Phosphate transporters OsPHT1;9 and OsPHT1;10 are involved in phosphate uptake in rice

We characterized the function of two rice phosphate (Pi) transporters: OsPHT1;9 (OsPT9) and OsPHT1;10 (OsPT10). OsPT9 and OsPT10 were expressed in the root epidermis, root hairs and lateral roots, with their expression being specifically induced by Pi starvation. In leaves, expression of the two genes was observed in both mesophyll and vasculature. High‐affinity Km values for Pi transport of OsPT9 and OsPT10 were determined by yeast experiments and two‐electrode voltage clamp analysis of anion transport in Xenopus oocytes expressing OsPT9 and OsPT10. Pi uptake and Pi concentrations in transgenic plants harbouring overexpressed OsPT9 and OsPT10 were determined by Pi concentration analysis and ³³P‐labelled Pi uptake rate analysis. Significantly higher Pi uptake rates in transgenic plants compared with wild‐type plants were observed under both high‐Pi and low‐Pi solution culture conditions. Conversely, although no alterations in Pi concentration were found in OsPT9 or OsPT10 knockdown plants, a significant reduction in Pi concentration in both shoots and roots was observed in double‐knockdown plants grown under both high‐ and low‐Pi conditions. Taken together, our results suggest that OsPT9 and OsPT10 redundantly function in Pi uptake.     

Light induces jasmonate‐isoleucine conjugation via OsJAR1‐dependent and ‐independent pathways in rice

The bioactive form of jasmonate is the conjugate of the amino acid isoleucine (Ile) with jasmonic acid (JA), which is biosynthesized in a reaction catalysed by the GH3 enzyme JASMONATE RESISTANT 1 (JAR1). We examined the biochemical properties of OsJAR1 and its involvement in photomorphogenesis of rice (Oryza sativa). OsJAR1 has a similar substrate specificities as its orthologue in Arabidopsis. However, osjar1 loss‐of‐function mutants did not show as severe coleoptile phenotypes as the JA‐deficient mutants coleoptile photomorphogenesis 2 (cpm2) and hebiba, which develop long coleoptiles in all light qualities we examined. Analysis of hormonal contents in the young seedling stage revealed that osjar1 mutants are still able to synthesize JA‐Ile conjugate in response to blue light, suggesting that a redundantly active enzyme can conjugate JA and Ile in rice seedlings. A good candidate for this enzyme is OsJAR2, which was found to be able to catalyse the conjugation of JA with Ile as well as with some additional amino acids. In contrast, if plants in the vegetative stage were mechanically wounded, the content of JA‐Ile was severely reduced in osjar1, demonstrating that OsJAR1 is the most important JA‐Ile conjugating enzyme in the wounding response during the vegetative stage.     

The auxin response factor,OsARF19, controls rice leaf angles through positively regulating OsGH3‐5 and OsBRI1

Auxin and brassinosteroid (BR) are important phytohormones for controlling lamina inclination implicated in plant architecture and grain yield. But the molecular mechanism of auxin and BR crosstalk for regulating lamina inclination remains unknown. Auxin response factors (ARFs) control various aspects of plant growth and development. We here report that OsARF19‐overexpression rice lines show an enlarged lamina inclination due to increase of its adaxial cell division. OsARF19 is expressed in various organs including lamina joint and strongly induced by auxin and BR. Chromatin immunoprecipitation (ChIP) and yeast one‐hybrid assays demonstrate that OsARF19 binds to the promoter of OsGH3‐5 and brassinosteroid insensitive 1 (OsBRI1) directing their expression. OsGH3‐5‐overexpression lines show a similar phenotype as OsARF19‐O1. Free auxin contents in the lamina joint of OsGH3‐5‐O1 or OsARF19‐O1 are reduced. OsGH3‐5 is localized at the endoplasmic retieulum (ER) matching reduction of the free auxin contents in OsGH3‐5‐O1. osarf19‐TDNA and osgh3‐5‐Tos17 mutants without erected leaves show a function redundancy with other members of their gene family. OsARF19‐overexpression lines are sensitive to exogenous BR treatment and alter the expressions of genes related to BR signalling. These findings provide novel insights into auxin and BR signalling, and might have significant implications for improving plant architecture of monocot crops.     

