OsNAC103, a NAC Transcription Factor, Positively Regulates Leaf Senescence and Plant Architecture in Rice.

Leaf senescence, the last stage of leaf development, is essential for crop yield by promoting nutrition relocation from senescence leaves to new leaves and seeds. NAC (NAM/ATAF1/ATAF2/CUC2) proteins, one of the plant-specific transcription factors, widely distribute in plants and play important roles in plant growth and development. Here, we identified a new NAC member OsNAC103 and found that it plays critical roles in leaf senescence and plant architecture in rice. OsNAC103 mRNA levels were dramatically induced by leaf senescence as well as different phytohormones such as ABA, MeJA and ACC and abiotic stresses including dark, drought and high salinity. OsNAC103 acts as a transcription factor with nuclear localization signals at the N terminal and a transcriptional activation signal at the C terminal. Overexpression of OsNAC103 promoted leaf senescence while osnac103 mutants delayed leaf senescence under natural condition and dark-induced condition, meanwhile, senescence-associated genes (SAGs) were up-regulated in OsNAC103 overexpression (OsNAC103-OE) lines, indicating that OsNAC103 positively regulates leaf senescence in rice. Moreover, OsNAC103-OE lines exhibited loose plant architecture with larger tiller angles while tiller angles of osnac103 mutants decreased during the vegetative and reproductive growth stages due to the response of shoot gravitropism, suggesting that OsNAC103 can regulate the plant architecture in rice. Taken together, our results reveal that OsNAC103 plays crucial roles in the regulation of leaf senescence and plant architecture in rice.

Spatiotemporal evolution of dissolved organic matter (DOM) and its response to environmental factors and human activities.

The South-to-North Water Diversion East Project (SNWDP-E) is an effective way to realize the optimal allocation of water resources in China. The North Dasha River (NDR) is the reverse recharge section that receives water from the Yufu River to the Wohushan Reservoir transfer project line in the SNWDP. However, the dissolved organic matter (DOM) evolution mechanism of seasonal water transfer projects on tributary waters has not been fully elucidated. In this paper, the NDR is the main object, and the changes in the composition and distribution of spectral characteristics during the winter water transfer period (WT) as well as during the summer non-water transfer period (NWT) are investigated by parallel factor analysis (PARAFAC). The results showed that the water connectivity caused by water transfer reduces the environmental heterogeneity of waters in the basin, as evidenced by the ammonia nitrogen (NH4+-N) and total phosphorus (TP) in the water body were significantly lower (p<0.05, p<0.01) during the water transfer period than the non-water transfer period. In addition, the fluorescence intensity of DOM was significantly lower in the WT than the NWT (p<0.05) and was mainly composed of humic substances generated from endogenous sources with high stability. While the NWT was disturbed by anthropogenic activities leading to significant differences in DOM composition in different functional areas. Based on the redundancy analysis (RDA) and multiple regression analysis, it was found that the evolution of the protein-like components is dominated by chemical oxygen demand (COD) and NH4+-N factors during the WT. While the NWT is mainly dominated by total nitrogen (TN) and TP factors for the evolution of the humic-like components. This study helps to elucidate the impact of water transfer projects on the trunk basin and contribute to the regulation and management of inter-basin water transfer projects.

Treatment of atrazine-containing wastewater by algae-bacteria consortia: Signal transmission and metabolic mechanism.

