Scott A. Finlayson

Transcriptional Profiling of Sorghum Induced by Methyl Jasmonate, Salicylic Acid, and Aminocyclopropane Carboxylic Acid Reveals Cooperative Regulation and Novel Gene Responses

We have conducted a large-scale study of gene expression in the C4 monocot sorghum (Sorghum bicolor) L. Moench cv BTx623 in response to the signaling compounds salicylic acid (SA), methyl jasmonate (MeJA), and the ethylene precursor aminocyclopropane carboxylic acid. Expression profiles were generated from seedling root and shoot tissue at 3 and 27 h, using a microarray containing 12,982 nonredundant elements. Data from 102 slides and quantitative reverse transcription-PCR data on mRNA abundance from 171 genes were collected and analyzed and are here made publicly available. Numerous gene clusters were identified in which expression was correlated with particular signaling compound and tissue combinations. Many genes previously implicated in defense responded to the treatments, including numerous pathogenesis-related genes and most members of the phenylpropanoid pathway, and several other genes that may represent novel activities or pathways. Genes of the octadecanoic acid pathway of jasmonic acid (JA) synthesis were induced by SA as well as by MeJA. The resulting hypothesis that increased SA could lead to increased endogenous JA production was confirmed by measurement of JA content. Comparison of responses to SA, MeJA, and combined SA+MeJA revealed patterns of one-way and mutual antagonisms, as well as synergistic effects on regulation of some genes. These experiments thus help further define the transcriptional results of cross talk between the SA and JA pathways and suggest that a subset of genes coregulated by SA and JA may comprise a uniquely evolved sector of plant signaling responsive cascades.

Ethylene Biosynthesis during Aerenchyma Formation in Roots of Maize Subjected to Mechanical Impedance and Hypoxia

Germinated maize (Zea mays L.) seedlings were enclosed in modified triaxial cells in an artificial substrate and exposed to oxygen deficiency stress (4% oxygen, hypoxia) or to mechanical resistance to elongation growth (mechanical impedance) achieved by external pressure on the artificial substrate, or to both hypoxia and impedance simultaneously. Compared with controls, seedlings that received either hypoxia or mechanical impedance exhibited increased rates of ethylene evolution, greater activities of 1-aminocyclopropane-1-carboxylic acid (ACC) synthase, ACC oxidase, and cellulase, and more cell death and aerenchyma formation in the root cortex. Effects of hypoxia plus mechanical impedance were strongly synergistic on ethylene evolution and ACC synthase activity; cellulase activity, ACC oxidase activity, or aerenchyma formation did not exhibit this synergism. In addition, the lag between the onset of stress and increases in both ACC synthase activity and ethylene production was shortened by 2 to 3 h when mechanical impedance or impedance plus hypoxia was applied compared with hypoxia alone. The synergistic effects of hypoxia and mechanical impedance and the earlier responses to mechanical impedance than to hypoxia suggest that different mechanisms are involved in the promotive effects of these stresses on maize root ethylene biosynthesis.

Phytochrome regulation of branching in Arabidopsis.

The red light:far-red light ratio perceived by phytochromes controls plastic traits of plant architecture, including branching. Despite the significance of branching for plant fitness and productivity, there is little quantitative and mechanistic information concerning phytochrome control of branching responses in Arabidopsis (Arabidopsis thaliana). Here, we show that in Arabidopsis, the negative effects of the phytochrome B mutation and of low red light:far-red light ratio on branching were largely due to reduced bud outgrowth capacity and an increased degree of correlative inhibition acting on the buds rather than due to a reduced number of leaves and buds available for branching. Phytochrome effects on the degree of correlative inhibition required functional BRANCHED1 (BRC1), BRC2, AXR1, MORE AXILLARY GROWTH2 (MAX2), and MAX4. The analysis of gene expression in selected buds indicated that BRC1 and BRC2 are part of different gene networks. The BRC1 network is linked to the growth capacity of specific buds, while the BRC2 network is associated with coordination of growth among branches. We conclude that the branching integrators BRC1 and BRC2 are necessary for responses to phytochrome, but they contribute differentially to these responses, likely acting through divergent pathways.