Tissue‐specific and pathogen‐inducible expression of a fusion protein containing a Fusarium‐specific antibody and a fungal chitinase protects wheat against Fusarium pathogens and mycotoxins

Fusarium head blight (FHB) in wheat and other small grain cereals is a globally devastating disease caused by toxigenic Fusarium pathogens. Controlling FHB is a challenge because germplasm that is naturally resistant against these pathogens is inadequate. Current control measures rely on fungicides. Here, an antibody fusion comprised of the Fusarium spp.‐specific recombinant antibody gene CWP2 derived from chicken, and the endochitinase gene Ech42 from the biocontrol fungus Trichoderma atroviride was introduced into the elite wheat cultivar Zhengmai9023 by particle bombardment. Expression of this fusion gene was regulated by the lemma/palea‐specific promoter Lem2 derived from barley; its expression was confirmed as lemma/palea‐specific in transgenic wheat. Single‐floret inoculation of independent transgenic wheat lines of the T₃ to T₆ generations revealed significant resistance (type II) to fungal spreading, and natural infection assays in the field showed significant resistance (type I) to initial infection. Gas chromatography–mass spectrometry analysis revealed marked reduction of mycotoxins in the grains of the transgenic wheat lines. Progenies of crosses between the transgenic lines and the FHB‐susceptible cultivar Huamai13 also showed significantly enhanced FHB resistance. Quantitative real‐time PCR analysis revealed that the tissue‐specific expression of the antibody fusion was induced by salicylic acid drenching and induced to a greater extent by F. graminearum infection. Histochemical analysis showed substantial restriction of mycelial growth in the lemma tissues of the transgenic plants. Thus, the combined tissue‐specific and pathogen‐inducible expression of this Fusarium‐specific antibody fusion can effectively protect wheat against Fusarium pathogens and reduce mycotoxin content in grain.     

Integrated metabolite and gene expression profiling revealing phytochrome A regulation of polyamine biosynthesis of Arabidopsis thaliana

In this study, metabolite profiling was demonstrated as a usefultool to plot a specific metabolic pathway, which is regulatedby phytochrome A (phyA). Etiolated Arabidopsis wild-type (WT)and phyA mutant seedlings were irradiated with either far-redlight (FR) or white light (W). Primary metabolites of the irradiatedseedlings were profiled by gas chromatography time-of-flightmass spectrometry (GC/TOF-MS) to obtain new insights on phyA-regulatedmetabolic pathways. Comparison of metabolite profiles in phyAand WT seedlings grown under FR revealed a number of metabolitesthat contribute to the differences between phyA and the WT.Several metabolites, including some amino acids, organic acids,and major sugars, as well as putrescine, were found in smalleramounts in WT compared with the content in phyA seedlings grownunder FR. There were also significant differences between metaboliteprofiles of WT and phyA seedlings during de-etiolation underW. The polyamine biosynthetic pathway was investigated further,because putrescine, one of the polyamines existing in a widevariety of living organisms, was found to be present in loweramounts in WT than in phyA under both light conditions. Theexpression levels of polyamine biosynthesis-related genes wereinvestigated by quantitative real-time RT-PCR. The gene expressionprofiles revealed that the arginine decarboxylase 2 (ADC2) genewas transcribed less in the WT than in phyA seedlings underboth light conditions. This finding suggests that ADC2 is negativelyregulated by phyA during photomorphogenesis. In addition, S-adenosylmethioninedecarboxylase 2 and 4 (SAMDC2 and SAMDC4) were found to be regulatedby phyA but in a different manner from the regulation of ADC2. Key words: Arabidopsis thaliana, gene expression profiling, metabolite profiling, phytochrome A, polyamine biosynthesis Received 19 October 2007; Revised 17 January 2008 Accepted 18 January 2008     