Atrazine is a toxic endocrine disruptor. Biological treatment methods are considered to be effective. In the present study, a modified version of the algae-bacteria consortia (ABC) was established and a control was simultaneously set up to investigate the synergistic relationship between bacteria and algae and the mechanism by which atrazine is metabolized by those microorganisms. The total nitrogen (TN) removal efficiency of the ABC reached 89.24% and the atrazine concentration was reduced to below the level recommended by the Environment Protection Agency (EPA) regulatory standards within 25 days. The protein signal released from the extracellular polymeric substances (EPS) secreted by the microorganisms triggered the resistance mechanism of the algae, and the conversion of humic acid to fulvic acid and electron transfer constituted the synergistic mechanism between the bacteria and algae. The mechanism by which atrazine is metabolized by the ABC mainly consists of hydrogen bonding, H-pi interactions, and cation exchange with atzA for hydrolysis, followed by a reaction with atzC for decomposition to non-toxic cyanuric acid. Proteobacteria was the dominant phylum for bacterial community evolution under atrazine stress, and the analysis revealed that the removal of atrazine within the ABC was mainly dependent on the proportion of Proteobacteria and the expression of degradation genes (p < 0.01). EPS played a major role in the removal of atrazine within the single bacteria group (p < 0.01).

OsFTL12, a member of FT-like family, modulates the heading date and plant architecture by florigen repression complex in rice.

FLOWERING LOCUS T (FT), a florigen in Arabidopsis, plays critical roles in floral transition. Among 13 FT-like members in rice, OsFTL2 (Hd3a) and OsFTL3 (RFT1), two rice homologues of FT, have been well characterized to act as florigens to induce flowering under short-day (SD) and long-day (LD) conditions, respectively, but the functions of other rice FT-like members remain largely unclear. Here, we show that OsFTL12 plays an antagonistic function against Hd3a and RFT1 to modulate the heading date and plant architecture in rice. Unlike Hd3a and RFT1, OsFTL12 is not regulated by daylength and highly expressed in both SD and LD conditions, and delays the heading date under either SD or LD conditions. We further demonstrate that OsFTL12 interacts with GF14b and OsFD1, two key components of the florigen activation complex (FAC), to form the florigen repression complex (FRC) by competing with Hd3a for binding GF14b. Notably, OsFTL12-FRC can bind to the promoters of the floral identity genes OsMADS14 and OsMADS15 and suppress their expression. The osmads14 osmads15 double mutants could not develop panicles and showed erect leaves. Taken together, our results reveal that different FT-like members can fine-tune heading date and plant architecture by regulating the balance of FAC and FRC in rice.

Cladophora can mitigate the shock of glyphosate-containing wastewater on constructed wetlands coupled with microbial fuel cells.

This study investigated the performance of constructed wetlands coupled with microbial fuel cells (CW-MFCs) treating agricultural wastewater containing glyphosate (N-phosphonomethyl glycine, PMG), and the use of Cladophora as a cathode plant in this system. Ten devices were divided into Cladophora groups (CGs) and no Cladophora groups (NGs), with five PMG concentrations (0, 10, 25, 50, and 100 mg/L). PMG removal efficiency significantly decreased with increasing PMG (P < 0.01) and was higher in CG devices than in NG devices at low PMG concentrations (<50 mg/L). The removal efficiency of chemical oxygen demand (COD) and NH4+ in CGs was significantly higher than in NGs (P < 0.01). The highest power densities of 6.37 (CGs) and 6.26 mW/m2 (NGs) were obtained at 50 mg/L PMG, and the average voltage was significantly higher in CGs than in NGs (p < 0.01). Moreover, PMG had a negative effect on the enrichment of electrochemically active bacteria, but Cladophora could mitigate this effect. The abundance of the resistance gene epsps was stabilized; The phnJ gene increased with increasing PMG in NGs and was downregulated at high PMG concentration in CGs, indicating better microbial adaptation to PMG in CGs throughout the experiment.

SDG712, a Putative H3K9-Specific Methyltransferase Encoding Gene, Delays Flowering through Repressing the Expression of Florigen Genes in Rice.