Suppression of sorghum axillary bud outgrowth by shade, phyB and defoliation signalling pathways

In recent years, several genetic components of vegetative axillary bud development have been defined in both monocots and eudicots, but our understanding of environmental inputs on branching remains limited. Recent work in sorghum (Sorghum bicolor) has revealed a role for phytochrome B (phyB) in the control of axillary bud outgrowth through the regulation of Teosinte Branched1 (TB1) gene. In maize (Zea mays), TB1 is a dosage-dependent inhibitor of axillary meristem progression, and the expression level of TB1 is a sensitive measure of axillary branch development. To further explore the mechanistic basis of branching, the expression of branching and cell cycle-related genes were examined in phyB-1 and wild-type sorghum axillary buds following treatment with low-red : far-red light and defoliation. Although defoliation inhibited bud outgrowth, it did not influence the expression of sorghum TB1 (SbTB1), whereas changes in SbMAX2 expression, a homolog of the Arabidopsis (Arabidopsis thaliana) branching inhibitor MAX2, were associated with the regulation of bud outgrowth by both light and defoliation. The expression of several cell cycle-related genes was also decreased dramatically in buds repressed by defoliation, but not by phyB deficiency. The data suggest that there are at least two distinct molecular pathways that respond to light and endogenous signals to regulate axillary bud outgrowth.

Apyrase (Nucleoside Triphosphate-Diphosphohydrolase) and Extracellular Nucleotides Regulate Cotton Fiber Elongation in Cultured Ovules

Ectoapyrase enzymes remove the terminal phosphate from extracellular nucleoside tri- and diphosphates. In Arabidopsis (Arabidopsis thaliana), two ectoapyrases, AtAPY1 and AtAPY2, have been implicated as key modulators of growth. In fibers of cotton (Gossypium hirsutum), transcript levels for GhAPY1 and GhAPY2, two closely related ectoapyrases that have high sequence similarity to AtAPY1 and AtAPY2, are up-regulated when fibers enter their rapid growth phase. In an ovule culture system, fibers release ATP as they grow, and when their ectoapyrase activity is blocked by the addition of polyclonal anti-apyrase antibodies or by two different small molecule inhibitors, the medium ATP level rises and fiber growth is suppressed. High concentrations of the poorly hydrolyzable nucleotides ATPγS and ADPβS applied to the medium inhibit fiber growth, and low concentrations of them stimulate growth, but treatment with adenosine 5′-O-thiomonophosphate causes no change in the growth rate. Both the inhibition and stimulation of growth by applied nucleotides can be blocked by an antagonist that blocks purinoceptors in animal cells, and by adenosine. Treatment of cotton ovule cultures with ATPγS induces increased levels of ethylene, and two ethylene antagonists, aminovinylglycine and silver nitrate, block both the growth stimulatory and growth inhibitory effects of applied nucleotides. In addition, the ethylene precursor, 1-aminocyclopropane-1-carboxylic acid, lowers the concentration of nucleotide needed to promote fiber growth. These data indicate that ectoapyrases and extracellular nucleotides play a significant role in regulating cotton fiber growth and that ethylene is a likely downstream component of the signaling pathway.

Abscisic Acid Regulates Axillary Bud Outgrowth Responses to the Ratio of Red to Far-Red Light