Circumnutation of rice coleoptiles: its occurrence, regulation by phytochrome, and relationship with gravitropism

It has been found that coleoptiles of dark-grown rice (Oryza sativa L.) seedlings undergo regular circumnutation in circular orbits with periods of about 180 min. Both clockwise and counter-clockwise movements were observed, but individual coleoptiles continued to rotate only in one direction. Light-grown seedlings did not show circumnutation. In fact, dark-grown seedlings were found to cease circumnutating in response to a pulse of red light (R). This light-induced inhibition of circumnutation was demonstrated to involve both a FR-inducible very-low-fluence response, solely mediated by phytochrome A, and a FR-reversible low-fluence response, mediated by phytochrome B and/or C. The R-induced inhibition of circumnutation showed temporal agreement with the R-induced inhibition of coleoptile growth, suggesting that the former results from the latter. However, about 25% of growth activity remained after R treatment, indicating that circumnutation is more specifically regulated by phytochrome. The R-treated coleoptile showed gravitropism. Investigation of the growth differential for gravitropic curvature revealed that gravitropic responsiveness was rather enhanced by R. The results suggested that gravitropism is not a cause of circumnutation. It remained probable, however, that gravity perception is a part of the mechanism of circumnutation. It is speculated that the circumnutation investigated aids the seedling shoot in growing through the soil.     

Allelic imbalance metre (Allim), a new tool for measuring allele‐specific gene expression with RNA‐seq data

Estimating differences in gene expression among alleles is of high interest for many areas in biology and medicine. Here, we present a user‐friendly software tool, Allim, to estimate allele‐specific gene expression. Because mapping bias is a major problem for reliable estimates of allele‐specific gene expression using RNA‐seq, Allim combines two different strategies to account for the mapping biases. In order to reduce the mapping bias, Allim first generates a polymorphism‐aware reference genome that accounts for the sequence variation between the alleles. Then, a sequence‐specific simulation tool estimates the residual mapping bias. Statistical tests for allelic imbalance are provided that can be used with the bias corrected RNA‐seq data.     

PhotoMorphs™: A novel light‐activated reagent for controlling gene expression in zebrafish

Manipulating gene expression in zebrafish is critical for exploiting the full potential of this vertebrate model organism. Morpholino oligos are the most commonly used antisense technology for knocking down gene expression. However, morpholinos suffer from a lack of control over the timing and location of knockdown. In this report, we describe a novel light‐ activatable knockdown reagent called PhotoMorph?. PhotoMorphs can be generated from existing morpholinos by hybridization with a complementary caging strand containing a photocleavable linkage. The caging strand neutralizes the morpholino activity until irradiation of the PhotoMorph with UV light releases the morpholino. We generated PhotoMorphs to target genes encoding enhanced green fluorescent protein, No tail, and E‐cadherin to illustrate the utility of this approach. Temporal control of gene expression with PhotoMorphs permitted us to circumvent the early lethal phenotype of E‐cadherin knockdown. A splice‐blocking PhotoMorph directed to the rheb gene showed light‐dependent gene knockdown up to 72 hpf. PhotoMorphs thus offer a new class of laboratory reagents suitable for the spatiotemporal control of gene expression in the zebrafish. genesis 47:736–743, 2009. © 2009 Wiley‐Liss, Inc.     

Regulation of phytochrome A mRNA abundance in parsley seedlings and cell-suspension cultures

A cDNA clone encoding the apoprotein of a parsley phytochrome was isolated and classified as parsley PHYA phytochrome, on the basis of a sequence homology comparison with all available phytochrome sequences. Red light pulses led to a phytochrome-dependent down-regulation of PHYA mRNA abundance in etiolated parsley seedlings to a level of 10–20% compared with the dark control. The PHYA mRNA abundance in a parsley cell suspension culture was also down-regulated by light pulses. Transient expression assays in parsley protoplasts showed light regulation of a chimeric pea PHYA promoter uidA-gene construct.     

