Characterization of Peroxidase and Laccase Gene Families and In Silico Identification of Potential Genes Involved in Upstream Steps of Lignan Formation in Sesame.

Peroxidases and laccases are oxidative enzymes involved in physiological processes in plants, covering responses to biotic and abiotic stress as well as biosynthesis of health-promoting specialized metabolites. Although they are thought to be involved in the biosynthesis of (+)-pinoresinol, a comprehensive investigation of this class of enzymes has not yet been conducted in the emerging oil crop sesame and no information is available regarding the potential (+)-pinoresinol synthase genes in this crop. In the present study, we conducted a pan-genome-wide identification of peroxidase and laccase genes coupled with transcriptome profiling of diverse sesame varieties. A total of 83 and 48 genes have been identified as coding for sesame peroxidase and laccase genes, respectively. Based on their protein domain and Arabidopsis thaliana genes used as baits, the genes were classified into nine and seven groups of peroxidase and laccase genes, respectively. The expression of the genes was evaluated using dynamic transcriptome sequencing data from six sesame varieties, including one elite cultivar, white vs black seed varieties, and high vs low oil content varieties. Two peroxidase genes (SiPOD52 and SiPOD63) and two laccase genes (SiLAC1 and SiLAC39), well conserved within the sesame pan-genome and exhibiting consistent expression patterns within sesame varieties matching the kinetic of (+)-pinoresinol accumulation in seeds, were identified as potential (+)-pinoresinol synthase genes. Cis-acting elements of the candidate genes revealed their potential involvement in development, hormonal signaling, and response to light and other abiotic triggers. Transcription factor enrichment analysis of promoter regions showed the predominance of MYB binding sequences. The findings from this study pave the way for lignans-oriented engineering of sesame with wide potential applications in food, health and medicinal domains.

Rice Genome Resequencing Reveals a Major Quantitative Trait Locus for Resistance to Bakanae Disease Caused by Fusarium fujikuroi.

Bakanae disease (BD), caused by the fungal pathogen Fusarium fujikuroi, has become a serious threat in rice-cultivating regions worldwide. In the present study, quantitative trait locus (QTL) mapping was performed using F2 and F3 plants derived after crossing a BD-resistant and a BD-susceptible Korean japonica rice variety, 'Samgwang' and 'Junam', respectively. Resequencing of 'Junam' and 'Samgwang' genomes revealed 151,916 DNA polymorphisms between the two varieties. After genotyping 188 F2 plants, we constructed a genetic map comprising 184 markers, including 175 kompetitive allele-specific PCR markers, eight cleaved amplified polymorphic sequence (CAPS) markers, and a derived CAPS (dCAPS) marker. The degree of BD susceptibility of each F2 plant was evaluated on the basis of the mortality rate measured with corresponding F3 progeny seedlings by in vitro screening. Consequently, qFfR9, a major QTL, was discovered at 30.1 centimorgan (cM) on chromosome 9 with a logarithm of the odds score of 60.3. For the QTL interval, 95% probability lay within a 7.24-7.56 Mbp interval. In this interval, we found that eight genes exhibited non-synonymous single nucleotide polymorphisms (SNPs) by comparing the 'Junam' and 'Samgwang' genome sequence data, and are possibly candidate genes for qFfR9; therefore, qFfR9 could be utilized as a valuable resource for breeding BD-resistant rice varieties.

Heterometal-Coordinated Monomeric Concanavalin A at pH 7.5 from Canavalia ensiformis.

The structure of concanavalin A (ConA) has been studied intensively owing to its specific interactions with carbohydrates and its heterometal (Ca²âº and Mn²âº) coordination. Most structures from X-ray crystallography have shown ConA as a dimer or tetramer, because the complex formation requires specific crystallization conditions. Here, we reported the monomeric structure of ConA with a resolution of 1.6 Å, which revealed that metal coordination could trigger sugar-binding ability. The calcium coordination residue, Asn14, changed the orientation of carbohydrate-binding residues and biophysical details, including structural information, providing valuable clues for the development and application of detection kits using ConA.

Oxidative defense metabolites induced by salinity stress in roots of Salicornia herbacea.

