Genomic DNA Methylation Analyses Reveal the Distinct Profiles in Castor Bean Seeds with Persistent Endosperms

Investigations of genomic DNA methylation in seeds have been restricted to a few model plants. The endosperm genomic DNA hypomethylation has been identified in angiosperm, but it is difficult to dissect the mechanism of how this hypomethylation is established and maintained because endosperm is ephemeral and disappears with seed development in most dicots. Castor bean (Ricinus communis), unlike Arabidopsis (Arabidopsis thaliana), endosperm is persistent throughout seed development, providing an excellent model in which to dissect the mechanism of endosperm genomic hypomethylation in dicots. We characterized the DNA methylation-related genes encoding DNA methyltransferases and demethylases and analyzed their expression profiles in different tissues. We examined genomic methylation including CG, CHG, and CHH contexts in endosperm and embryo tissues using bisulfite sequencing and revealed that the CHH methylation extent in endosperm and embryo was, unexpectedly, substantially higher than in previously studied plants, irrespective of the CHH percentage in their genomes. In particular, we found that the endosperm exhibited a global reduction in CG and CHG methylation extents relative to the embryo, markedly switching global gene expression. However, CHH methylation occurring in endosperm did not exhibit a significant reduction. Combining with the expression of 24-nucleotide small interfering RNAs (siRNAs) mapped within transposable element (TE) regions and genes involved in the RNA-directed DNA methylation pathway, we demonstrate that the 24-nucleotide siRNAs played a critical role in maintaining CHH methylation and repressing the activation of TEs in persistent endosperm development. This study discovered a novel genomic DNA methylation pattern and proposes the potential mechanism occurring in dicot seeds with persistent endosperm.

A novel fluorescent conjugate applicable to visualize the translocation of glucose-fipronil

The ability to visualize the movement of glycosyl insecticides contributes to learning their translocation and distribution in plants. In our present work, a novel fluorescent glucose-fipronil conjugate N-[3-cyano-1-[2,6-dichloro-4-(trifluoromethyl)phenyl]-4-[(trifluoromethyl)sulfinyl]-1H-pyrazol-5-yl]-1-(2-[N-(7-nitrobenz-2-oxa-1,3-diazol-4-yl)amino]-2-deoxy-β-D-glucopyranosyl)-1H-1,2,3-triazole-4-methanamine (2-NBDGTF), was obtained via click chemistry. Disk uptake experiments showed that an active carrier-mediated system was involved in the 2-NBDGTF uptake process. Meanwhile, 2-NBDGTF exhibited comparable phloem mobility with GTF in castor bean seedlings. Visualization of 2-NBDGTF uptake and transport experiment showed that this fluorescent glucose-fipronil conjugate could be loaded into sieve tubes after transiting through epidermal cells and mesophyll cells and then translocate from cotyledon to hypocotyl via phloem in castor bean seedlings. The results above determined that it is a promising fluorescence tagging approach for revealing the activities of glycosyl insecticides and 2-NBDGTF is a reasonable and feasible fluorescent surrogate of GTF for tracing the distribution of glucose-fipronil conjugates.

Genomic imprinting, methylation and parent-of-origin effects in reciprocal hybrid endosperm of castor bean

Genomic imprinting often results in parent-of-origin specific differential expression of maternally and paternally inherited alleles. In plants, the triploid endosperm is where gene imprinting occurs most often, but aside from studies on Arabidopsis, little is known about gene imprinting in dicotyledons. In this study, we inspected genomic imprinting in castor bean (Ricinus communis) endosperm, which persists throughout seed development. After mapping out the polymorphic SNP loci between accessions ZB306 and ZB107, we generated deep sequencing RNA profiles of F1 hybrid seeds derived from reciprocal crosses. Using polymorphic SNP sites to quantify allele-specific expression levels, we identified 209 genes in reciprocal endosperms with potential parent-of-origin specific expression, including 200 maternally expressed genes and 9 paternally expressed genes. In total, 57 of the imprinted genes were validated via reverse transcriptase-polymerase chain reaction sequencing, and analysis of the genomic DNA methylation distribution between embryo and endosperm tissues showed significant hypomethylation in the endosperm and an enrichment of differentially methylated regions around the identified genes. Curiously, the expression of the imprinted genes was not tightly linked to DNA methylation. These results largely extended gene imprinting information existing in plants, providing potential directions for further research in gene imprinting.