SET domain group (SDG) proteins have been identified to be involved in histone modification and participate in diverse biological processes. Rice contains 41 SDG genes, however, most of which have not been functionally characterized. Here, we report the identification and functional investigation of rice SDG712 gene. Phylogenic analysis revealed that SDG712 belongs to the H3K9-specific SDG subclade. SDG712 is highly expressed in leaves during reproductive growth stage with obvious circadian rhythmic pattern. Mutation of SDG712 promotes rice flowering, while overexpression of SDG712 delays rice flowering. Gene expression analysis suggested that SDG712 acts downstream of Hd1, while acts upstream of Ehd1, Hd3a and RFT1. Subcellular localization assay demonstrated that SDG712 is localized in the nucleus. Chromatin immunoprecipitation (ChIP) assay showed that the H3K9me2 levels at Hd3a and RFT1 loci were increased in SDG712 overexpression transgenic plants, indicating that SDG712 may mediate the H3K9 di-methylation on these loci to repress rice flowering. Taken together, our findings demonstrated that SDG712 is a negative flowering regulatory gene in rice, and it delays flowering through repressing key flowering regulator gene Ehd1 and the florigen genes Hd3a and RFT1.

TarDB: an online database for plant miRNA targets and miRNA-triggered phased siRNAs.

BACKGROUND: In plants, microRNAs (miRNAs) are pivotal regulators of plant development and stress responses. Different computational tools and web servers have been developed for plant miRNA target prediction; however, in silico prediction normally contains false positive results. In addition, many plant miRNA target prediction servers lack information for miRNA-triggered phased small interfering RNAs (phasiRNAs). Creating a comprehensive and relatively high-confidence plant miRNA target database is much needed. RESULTS: Here, we report TarDB, an online database that collects three categories of relatively high-confidence plant miRNA targets: (i) cross-species conserved miRNA targets; (ii) degradome/PARE (Parallel Analysis of RNA Ends) sequencing supported miRNA targets; (iii) miRNA-triggered phasiRNA loci. TarDB provides a user-friendly interface that enables users to easily search, browse and retrieve miRNA targets and miRNA initiated phasiRNAs in a broad variety of plants. TarDB has a comprehensive collection of reliable plant miRNA targets containing previously unreported miRNA targets and miRNA-triggered phasiRNAs even in the well-studied model species. Most of these novel miRNA targets are relevant to lineage-specific or species-specific miRNAs. TarDB data is freely available at http://www.biosequencing.cn/TarDB . CONCLUSIONS: In summary, TarDB serves as a useful web resource for exploring relatively high-confidence miRNA targets and miRNA-triggered phasiRNAs in plants.

Extensive profiling of the expressions of tRNAs and tRNA-derived fragments (tRFs) reveals the complexities of tRNA and tRF populations in plants.

Evidence is emerging that tRNA-derived fragments (tRFs) are regulatory molecules. Studies of tRFs in plants have been based on conventional small RNA sequencing, and focused on profiling of tRF-5 and tRF-3 species. A more comprehensive and quantitative analysis of the entire tRF population is highly necessary. Here, we employ tRNA-seq and YAMAT-seq, and develop a bioinformatics tool to comprehensively profile the expressions of tRNAs and tRFs in plants. We show that in Arabidopsis, approximately half of tRNA genes are extremely weakly expressed, accounting for only 1% of total tRNA abundance, while ~12% of tRNA genes contribute to ~80% of tRNA abundance. Our tRNA sequencings in various plants reveal that tRNA expression profiles exhibit a cross-species conserved pattern. By characterizing the composition of a highly heterogeneous tRF population, we show that tRNA halves and previously unnoticed 10-16-nt tiny tRFs represent substantial portions. The highly accumulated 13-nt and 16-nt tiny tRFs in Arabidopsis indicate that tiny tRFs are not random tRNA degradation products. Finally, we provide a user-friendly database for displaying the dynamic spatiotemporal expressions of tRNAs and tRFs in the model plants Arabidopsis and rice.

Overexpression of OsARD1 Improves Submergence, Drought, and Salt Tolerances of Seedling Through the Enhancement of Ethylene Synthesis in Rice.

