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An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Plant seeds accumulate large amounts of storage reserves comprising biodegradable organic matter. Humans rely on seed storage reserves for food and as ...

national institute for basic biology

Common reed (Phragmites australis) is a well known salt-tolerant plant and it is suggested that reeds recover Na(+) in the xylem sap of the shoot base (basal part of the shoot), store it temporarily in the shoot base, release it into the phloem sap, and then retranslocate it to the roots. To investigate whether Na(+) is retained in the shoot base of reeds, confocal laser scanning microscope (CLSM) observations were conducted using an intracellular Na(+)-specific fluorescent probe. The CLSM observations revealed that reeds produced a large number of the starch granules at the shoot base when salt-stressed, and that the fluorescence indicating the location of intracellular free Na(+) was observed in the same position as the starch granules. The Na content of starch granules was considerably greater than that of the shoot base, whereas the potassium (K) contents of the granules was only slightly greater than that of the shoot base. Reeds produced Na(+)-binding starch granules in the parenchyma cells of the shoot base when salt-stressed; these starch granules may decrease intracellular free Na(+). It is proposed that the site-specific production of Na(+)-binding starch granules constitutes a novel salt tolerance mechanism.

Common reed produces starch granules at the shoot base in response to salt stress.

Seed dormancy is essential for most plants to control the timing of germination. In Arabidopsis thaliana, PED3 is a single-copy gene encoding an ATP-binding cassette transporter that is required for peroxisomal fatty acid beta-oxidation. PED3 is involved in the import of several biologically important molecules into the peroxisome, including very-long-chain fatty acids associated with the breakdown of seed-reserve lipids, and precursors of auxin and jasmonic acid. The germination of ped3 mutants is significantly impaired, suggesting that PED3 regulates dormancy and germination. A transcriptome analysis revealed that many genes containing the core motif of the ABA responsive element (ABRE) in their promoter regions, and the ABA insensitive 5 (ABI5) transcription factor that binds to ABRE, are abnormally up-regulated in imbibed ped3 seeds. Expression of polygalacturonase inhibiting proteins (PGIPs) is also up-regulated specifically in ped3 after imbibition. By contrast, the ped3 abi5 double mutant does not show any of these expression patterns. The results indicate that the abi5 mutation normalizes PGIP expression and rescues the impaired germination phenotype of the ped3 mutant. PGIPs are known to act as inhibitors of polygalacturonases that degrade pectin. The amount of PGIP1 transcript regulates the timing of radicle protrusion. The impaired germination of ped3 could also be rescued by removal of pectin from the seed coat using exogenous polygalacturonase or acidic conditions. Overall, our results suggest that PED3, a peroxisomal ABC transporter, promotes seed germination by suppressing PGIPs under the control of ABI5.

A peroxisomal ABC transporter promotes seed germination by inducing pectin degradation under the control of ABI5.

Hydrangea (Hydrangea macrophylla) is tolerant of acidic soils in which toxicity generally arises from the presence of the soluble aluminum (Al) ion. When hydrangea is cultivated in acidic soil, its resulting blue sepal color is caused by the Al complex formation of anthocyanin. The concentration of vacuolar Al in blue sepal cells can reach levels in excess of approximately 15 mM, suggesting the existence of an Al-transport and/or storage system. However, until now, no Al transporter has been identified in Al hyperaccumulating plants, animals or microorganisms. To identify the transporter being responsible for Al hyperaccumulation, we prepared a cDNA library from blue sepals according to the sepal maturation stage, and then selected candidate genes using a microarray analysis and an in silico study. Here, we identified the vacuolar and plasma membrane-localized Al transporters genes vacuolar Al transporter (VALT) and plasma membrane Al transporter 1 (PALT1), respectively, which are both members of the aquaporin family. The localization of each protein was confirmed by the transient co-expression of the genes. Reverse transcription-PCR and immunoblotting results indicated that VALT and PALT1 are highly expressed in sepal tissue. The overexpression of VALT and PALT1 in Arabidopsis thaliana conferred Al-tolerance and Al-sensitivity, respectively.

Tonoplast- and plasma membrane-localized aquaporin-family transporters in blue hydrangea sepals of aluminum hyperaccumulating plant.