Identification of a potential bottleneck in branched chain fatty acid incorporation into triacylglycerol for lipid biosynthesis in agronomic plants

In plant, unusual fatty acids are produced by a limited number of species. The industrial benefits of these unusual structures have led several groups to study their production in transgenic plants. Their research results led to very modest accumulation in seeds which was largely due to a limited knowledge of the lipid metabolism and fatty acid transfer in plants. More specifically we need to better understand the substrate specificity and selectivity of acyltransferases which are required for the incorporation of these unusual fatty acids into storage triacylglycerols. In our studies we have compared the incorporation of [(14)C] Oleoyl-CoA and Branched Chain Acyls-CoA into [(3)H] LPA-C18:1 by the Lysophosphatidic acid Acyltransferase (LPAAT) from developing seeds of agronomic plants (flax (Linum usitatissimum) and rape (Brassica napus)) and from a plant capable of producing high amounts of hydroxy fatty acids (castor bean (Ricinus communis)). Our assays demonstrate that LPAATs of the three studied species (1) incorporated preferentially oleyl-CoA, (2) could incorporate cyclopropane acyl-CoA when added alone as a substrate, however very weakly for rapeseed and castor bean seeds, (3) presented a low capacity to incorporate methyl branched acyl-CoA when added alone as a substrate (4) weakly incorporated cyclopropane acyl-CoA and was unable to incorporate methyl branched acyl-CoA when presented with an equimolar mix of oleyl-CoA and branched chain acyl-CoA. In all cases, the LPAAT had a low affinity for branched chain acyl-CoAs. The results show that LPAAT activity from agronomic plants constitutes a bottleneck for the incorporation of branched Chain acyl-CoA into PA.

Stable genetic transformation of castor (Ricinus communis L.) via particle gun-mediated gene transfer using embryo axes from mature seeds

The first successful attempt to produce stably transformed castor plants through direct gene transfer using particle gun (BioRad) is described. Decotyledonated embryos from mature seeds were germinated and the embryonic axis was induced to proliferate on Murashige and Skoog (MS) medium supplemented with 0.5 mg l(-1) thidiazuron (TDZ) and subjected to bombardment after 5-7 days of pre-incubation. The physical parameters for transient transformation were optimized using the UidA gene encoding beta-glucuronidase (GUS) as the reporter gene and with hygromycin-phosphotransferase (hptII) gene as selectable marker. Statistical analysis revealed that helium pressure, target distance, osmoticum, microcarrier type and size, DNA quantity, explant type and number of bombardments had significant influence on transformation efficiency, while the effect of genotype was non-significant. Of the different variables evaluated, embryonic axes from mature seeds, a target distance of 6.0 cm, helium pressure of 1,100 psi, 0.6 microm gold microcarriers, single time bombardment and with both pre- and post-osmoticum were found ideal. Selection of putative transformants was done on MS medium supplemented with 0.5 mg l(-1) BA and hygromycin (20, 40 and 60 mg l(-1)) for 3 cycles. The stable integration of the incorporated gene into castor genome was confirmed with PCR and Southern analysis of T0 and T1 plants. Transformation frequency in terms of plants grown to maturity and showing the presence of the introduced genes was 1.4%. The present results demonstrate the possibility of transformation of embryonic meristematic tissues of castor through particle delivery system.

An analysis of expressed sequence tags of developing castor endosperm using a full-length cDNA library

BACKGROUND

Castor seeds are a major source for ricinoleate, an important industrial raw material. Genomics studies of castor plant will provide critical information for understanding seed metabolism, for effectively engineering ricinoleate production in transgenic oilseeds, or for genetically improving castor plants by eliminating toxic and allergic proteins in seeds.