Acireductone dioxygenase (ARD) is a metal-binding metalloenzyme and involved in the methionine salvage pathway. In rice, OsARD1 binds Fe2+ and catalyzes the formation of 2-keto-4-methylthiobutyrate (KMTB) to produce methionine, which is an initial substrate in ethylene synthesis pathway. Here, we report that overexpression of OsARD1 elevates the endogenous ethylene release rate, enhances the tolerance to submergence stress, and reduces the sensitivity to drought, salt, and osmotic stresses in rice. OsARD1 is strongly induced by submergence, drought, salinity, PEG6000, and mechanical damage stresses and exhibits high expression level in senescent leaves. Transgenic plants overexpressing OsARD1 (OsARD1-OE) display fast elongation growth to escape submergence stress. The ethylene content is significantly maximized in OsARD1-OE plants compared with the wide type. OsARD1-OE plants display increased shoot elongation and inhibition of root elongation under the submergence stress and grow in dark due to increase of ethylene. The elongation of coleoptile under anaerobic germination is also significantly promoted in OsARD1-OE lines due to the increase of ethylene content. The sensitivity to drought and salt stresses is reduced in OsARD1-OE transgenic lines. Water holding capacity is enhanced, and the stomata and trichomes on leaves increase in OsARD1-OE lines. Drought and salt tolerance and ethylene synthesis-related genes are upregulated in OsARD1-OE plants. Subcellular localization shows that OsARD1 displays strong localization signal in cell nucleus, suggesting OsARD1 may interact with the transcription factors. Taken together, the results provide the understanding of the function of OsARD1 in ethylene synthesis and abiotic stress response in rice.

Identification of quantitative trait loci affecting hemicellulose characteristics based on cell wall composition in a wild and cultivated rice species.

Cell wall hemicellulosic polysaccharides are structurally complex and diverse. Knowledge about the synthesis of cell wall hemicelluloses and their biological roles is limited. Quantitative trait loci (QTL) mapping is a helpful tool for the dissection of complex phenotypes for gene identification. In this study, we exploited the natural variation in cell wall monosaccharide levels between a common wild rice, Yuanj, and an elite indica cultivar, Teqing, and performed QTL mapping with their introgression lines (ILs). Chemical analyses conducted on the culms of Yuanj and Teqing showed that the major alterations are found in glucose and xylose levels, which are correlated with specific hemicellulosic polymers. Glycosidic linkage examination revealed that, in Yuanj, an increase in glucose content results from a higher level of mixed linkage ß-glucan (MLG), whereas a reduction in xylose content reflects a low level of xylan backbone and a varied arabinoxylan (AX) structure. Seventeen QTLs for monosaccharides have been identified through composition analysis of the culm residues of 95 core ILs. Four major QTLs affecting xylose and glucose levels are responsible for 19 and 21% of the phenotypic variance, respectively. This study provides a unique resource for the genetic dissection of rice cell wall formation and remodeling in the vegetative organs.

[The determination of echinacoside and acteoside in herbs of Cistanche tubulosa].

OBJECTIVE: To analyse the echinacoside and acteoside content of Cistanche tubulosa, collected from different hosts and different size of the cultivated, which is compared to the wilding by RP-HPLC method. METHOD: An Agilent Eclipse XDB-C18(4.6 mm x 250 mm, 5 microm) column was used and a mixture of methanol-acetonitrile-1% acetic acid (15:10:75) was used as the mobile phase at a flow rate of 0.6 mL x min(-1). The column temperature was 30 degrees C and the UV detection wavelength was 334 nm. RESULT: The calibration curves of echinacoside and acteoside were in good linearity over the range of 0.904-9.04 microg (r = 0.999 9), and 1.27-12.7 microg (r = 0.999 9) respectively and the average recoveries of echinacoside (and acteoside) were 98.9% (n = 5, RSD 1.9%), and 97.0% (n = 5, RSD 0.97%). CONCLUSION: The method is simple, quick, acurate. In all of the samples, the contents of echinacoside is markedly more than that of acteoside, the content of the two active component in the wilding is higher than that in the planting. The content of sample in the different sizes gradually increase from the big to the small, and the contents of samples collected from the different hosts vary markedly. These results are useful for the quality evaluation of medicinal materials of C. tubulosa.