation of subsequent sprout growth.

Physiological regulation of potato tuber dormancy

The factors that regulate storage organ carotenoid content remain to be fully elucidated, despite the nutritional and economic importance of this class of compound. Recent findings suggest that carotenoid pool size is determined, at least in part, by the activity of carotenoid cleavage dioxygenases. The aim of this study was to investigate whether Carotenoid Cleavage Dioxygenase4 (CCD4) activity affects potato (Solanum tuberosum) tuber carotenoid content. Microarray analysis revealed elevated expression of the potato CCD4 gene in mature tubers from white-fleshed cultivars compared with higher carotenoid yellow-fleshed tubers. The expression level of the potato CCD4 gene was down-regulated using an RNA interference (RNAi) approach in stable transgenic lines. Down-regulation in tubers resulted in an increased carotenoid content, 2- to 5-fold higher than in control plants. The increase in carotenoid content was mainly due to elevated violaxanthin content, implying that this carotenoid may act as the in vivo substrate. Although transcript level was also reduced in plant organs other than tubers, such as leaves, stems, and roots , there was no change in carotenoid content in these organs. However, carotenoid levels were elevated in flower petals from RNAi lines. As well as changes in tuber carotenoid content, tubers from RNAi lines exhibited phenotypes such as heat sprouting, formation of chain tubers, and an elongated shape. These results suggest that the product of the CCD4 reaction may be an important factor in tuber heat responses.

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The metabolic and developmental roles of Carotenoid Cleavage Dioxygenase4 from potato.

The effect of ethylene treatment on polar indole-3-acetic acid (IAA) transport, net IAA uptake in the presence and absence of N-1-naphthylphthalamic acid (NPA) and [3H]NPA binding characteristics was investigated in tissue segments or microsomes isolated from etiolated pea (Pisum sativum L cv Alaska) epicotyls Basipetal IAA transport in 5 millimeter segments isolated from ethylene-treated seedlings was inhibited by ethylene in a dose-dependent manner Threshold, half-maximal and saturating concentrations of ethylene were 001, 055, 100 microliters per liter, respectively This inhibition became apparent after 6 to 8 hours of ethylene treatment Transport velocity in both control and ethylene-treated tissues was estimated to be 5 millimeters per hour Net IAA uptake was stimulated in ethylene-treated tissues and the relative ability of the phytotropin NPA to enhance net IAA uptake was reduced in treated tissues Specific binding of [3H]NPA to microsomes prepared from both control and ethylene-treated tissues was saturable and consistent with the existence of a single class of binding sites with an apparent affinity (Kd) toward NPA of 8 to 9 nanomolar The density of these binding sites (per milligram protein) was lower (36% of control) in ethylene-treated tissues Direct application of ethylene to microsomal preparations isolated from untreated seedlings had no effect on the level of specific [3H]NPA binding

Effect of Ethylene Treatment on Polar IAA Transport, Net IAA Uptake and Specific Binding of N-1-Naphthylphthalamic Acid in Tissues and Microsomes Isolated from Etiolated Pea Epicotyls

Potato (Solanum tuberosum L. cv Russet Burbank) microtubers generated in vitro from single-node explants contained substantial amounts (approximately 250 pmol/g fresh weight) of free abscisic acid (ABA) and were completely dormant for a minimum of 12 weeks. Microtubers that developed in the presence of 10 [mu]M fluridone (FLD) contained considerably reduced amounts (approximately 5-25 pmol/g fresh weight) of free ABA and exhibited a precocious loss of dormancy. Inclusion of exogenous racemic ABA in the FLD-containing medium suppressed the premature sprouting of these microtubers in a dose-dependent manner. At a concentration of 50 [mu]M, exogenous ABA restored internal ABA levels to control values and completely inhibited FLD-induced precocious sprouting. Exogenous jasmonic acid was ineffective in suppressing FLD-induced sprouting. Application of FLD to preformed, fully dormant microtubers also resulted in a reduction in internal ABA content and precocious sprouting. These results indicate that endogenous ABA is essential for the induction and maintenance of potato microtuber dormancy.

Jeffrey C. Suttle

Papers

Transcriptome analysis identifies novel responses and potential regulatory genes involved in seasonal dormancy transitions of leafy spurge (Euphorbia esula L.)

Physiological regulation of potato tuber dormancy

The metabolic and developmental roles of Carotenoid Cleavage Dioxygenase4 from potato.

Effect of Ethylene Treatment on Polar IAA Transport, Net IAA Uptake and Specific Binding of N-1-Naphthylphthalamic Acid in Tissues and Microsomes Isolated from Etiolated Pea Epicotyls

Role of Endogenous Abscisic Acid in Potato Microtuber Dormancy.