RESULTS

Full-length cDNAs are useful resources in annotating genes and in providing functional analysis of genes and their products. We constructed a full-length cDNA library from developing castor endosperm, and obtained 4,720 ESTs from 5'-ends of the cDNA clones representing 1,908 unique sequences. The most abundant transcripts are genes encoding storage proteins, ricin, agglutinin and oleosins. Several other sequences are also very numerous, including two acidic triacylglycerol lipases, and the oleate hydroxylase (FAH12) gene that is responsible for ricinoleate biosynthesis. The role(s) of the lipases in developing castor seeds are not clear, and co-expressing of a lipase and the FAH12 did not result in significant changes in hydroxy fatty acid accumulation in transgenic Arabidopsis seeds. Only one oleate desaturase (FAD2) gene was identified in our cDNA sequences. Sequence and functional analyses of the castor FAD2 were carried out since it had not been characterized previously. Overexpression of castor FAD2 in a FAH12-expressing Arabidopsis line resulted in decreased accumulation of hydroxy fatty acids in transgenic seeds.

CONCLUSION

Our results suggest that transcriptional regulation of FAD2 and FAH12 genes maybe one of the mechanisms that contribute to a high level of ricinoleate accumulation in castor endosperm. The full-length cDNA library will be used to search for additional genes that affect ricinoleate accumulation in seed oils. Our EST sequences will also be useful to annotate the castor genome, which whole sequence is being generated by shotgun sequencing at the Institute for Genome Research (TIGR).

Adenosine stimulates anabolic metabolism in developing castor bean (Ricinus communis L.) cotyledons

In previous experiments it was shown that Castor-bean (Ricinus communis) endosperm releases carbohydrates, amino acids and nucleoside derivatives, which are subsequently imported into the developing cotyledons (Kombrink and Beevers in Plant Physiol 73:370-376, 1983). To investigate the importance of the most prominent nucleoside adenosine for the metabolism of growing Ricinus seedlings, we supplied adenosine to cotyledons of 5-days-old seedlings after removal of the endosperm. This treatment led to a 16% increase in freshweight of intact seedlings within 16 h, compared to controls. Using detached cotyledons, we followed uptake of radiolabelled adenosine and identified 40% of label in solubles (mostly ATP and ADP), 46% incorporation in RNA and 2.5% in DNA, indicating a highly active salvage pathway. About 7% of freshly imported adenosine entered the phloem, which indicates a major function of adenosine for cotyledon metabolism. Import and conversion of adenosine improved the energy content of cotyledons as revealed by a substantially increased ATP/ADP ratio. This effect was accompanied by slight increases in respiratory activity, decreased levels of hexose phosphates and increased levels of fructose-1,6-bisphosphate and triose phosphates. These alterations indicate a stimulation of glycolytic flux by activation of phosphofructokinase, and accordingly we determined a higher activity of this enzyme. Furthermore the rate of [(14)C]-sucrose driven starch biosynthesis in developing castor-bean is significantly increased by feeding of adenosine. In conclusion, our data indicate that adenosine imported from mobilizing endosperm into developing castor-bean cotyledons fulfils an important function as it promotes anabolic reactions in this rapidly developing tissue.

Polyamines are essential for the synthesis of 2-ricinoleoyl phosphatidic acid in developing seeds of castor

