Integrated analysis of transcriptomic and proteomic data from tree peony (P. ostii) seeds reveals key developmental stages and candidate genes related to oil biosynthesis and fatty acid metabolism.

Tree peony (Paeonia section Moutan DC.) seeds are an excellent source of beneficial natural compounds that promote health, and they contain high levels of alpha-linolenic acid (ALA). In recent years, tree peony has been emerging as an oil crop. Therefore, combined analysis of the transcriptome and proteome of tree peony (P. ostii) seeds at 25, 32, 39, 53, 67, 81, 88, 95, and 109 days after pollination (DAP) was conducted to better understand the transcriptional and translational regulation of seed development and oil biosynthesis. A total of 38,482 unigenes and 2841 proteins were identified. A total of 26,912 differentially expressed genes (DEGs) and 592 differentially expressed proteins (DEPs) were clustered into three groups corresponding to the rapid growth, seed inclusion enrichment and conversion, and late dehydration and mature stages of seed development. Fifteen lipid metabolism pathways were identified at both the transcriptome and proteome levels. Pathway enrichment analysis revealed that a period of rapid fatty acid biosynthesis occurred at 53-88 DAP. Furthermore, 211 genes and 35 proteins associated with the fatty acid metabolism pathway, 63 genes and 11 proteins associated with the biosynthesis of unsaturated fatty acids (UFAs), and 115 genes and 24 proteins associated with ALA metabolism were identified. Phylogenetic analysis revealed that 16 putative fatty acid desaturase (FAD)-encoding genes clustered into four FAD groups, eight of which exhibited the highest expression at 53 DAP, suggesting that they play an important role in ALA accumulation. RT-qPCR analysis indicated that the temporal expression patterns of oil biosynthesis genes were largely similar to the RNA-seq results. The expression patterns of fatty acid metabolism- and seed development-related proteins determined by MRM were also highly consistent with the results obtained in the proteomic analysis. Correlation analysis indicated significant differences in the number and abundance of DEGs and DEPs but a high level of consistency in expression patterns and metabolic pathways. The results of the present study represent the first combined transcriptomic and proteomic analysis of tree peony seeds and provide insight into tree peony seed development and oil accumulation.

Effects of Growing Location on the Contents of Main Active Components and Antioxidant Activity of Dasiphora fruticosa (L.) Rydb. by Chemometric Methods.

Traditional Chinese Medicine (TCM) is a very important raw material source for natural medicines in China. The content and activity of active component are main indexes that evaluate the quality of TCM, however, they may vary with environmental factors. In this study, the effects of environmental factors on the active component contents and antioxidant activity of Dasiphora fruticosa collected from the five main growing areas of China were investigated. The contents of tannin, total flavonoids and rutin were determined to be 7.65 - 10.69%, 2.30 - 5.39% and 0.18 - 0.81%, respectively. Antioxidant activity was determined by DPPH assay, with the DPPH IC50 values ranged from 8.791 to 32.534 µg mL-1 . In order to further explore the cause of these significant geographical variations, the chemometric methods including correlation analysis, principal component analysis, gray correlation analysis and path analysis were applied. The results showed that environmental factors had significant effect on the contents of active components and antioxidant activity. Rapidly available phosphorus (RAP) and rapidly available nitrogen (RAN) were common dominant factors, and a significant positive action existed between RAP and active components and antioxidant activity (P < 0.05). Contributed by their high active components and strong antioxidant activity, Bange in Tibet and Geermu in Qinghai Province were selected as a favorable growing location, respectively.

Arabidopsis AT-hook protein TEK positively regulates the expression of arabinogalactan proteins for Nexine formation.

Nexine is a conserved layer of the pollen wall. We previously reported that the nexine layer is absent in the knockout mutant of Arabidopsis TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK) gene. In this study, we investigated the molecular regulatory functions of TEK in pollen development and identified the genes encoding Arabinogalactan proteins (AGPs) as direct targets of TEK, which are essential for nexine formation. Phenotypic similarity between tek and the TEK-SRDX transgenic lines suggest that TEK plays a role in transcriptional activation in anther development. Microarray analysis identified a total of 661 genes downregulated in tek, including four genes encoding AGPs, AGP6, AGP11, AGP23, and AGP40. Electrophoretic mobility shift assays showed that TEK could directly bind the nuclear matrix attachment region (MAR) and the promoter of AGP6. Chromatin immunoprecipitation followed by PCR analysis demonstrated that TEK is enriched in the promoters of the four AGP genes. Expression of AGP6 driven by the TEK promoter in tek partially rescued both nexine formation and plant fertility. These results indicate that TEK directly regulates AGP expression in the anther to control nexine layer formation. We also proposed that glycoproteins might be essential components of the nexine layer in the pollen wall.