High salinity is a major abiotic stress that affects the growth and development of plants. This type of stress can influence flowering, the production of crops, defense mechanisms and other physiological processes. Previous studies have attempted to elucidate salt-tolerance mechanisms to improve plant growth and productivity in the presence of sodium chloride. One such plant that has been studied in detail is Salicornia, a well-known halophyte, which has adapted to grow in the presence of high salt. To further the understanding of how Salicornia grows and develops under high saline conditions, Salicornia herbacea (S. herbacea) was grown under varying saline concentrations (0, 50, 100, 200, 300, and 400mM), and the resulting phenotype, ion levels, and metabolites were investigated. The optimal condition for the growth of S. herbacea was determined to be 100mM NaCl, and increased salt concentrations directly decreased the internal concentrations of other inorganic ions including Ca2+, K+, and Mg2+. Metabolomics were performed on the roots of the plant as a systematic metabolomics study has not yet been reported for Salicornia roots. Using ethylacetate and methanol extraction followed by high resolution ultra-performance liquid chromatography coupled with mass spectrometry (UPLC-MS), 1793 metabolites were identified at different NaCl levels. Structural and functional analyses demonstrated that the concentration of 53 metabolites increased as the concentration of NaCl increased. These metabolites have been linked to stress responses, primarily oxidative stress responses, which increase under saline stress. Most metabolites can be classified as polyols, alkaloids, and steroids. Functional studies of these metabolites show that shikimic acid, vitamin K1, and indole-3-carboxylic acid are generated as a result of defense mechanisms, including the shikimate pathway, to protect against reactive oxygen species (ROS) generated by salt stress. This metabolite profiling provides valuable information on the salt-tolerance mechanisms of S. herbacea and may be applied to bioengineer plants with improved salt tolerance.

Rice hull extracts inhibit proliferation of MCF-7 cells with G1 cell cycle arrest in parallel with their antioxidant activity.

Rice (Oryza sativa L.) has been a major dietary staple worldwide for centuries. Growing interest in the beneficial effects of antioxidants has inspired investigation of rice hulls as an attractive source of chemopreventive compounds for breast cancer intervention. We prepared methanol extracts from rice hulls of three Korean bred cultivars (japonica), Ilpum, Heugjinju, and Jeogjinju, and one japonica weedy rice, WD-3. We examined the antiproliferative potential of the hull extracts on MCF-7 human breast cancer cells and the related mechanisms thereof. Hull extracts inhibited proliferation of the cells and mediated G0/G1 phase arrest by suppressing cyclins and cyclin-dependent kinases, where WD-3 extract showed the most potent. Blockage of p21 expression by small interfering RNA transfection attenuated G1 phase arrest induced by WD-3 extract. The WD-3 extract exhibited greater antioxidant potential and total phenolic compounds, compared with other rice hulls. Gas chromatography-mass spectrometry analysis for the F4 fractioned from WD-3 extract revealed that cinnamic acid derivatives were the major active constituents. The F4 fraction most potently inhibited proliferation of MCF-7 cells than WD-3 extract through the suppression of cell cycle regulatory factors. Collectively, our results suggest that the pigmented rice hulls possess greater antioxidant and chemopreventive activity against breast cancer than the other rice cultivars tested, demonstrating that WD-3 rice hulls are an attractive source of chemopreventive bioactive compounds.

Seed wintering and deterioration characteristics between weedy and cultivated rice.

BACKGROUND: Incidences of weedy rice continuously occurred in paddy fields because its shattering seeds were able to over-winter. In this research, the seed deterioration of weedy rice was investigated compared with cultivated rice, and the wintering characteristics of these two types of rice were investigated with the field wintering test, freezing resistance test, and accelerated aging test. RESULTS: For the wintering test, the seeds of weedy rice were placed on the soil surface of a paddy with cultivated rice seeds during the 2008/2009 and 2009/2010 winter seasons from November to April. The viability of seeds after wintering was 4.3% for cultivated rice, but 92.7% for weedy rice in 2008/2009. In the second wintering test, the seeds were placed under flooded and dry paddy conditions. The seed viability of cultivated rice was 5% in dry paddy and 0.5% in flooded paddy, but weedy rice maintained a high viability during winter of 90% in the dry paddy and 61% in the flooded paddy. Following freezing treatment of the imbibed seeds, the seed viability was 78% for weedy rice and 16% for cultivated rice. The deterioration of seed tissue induced by freezing treatment was observed by the tetrazolium test. In an accelerated aging test at low temperature and soaking conditions, the seed viability of the weedy rice was 40% higher than the cultivated rice 90 days after treatment. During accelerated aging of seeds, the protein content remained higher in the weedy rice compared to the cultivated rice, and fat acidity remained lower in the weedy rice compared to the cultivated rice. Catalase and superoxide dismutase activity of the weedy rice was 4 times higher than that of the cultivated rice, and DPPH radical scavenging activity of the weedy rice was also much higher than for the cultivated rice. CONCLUSION: In conclusion, the superior ability of seed wintering in weedy rice was based on freezing resistibility of embryo cellular tissue and higher antioxidant activity to protect seed deterioration during the winter season.