The major fatty acid component of castor (Ricinus communis L.) oil is ricinoleic acid (12-hydroxy-cis-9-octadecenoic acid), and unsaturated hydroxy acid accounts for >85% of the total fatty acids in triacylglycerol (TAG). TAG had a higher ricinoleate content at position 2 than at positions 1 and 3. Although lysophosphatidic acid (LPA) acyltransferase (EC 2.3.1.51), which catalyzes acylation of LPA at position 2, was expected to utilize ricinoleoyl-CoA preferentially over other fatty acyl-CoAs, no activity was found for ricinoleoyl-CoA in vitro at concentrations at which other unsaturated acyl-CoAs were incorporated rapidly. However, activity for ricinoleoyl-CoA appeared with addition of polyamines (putrescine, spermidine, and spermine), while polyamines decreased the rates of incorporation of other acyl-CoAs into position 2. The order of effect of polyamines on LPA acyltransferase activity was spermine > spermidine >> putrescine. At concentrations of spermine and spermidine of >0.1 mM, ricinoleoyl-CoA served as an effective substrate for LPA acyltransferase reaction. The concentrations of spermine and spermidine in the developing seeds were estimated at approximately 0.09 and approximately 0.63 mM, respectively. These stimulatory effects for incorporation of ricinoleate were specific to polyamines, but basic amino acids were ineffective as cations. In contrast, in microsomes from safflower seeds that do not contain ricinoleic acid, spermine and spermidine stimulated the LPA acyltransferase reaction for all acyl-CoAs tested, including ricinoleoyl-CoA. Although the fatty acid composition of TAG depends on both acyl-CoA composition in the cell and substrate specificity of acyltransferases, castor bean polyamines are crucial for incorporation of ricinoleate into position 2 of LPA. Polyamines are essential for synthesis of 2-ricinoleoyl phosphatidic acid in developing castor seeds.

In vitro proteolysis of phosphoenolpyruvate carboxylase from developing castor oil seeds by an endogenous thiol endopeptidase

Two novel phosphoenolpyruvate carboxylase (PEPC) isoforms have been biochemically characterized from endosperm of developing castor oil seeds (COS). The association of a 107 kDa PEPC subunit (p107) with an immunologically unrelated bacterial PEPC-type 64 kDa polypeptide leads to marked physical and kinetic differences between the PEPC1 p107 homotetramer and PEPC2 p107/p64 heterooctamer. COS p107 is quite susceptible to limited proteolysis during PEPC purification. An endogenous asparaginyl endopeptidase appears to catalyze the in vitro cleavage of an approximately 120 amino acid polypeptide from the N-terminal end of p107, producing a truncated 98 kDa polypeptide (p98). Immunoblotting was used to estimate proteolytic activity by following the disappearance of p107 and concomitant appearance of p98 during incubation of clarified COS extracts at 4 degrees C. The in vitro proteolysis of p107 to p98 only occurred in the combined presence of 2 mM dithiothreitol and high salt concentrations (particularly SO(4) (2-) and PO(4) (2-) salts). Although p107-degrading activity was present throughout COS development, it was most pronounced in endosperm extracts from older beans. Several protease inhibitors, including two commercially available protease inhibitor cocktails, were tested for their ability to prevent p107 proteolysis. All of the inhibitors were ineffective except for 2,2'-dipyridyl disulfide (DPDS), a relatively inexpensive and underutilized active site inhibitor of plant thiol proteases. Asparaginyl endopeptidase activity of COS extracts was unaffected by 20% (NH(4))(2)SO(4) when determined in the presence or absence of 2 mM dithiothreitol using a spectrophotometric assay based upon the hydrolysis of benzoyl-L-Asn-p-nitroanilide. Thus, we propose that the combined presence of 2 mM dithiothreitol and 20% (NH(4))(2)SO(4) promotes a p107 conformational change that exposes the N-terminal region asparaginyl residue where p107 hydrolysis is believed to occur.

Purification and characterization of cytosolic fructose-1, 6-bisphosphate aldolase from endosperm of germinated castor oil seeds

Cytosolic fructose-1,6-bisphosphate (FBP) aldolase (ALDc) from the endosperm of 4- to 5-day germinated castor oil seeds (COS) has been purified 83-fold to electrophoretic homogeneity and a final specific activity of 2.5 micromol FBP cleaved/min/mg protein. SDS-PAGE and denaturing isoelectric focusing of the final preparation revealed a single protein-staining band of 40 kDa and pI value 7.2. The native Mr was determined by gel-filtration chromatography and multiangle laser light scattering to be 160-175 kDa, indicating that the enzyme is homotetrameric. The enzyme (a) is a class I aldolase, since EDTA or Mg2+ had no effect on its activity; and (b) was relatively heat stable and had an activation energy of 100 kJ/mol. It exhibited a broad pH-activity optima of 7.2, a relatively high affinity for FBP (Km = 0.16 microM), and a forward:reverse Vmax ratio of 0.77. Rabbit anti-(COS ALDc) antibodies cross-reacted with COS ALDc, but not with the corresponding plastidic isozyme. Time-course studies revealed that (a) the increase in total ALD activity that occurs during COS development and early germination coincides with an increase in ALDc concentration and (b) the latter stages of COS maturation and germination are accompanied by marked reductions in ALD activity and ALDc concentration. The most significant elevation in ALDc concentration occurred over the first 4 days of germination when COS initiates the gluconeogenic conversion of P-enolpyruvate and triose-P, derived from reserve triacylglycerols, into the sucrose required to support early seedling growth.