Plants accumulate large amounts of storage products in seeds to provide an energy reserve and to supply nutrients for germination and post-germinative growth. Arabidopsis thaliana belongs to the Brassica family, and oil is the main storage product in Arabidopsis seeds. To elucidate the regulatory mechanisms of oil biosynthesis in seeds, we screened for high density seeds (heavy seed) that have a low oil content. HS3 (heavy seed 3) encodes the DEAD-box RNA helicase 22 that is localized to plastids. The triacylglycerol (TAG) content of hs3-1 seeds was 10% lower than that of wild-type (WT) seeds, while the protein content was unchanged. The hs3-1 plants displayed a pale-green phenotype in developing seeds and seedlings, but not in adult leaves. The HS3 expression level was high in developing seeds and seedlings, but was low in stems, rosette leaves and flowers. The plastid gene expression profile of WT developing seeds and seedlings differed from that of hs3-1 developing seeds and seedlings. The expression of several genes was reduced in developing hs3-1 seeds, including accD, a gene that encodes the β subunit of carboxyltransferase, which is one component of acetyl-CoA carboxylase in plastids. In contrast, no differences were observed between the expression profiles of WT and hs3-1 rosette leaves. These results show that HS3 is essential for proper mRNA accumulation of plastid genes during seed development and seedling growth, and suggest that HS3 ensures seed oil biosynthesis by maintaining plastid mRNA levels.

The plastidic DEAD-box RNA helicase 22, HS3, is essential for plastid functions both in seed development and in seedling growth.

Common reed (Phragmites australis) is a phytoremediator tolerant to heavy metals. In this study, we found that 70% of the cadmium (Cd) found in the stem of common reed exists in a soluble form, with more than half of the soluble Cd in the 10- to 50-kDa fraction. Based on an enzyme degradation assay, the major component of the Cd-associated molecule is assumed to be an amylopectin-like α-glucan. This molecule may associate with Cd via the carboxyl group, rather than the thiol group. The conditions required for the disengagement of Cd from the 10- to 50-kDa fraction indicated that disulfide bonds and other intramolecular interactions may contribute to maintaining the proper conformation of the molecule and to stabilizing its association with Cd. Accumulation of the Cd-associated molecule was induced by Cd stress, and the molecule was found to be also associated with Cu and Fe. Thus, we have identified a novel mechanism of Cd-pooling, namely, the association of Cd with an α-glucan-like molecule in reed stem.

Detoxification of cadmium (Cd) by a novel Cd-associated and Cd-induced molecule in the stem of common reed.

In a previous study, we reported that the common reed accumulates water-soluble Cd complexed with an α-glucan-like molecule, and that the synthesis of this molecule is induced in the stem of the common reed under Cd stress. We studied the metabolic background to ensure α-glucan accumulation under the Cd stress conditions that generally inhibit photosynthesis. We found that the common reed maintained an adequate CO2 assimilation rate, tended to allocate more assimilated (11)C to the stem, and accumulated starch granules in its stem under Cd stress conditions. AGPase activity, which is the rate-limiting enzyme for starch synthesis, increased in the stem of common reed grown in the presence of Cd. Starch accumulation in the stem of common reed was not obvious under other excess metal conditions. Common reed may preferentially allocate assimilated carbon as the carbon source for the formation of Cd and α-glucan complexes in its stem followed by prevention of Cd transfer to leaves acting as the photosynthetic organ. These responses may allow the common reed to grow even under severe Cd stress conditions.

Common reed accumulates starch in its stem by metabolic adaptation under Cd stress conditions.

Regulation of oil biosynthesis in plant seeds has been extensively studied, and biotechnological approaches have been designed to increase seed oil content. Oil and protein synthesis is negatively correlated in seeds, but the mechanisms controlling interactions between these two pathways are unknown. Here, we identify the molecular mechanism controlling oil and protein content in seeds. We utilized transgenic Arabidopsis thaliana plants overexpressing WRINKLED1 (WRI1), a master transcription factor regulating seed oil biosynthesis, and knockout mutants of major seed storage proteins. Oil and protein biosynthesis in wild-type plants was sequentially activated during early and late seed development, respectively. The negative correlation between oil and protein contents in seeds arises from competition between the pathways. Extension of WRI1 expression during mid-phase of seed development significantly enhanced seed oil content. This study demonstrates that temporal activation of genes involved in oil or storage protein biosynthesis determines the oil/protein ratio in Arabidopsis seeds. These results provide novel insights into potential breeding strategies to generate crops with high oil contents in seeds.

Masatake Kanai

Laboratory of Biological Diversity,
Department of Evolutionary Biology and Biodiversity,
Laboratory of Biological Diversity, Department of Evolutionary Biology and Biodiversity

national institute for basic biology

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Masatake Kanai

Laboratory of Biological Diversity,Department of Evolutionary Biology and Biodiversity,Laboratory of Biological Diversity, Department of Evolutionary Biology and Biodiversity

national institute for basic biology

An Efficient Method for the Isolation of Highly Purified RNA from Seeds for Use in Quantitative Transcriptome Analysis

Laboratory of Biological Diversity,
Department of Evolutionary Biology and Biodiversity,
Laboratory of Biological Diversity, Department of Evolutionary Biology and Biodiversity