Genome-Wide Identification and Expression Analysis of OsbZIP09 Target Genes in Rice Reveal Its Mechanism of Controlling Seed Germination.

Seed dormancy and germination are key events in plant development and are critical for crop production, and defects in seed germination or the inappropriate release of seed dormancy cause substantial losses in crop yields. Rice is the staple food for more than half of the world's population, and preharvest sprouting (PHS) is one of the most severe problems in rice production, due to a low level of seed dormancy, especially under warm and damp conditions. Therefore, PHS leads to yield loss and a decrease in rice quality and vitality. We reveal that mutation of OsbZIP09 inhibited rice PHS. Analysis of the expression of OsbZIP09 and its encoded protein sequence and structure indicated that OsbZIP09 is a typical bZIP transcription factor that contains conserved bZIP domains, and its expression is induced by ABA. Moreover, RNA sequencing (RNA-seq) and DNA affinity purification sequencing (DAP-seq) analyses were performed and 52 key direct targets of OsbZIP09 were identified, including OsLOX2 and Late Embryogenesis Abundant (LEA) family genes, which are involved in controlling seed germination. Most of these key targets showed consistent changes in expression in response to abscisic acid (ABA) treatment and OsbZIP09 mutation. The data characterize a number of key target genes that are directly regulated by OsbZIP09 and contribute to revealing the molecular mechanism that underlies how OsbZIP09 controls rice seed germination.

Enhancing 5-aminolevulinic acid tolerance and production by engineering the antioxidant defense system of Escherichia coli.

5-Aminolevulinic acid (ALA) is a value-added compound with potential applications in the fields of agriculture and medicine. Although massive efforts have recently been devoted to building microbial producers of ALA through metabolic engineering, few studies focused on the cellular response and tolerance to ALA. In this study, we demonstrated that ALA caused severe cell damage and morphology change of Escherichia coli via generating reactive oxygen species (ROS), which were further determined to be mainly hydrogen peroxide and superoxide anion radical. ALA treatment activated the native antioxidant defense system by upregulating catalase (CAT) and superoxide dismutase (SOD) expression to combat ROS. Further overexpressing CAT (encoded by katG and katE) and SOD (encoded by sodA, sodB, and sodC) not only improved ALA tolerance but also its production level. Notably, coexpression of katE and sodB in an ALA synthase expressing strain enhanced the biomass and final ALA titer by 81% and 117% (11.5 g/L) in a 5 L bioreactor, respectively. This study demonstrates the importance of tolerance engineering in strain development. Reinforcing the antioxidant defense system holds promise to improve the bioproduction of chemicals that cause oxidative stress.

3D-QSAR studies of HDACs inhibitors using pharmacophore-based alignment.

Histone deacetylases (HDACs) enzyme is a promising target for the development of anticancer drugs. The enzyme-bound conformation of Trichostatin A (TSA) (PDB ID:1C3R) as an inhibitor of HDACs was used to manually construct a pharmacophore model. This model was then successfully used to identify the bioactive conformation and align flexible and structurally diverse molecules. Comparative molecular field analysis (CoMFA) and comparative molecular similarity indices analysis (CoMSIA) were performed on hydroxamate-based HDACs inhibitors based on phamacophore alignment. The best predictions were obtained with CoMFA standard model (q(2) = 0.726, r(2) = 0.998) and CoMSIA model combined with steric, electrostatic, hydrophobic, hydrogen bond donor and acceptor fields (q(2) = 0.610, r(2) = 0.995). Both of the models were validated by an external test set, which gave a satisfactory predictive r(2) value of 0.800 and 0.732, respectively. Graphical interpretation of the results revealed important structural features of the inhibitors related to the active site of HDACs. The results may be exploited for further design and virtual screening for some novel HDACs inhibitors.