Different sets of cis-elements contribute to the expression of a catalase gene from castor bean during seed formation and postembryonic development in transgenic tobacco

Deletion analysis of the promoter region of a gene for catalase, cat2, from castor bean (Ricinus communis) was performed to identify the cis-regulatory elements responsible for the expression of a beta-glucuronidase (GUS) fusion gene during seed formation and postembryonic development in transgenic tobacco. The analysis showed that multiple cis-elements contribute to the activity of the cat2 promoter during seed formation and postembryonic development. The 5'-upstream regions from -1,241 to -816 bp, from -720 to -682 bp, and from -632 to -535 bp, relative to the site of initiation of translation of cat2, contributed positively to the activity of the cat2 promoter during both stages. By contrast, the region from -816 to -720 bp had a negative effect at both stages. The region from -682 to -632 bp contributed positively to the activity during seed formation but negatively during postembyonic development. Histochemical analysis revealed that the multiple cis-elements determined not only the level of expression of the chimeric gene but also the tissue-specificity of such expression. For example, the region from -1,241 to -816 bp allowed expression of the chimeric gene in the axis of the embryo of the dry seed, as well as in the cortex of the middle part of the hypocotyl and at the base of epicotyl in the young seedling.

Higher-plant cofactor-independent phosphoglyceromutase: purification, molecular characterization and expression

Cofactor-independent phosphoglyceromutase (PGM) was purified to homogeneity from developing castor seed endosperm. Immunological characterization using monospecific antisera raised against this protein indicates that the enzyme is located in the cytosol and that there is no immunologically related polypeptide in the leucoplast from this tissue. Isolation and sequence determination of full-length cDNA clones for castor and tobacco PGM demonstrate that the protein is highly conserved in these plants and is closely related to the maize enzyme. A comparison of the amino acid sequence of peptides derived from Neurospora crassa PGM with the cofactor-independent enzyme from higher plants demonstrated that they are related and may have diverged from a common ancestral gene. The previously proposed relationship between higher-plant PGM and alkaline phosphatases is not supported by sequence analysis of the castor and tobacco enzymes. Expression of the single castor cytosolic PGM gene correlates well with other cytosolic glycolytic genes in developing and germinating castor seeds, and with the appearance of enzyme activity and PGM polypeptides in these tissues.

Changes in stability of isocitrate dehydrogenase (NADP+) during germination of castor bean seeds

In crude extract of castor bean endosperm, isocitrate dehydrogenase (NADP+) (EC 1.1.1.42) was stable at 57 degrees C at the beginning of seed germination as well as in maturing and dry seeds. The enzyme gradually became less thermostable as germination proceeded and became unstable after 4 days. Extract from 5-day-old endosperm reduced the thermostability of the thermostable enzyme. The destabilizing factor accumulated in the endosperm as germination progressed and was identified as ricinoleate. Ricinoleate destabilized the purified enzyme which was stabilized by isocitrate and Mg2+, but ricinoleate did not affect the activity of NADP+-isocitrate dehydrogenase itself. Stearate, oleate, palmitate and myristate were similar to ricinoleate in their effect on the thermostability of the enzyme. The thermolabile enzyme in the crude extract of 5-day-old endosperm was readily inactivated by trypsin and in low concentrations of buffer. The thermostable enzyme in the crude extract of 2-day-old endosperm was not affected by these treatments. The thermostable enzyme treated with ricinoleate showed the same instabilities as the thermolabile enzyme. The role of ricinoleate in the germinating castor bean endosperm is discussed.