ABA regulates bud outgrowth responses to the ratio of red to far-red light, extending the known hormonal pathways associated with the regulation of branching and shade avoidance. Low red light/far-red light ratio (R:FR) serves as an indicator of impending competition and has been demonstrated to suppress branch development. The regulation of Arabidopsis (Arabidopsis thaliana) rosette bud outgrowth by the R:FR and the associated mechanisms were investigated at several levels. Growth under low R:FR suppressed outgrowth of the third from topmost bud (bud n-2) but not that of the topmost bud. Subsequently increasing the R:FR near the time of anthesis promoted bud n-2 outgrowth and reduced topmost bud growth. Buds from specific rosette positions, exhibiting divergent fates to increased R:FR, were harvested 3 h after modifying the R:FR and were used to conduct ATH1 microarray-based transcriptome profiling. Differentially expressed genes showed enrichment of light signaling and hormone-related Gene Ontology terms and promoter motifs, most notably those associated with abscisic acid (ABA). Genes associated with ABA biosynthesis, including the key biosynthetic gene NINE-CIS-EPOXYCAROTENOID DIOXYGENASE3 (NCED3), and with ABA signaling were expressed at higher levels in the responsive bud n-2, and increasing the R:FR decreased their expression only in bud n-2. ABA abundance in responsive buds decreased within 12 h of increasing the R:FR, while indole-3-acetic acid levels did not change. A role for ABA in repressing bud outgrowth from lower positions under low R:FR was demonstrated using the nced3-2 and aba2-1 ABA biosynthesis mutants, which showed enhanced branching and a defective bud n-2 outgrowth response to low R:FR. The results provide evidence that ABA regulates bud outgrowth responses to the R:FR and thus extend the known hormonal pathways associated with the regulation of branching and shade avoidance.

Stem Transcriptome Reveals Mechanisms to Reduce the Energetic Cost of Shade-Avoidance Responses in Tomato

While the most conspicuous response to low red/far-red ratios (R:FR) of shade light perceived by phytochrome is the promotion of stem growth, additional, less obvious effects may be discovered by studying changes in the stem transcriptome. Here, we report rapid and reversible stem transcriptome responses to R:FR in tomato (Solanum lycopersicum). As expected, low R:FR promoted the expression of growth-related genes, including those involved in the metabolism of cell wall carbohydrates and in auxin responses. In addition, genes involved in flavonoid synthesis, isoprenoid metabolism, and photosynthesis (dark reactions) were overrepresented in clusters showing reduced expression in the stem of low R:FR-treated plants. Consistent with these responses, low R:FR decreased the levels of flavonoids (anthocyanin, quercetin, kaempferol) and selected isoprenoid derivatives (chlorophyll, carotenoids) in the stem and severely reduced the photosynthetic capacity of this organ. However, lignin contents were unaffected. Low R:FR reduced the stem levels of jasmonate, which is a known inducer of flavonoid synthesis. The rate of stem respiration was also reduced in low R:FR-treated plants, indicating that by downsizing the stem photosynthetic apparatus and the levels of photoprotective pigments under low R:FR, tomato plants reduce the energetic cost of shade-avoidance responses.

Phytochrome B Promotes Branching in Arabidopsis by Suppressing Auxin Signaling

Phytochrome B promotes branching in Arabidopsis by suppressing auxin signaling. Many plants respond to competition signals generated by neighbors by evoking the shade avoidance syndrome, including increased main stem elongation and reduced branching. Vegetation-induced reduction in the red light:far-red light ratio provides a competition signal sensed by phytochromes. Plants deficient in phytochrome B (phyB) exhibit a constitutive shade avoidance syndrome including reduced branching. Because auxin in the polar auxin transport stream (PATS) inhibits axillary bud outgrowth, its role in regulating the phyB branching phenotype was tested. Removing the main shoot PATS auxin source by decapitation or chemically inhibiting the PATS strongly stimulated branching in Arabidopsis (Arabidopsis thaliana) deficient in phyB, but had a modest effect in the wild type. Whereas indole-3-acetic acid (IAA) levels were elevated in young phyB seedlings, there was less IAA in mature stems compared with the wild type. A split plate assay of bud outgrowth kinetics indicated that low auxin levels inhibited phyB buds more than the wild type. Because the auxin response could be a result of either the auxin signaling status or the bud’s ability to export auxin into the main shoot PATS, both parameters were assessed. Main shoots of phyB had less absolute auxin transport capacity compared with the wild type, but equal or greater capacity when based on the relative amounts of native IAA in the stems. Thus, auxin transport capacity was unlikely to restrict branching. Both shoots of young phyB seedlings and mature stem segments showed elevated expression of auxin-responsive genes and expression was further increased by auxin treatment, suggesting that phyB suppresses auxin signaling to promote branching.