Arabidopsis AT-hook protein TEK positively regulates the expression of arabinogalactan proteins in controlling nexine layer formation in the pollen wall.

Nexine is a conserved layer of the pollen wall. We previously reported that the nexine layer is absent in the knockout mutant of TRANSPOSABLE ELEMENT SILENCING VIA AT-HOOK (TEK). In this work, we characterized the molecular function of TEK in pollen development and identified direct targets of TEK, Arabinogalactan proteins (AGPs), which are responsible for nexine formation. Electrophoretic mobility shift assay (EMSA) showed that TEK can directly bind to the nuclear matrix attachment region (MAR). Phenotypic similarity between tek and the TEK-SRDX transgenic lines indicated that TEK plays a role in transcriptional activation in anther development. Microarray analysis identified a total of 661 genes downstream of TEK, including four genes encoding AGPs, AGP6, AGP11, AGP23 and AGP40. Chromatin immunoprecipitation (ChIP) followed by PCR analysis using the FLAG-tagged TEK complement lines suggested that TEK is enriched in the promoters of these four genes. EMSA further confirmed that TEK binds to the AGP6 promoter. The expression of AGP6 driven by the TEK promoter in tek can partially rescue both nexine formation and plant fertility. These results show that TEK directly regulates AGPs expression in the anther. It is proposed that glycoproteins are an essential component of the nexine layer in the pollen wall.

AUXIN RESPONSE FACTOR17 is essential for pollen wall pattern formation in Arabidopsis.

In angiosperms, pollen wall pattern formation is determined by primexine deposition on the microspores. Here, we show that AUXIN RESPONSE FACTOR17 (ARF17) is essential for primexine formation and pollen development in Arabidopsis (Arabidopsis thaliana). The arf17 mutant exhibited a male-sterile phenotype with normal vegetative growth. ARF17 was expressed in microsporocytes and microgametophytes from meiosis to the bicellular microspore stage. Transmission electron microscopy analysis showed that primexine was absent in the arf17 mutant, which leads to pollen wall-patterning defects and pollen degradation. Callose deposition was also significantly reduced in the arf17 mutant, and the expression of CALLOSE SYNTHASE5 (CalS5), the major gene for callose biosynthesis, was approximately 10% that of the wild type. Chromatin immunoprecipitation and electrophoretic mobility shift assays showed that ARF17 can directly bind to the CalS5 promoter. As indicated by the expression of DR5-driven green fluorescent protein, which is an synthetic auxin response reporter, auxin signaling appeared to be specifically impaired in arf17 anthers. Taken together, our results suggest that ARF17 is essential for pollen wall patterning in Arabidopsis by modulating primexine formation at least partially through direct regulation of CalS5 gene expression.

The GDC1 gene encodes a novel ankyrin domain-containing protein that is essential for grana formation in Arabidopsis.

In land-plant chloroplasts, the grana play multiple roles in photosynthesis, including the potential increase of photosynthetic capacity in light and enhancement of photochemical efficiency in shade. However, the molecular mechanisms of grana formation remain elusive. Here, we report a novel gene, Grana-Deficient Chloroplast1 (GDC1), required for chloroplast grana formation in Arabidopsis (Arabidopsis thaliana). In the chloroplast of knockout mutant gdc1-3, only stromal thylakoids were observed, and they could not stack together to form appressed grana. The mutant exhibited seedling lethality with pale green cotyledons and true leaves. Further blue native-polyacrylamide gel electrophoresis analysis indicated that the trimeric forms of Light-Harvesting Complex II (LHCII) were scarcely detected in gdc1-3, confirming previous reports that the LHCII trimer is essential for grana formation. The Lhcb1 protein, the major component of the LHCIIb trimer, was substantially reduced, and another LHCIIb trimer component, Lhcb2, was slightly reduced in the gdc1-3 mutant, although their transcription levels were not altered in the mutant. This suggests that defective LHCII trimer formation in gdc1-3 is due to low amounts of Lhcb1 and Lhcb2. GDC1 encodes a chloroplast protein with an ankyrin domain within the carboxyl terminus. It was highly expressed in Arabidopsis green tissues, and its expression was induced by photosignaling pathways. Immunoblot analysis of the GDC1-green fluorescent protein (GFP) fusion protein in 35S::GDC1-GFP transgenic plants with GFP antibody indicates that GDC1 is associated with an approximately 440-kD thylakoid protein complex instead of the LHCII trimer. This shows that GDC1 may play an indirect role in LHCII trimerization during grana formation.