Extensive allele‐level remodeling of histone methylation modification in reciprocal F1 hybrids of rice subspecies

Epigenetic mechanisms play a major role in heterosis, partly as a result of the remodeling of epigenetic modifications in F₁ hybrids. Based on chromatin immunoprecipitation‐sequencing (ChIP‐Seq) analyses, we show that at the allele level extensive histone methylation remodeling occurred for a subset of genomic loci in reciprocal F₁ hybrids of Oryza sativa (rice) cultivars Nipponbare and 93‐11, representing the two subspecies japonica and indica. Globally, the allele modification‐altered loci in leaf or root of the reciprocal F₁ hybrids involved ?12–43% or more of the genomic regions carrying either of two typical histone methylation markers, H3K4me3 (>21 000 genomic regions) and H3K27me3 (>11 000 genomic regions). Nevertheless, at the total modification level, the majority (from ?43 to >90%) of the modification‐altered alleles lay within the range of parental additivity in the hybrids because of concerted alteration in opposite directions, consistent with an overall attenuation of allelic differences in the modifications. Importantly, of the genomic regions that did show non‐additivity in total modification level by either marker in the two tissues of hybrids, >80% manifested transgressivity, which involved genes enriched in specific functional categories. Extensive allele‐level alteration of H3K4me3 alone was positively correlated with genome‐wide changes in allele‐level gene expression, whereas at the total level, both H3K4me3 and H3K27me3 remodeling, although affecting just a small number of genes, contributes to the overall non‐additive gene expression to variable extents, depending on tissue/marker combinations. Our results emphasize the importance of allele‐level analysis in hybrids to assess the remodeling of epigenetic modifications and their relation to changes in gene expression.     

Highly interactive nature of flower‐specific enhancers and promoters,and its potential impact on tissue‐specific expression and engineering of multiple genes or agronomic traits

Molecular stacking enables multiple traits to be effectively engineered in crops using a single vector. However, the co‐existence of distinct plant promoters in the same transgenic unit might, like their mammalian counterparts, interfere with one another. In this study, we devised a novel approach to investigate enhancer–promoter and promoter–promoter interactions in transgenic plants and demonstrated that three of four flower‐specific enhancer/promoters were capable of distantly activating a pollen‐ and stigma‐specific Pps promoter (fused to the cytotoxic DT‐A gene) in other tissues, as revealed by novel tissue ablation phenotypes in transgenic plants. The NtAGI1 enhancer exclusively activated stamen‐ and carpel‐specific DT‐A expression, thus resulting in tissue ablation in an orientation‐independent manner; this activation was completely abolished by the insertion of an enhancer‐blocking insulator (EXOB) between the NtAGI1 enhancer and Pps promoter. Similarly, AGL8 and AP1Lb1, but not AP1La, promoters also activated distinct tissue‐specific DT‐A expression and ablation, with the former causing global growth retardation and the latter ablating apical inflorescences. While the tissue specificity of the enhancer/promoters generally defined their activation specificities, the strength of their activity in particular tissues or developmental stages appeared to determine whether activation actually occurred. Our findings provide the first evidence that plant‐derived enhancer/promoters can distantly interact/interfere with one another, which could pose potential problems for the tissue‐specific engineering of multiple traits using a single‐vector stacking approach. Therefore, our work highlights the importance of adopting enhancer‐blocking insulators in transformation vectors to minimize promoter–promoter interactions. The practical and fundamental significance of these findings will be discussed.     

The light-dependent regulation of gene expression during plastid development in higher plants

In recent years there has been a considerable increase in our understanding of the manner by which light affects gene expression during chloroplast development. In most systems that have been studied, light acts through sensitive photoreceptor molecules and quantitatively increases or represses the level of expression of specific nuclear-and plastid-encoded genes. Although the mechanisms are obscure, a picture is beginning to emerge in which the coordination of nuclear and plastid gene expression is controlled by regulatory mechanisms originating within their respective subcellular compartments. This review summarizes some of our current knowledge concerning the nature of light-regulated gene expression in higher plants and provides a prospectus for future research in this area.