BOTRYTIS-INDUCED KINASE1 Modulates Arabidopsis Resistance to Green Peach Aphids via PHYTOALEXIN DEFICIENT4

Rapid HR-like cell death confers plant resistance to aphids. BOTRYTIS-INDUCED KINASE1 (BIK1) plays important roles in induced defense against fungal and bacterial pathogens in Arabidopsis (Arabidopsis thaliana). Its tomato (Solanum lycopersicum) homolog is required for host plant resistance to a chewing insect herbivore. However, it remains unknown whether BIK1 functions in plant defense against aphids, a group of insects with a specialized phloem sap-feeding style. In this study, the potential role of BIK1 was investigated in Arabidopsis infested with the green peach aphid (Myzus persicae). In contrast to the previously reported positive role of intact BIK1 in defense response, loss of BIK1 function adversely impacted aphid settling, feeding, and reproduction. Relative to wild-type plants, bik1 displayed higher aphid-induced hydrogen peroxide accumulation and more severe lesions, resembling a hypersensitive response (HR) against pathogens. These symptoms were limited to the infested leaves. The bik1 mutant showed elevated basal as well as induced salicylic acid and ethylene accumulation. Intriguingly, elevated salicylic acid levels did not contribute to the HR-like symptoms or to the heightened aphid resistance associated with the bik1 mutant. Elevated ethylene levels in bik1 accounted for an initial, short-term repellence. Introducing a loss-of-function mutation in the aphid resistance and senescence-promoting gene PHYTOALEXIN DEFICIENT4 (PAD4) into the bik1 background blocked both aphid resistance and HR-like symptoms, indicating bik1-mediated resistance to aphids is PAD4 dependent. Taken together, Arabidopsis BIK1 confers susceptibility to aphid infestation through its suppression of PAD4 expression. Furthermore, the results underscore the role of reactive oxygen species and cell death in plant defense against phloem sap-feeding insects.

Abscisic Acid Is a General Negative Regulator of Arabidopsis Axillary Bud Growth

The plant hormone abscisic acid functions as a general negative regulator of branching and may contribute to the effects of other hormones and proteins that control the process. Branching is an important process controlled by intrinsic programs and by environmental signals transduced by a variety of plant hormones. Abscisic acid (ABA) was previously shown to mediate Arabidopsis (Arabidopsis thaliana) branching responses to the ratio of red light (R) to far-red light (FR; an indicator of competition) by suppressing bud outgrowth from lower rosette positions under low R:FR. However, the role of ABA in regulating branching more generally was not investigated. This study shows that ABA restricts lower bud outgrowth and promotes correlative inhibition under both high and low R:FR. ABA was elevated in buds exhibiting delayed outgrowth resulting from bud position and low R:FR and decreased in elongating buds. ABA was reduced in lower buds of hyperbranching mutants deficient in auxin signaling (AUXIN RESISTANT1), MORE AXILLARY BRANCHING (MAX) signaling (MAX2), and BRANCHED1 (BRC1) function, and partial suppression of branch elongation in these mutants by exogenous ABA suggested that ABA may act downstream of these components. Bud BRC1 expression was not altered by exogenous ABA, consistent with a downstream function for ABA. However, the expression of genes encoding the indole-3-acetic acid (IAA) biosynthesis enzyme TRYPTOPHAN AMINOTRANSFERASE OF ARABIDOPSIS1, the auxin transporter PIN-FORMED1, and the cell cycle genes CYCLIN A2;1 and PROLIFERATING CELL NUCLEAR ANTIGEN1 in buds was suppressed by ABA, suggesting that it may inhibit bud growth in part by suppressing elements of the cell cycle machinery and bud-autonomous IAA biosynthesis and transport. ABA was found to suppress bud IAA accumulation, thus confirming this aspect of its action.