Identification of Auxiliary Organellar Targeting Signals for Plant Peroxisomes Using Bioinformatic Analysis of Large Protein Sequence Datasets Followed by Experimental Validation.

Eukaryotic cells are compartmentalized by membrane-bounded organelles to ensure that specific biochemical reactions and cellular functions occur in a spatially restricted manner. The subcellular localization of proteins is largely determined by their intrinsic targeting signals, which are mainly constituted by short peptides. A complete organelle targeting signal may contain a core signal (CoreS) as well as auxiliary signals (AuxiS). However, the AuxiS is often not as well characterized as the CoreS. Peroxisomes house many key steps in photorespiration, besides other crucial functions in plants. Peroxisome targeting signal type 1 (PTS1), which is carried by most peroxisome matrix proteins, was initially recognized as a C-terminal tripeptide with a "canonical" consensus of [S/A]-[K/R]-[L/M]. Many studies have shown the existence of auxiliary targeting signals upstream of PTS1, but systematic characterizations are lacking. Here, we designed an analytical strategy to characterize the auxiliary targeting signals for plant peroxisomes using large datasets and statistics followed by experimental validations. This method may also be applied to deciphering the auxiliary targeting signals for other organelles, whose organellar targeting depends on a core peptide with assistance from a nearby auxiliary signal.

Using Mercury Stable Isotopes to Quantify Bidirectional Water-Atmosphere Hg(0) Exchange Fluxes and Explore Controlling Factors.

In this study, exchange fluxes and Hg isotope fractionation during water-atmosphere Hg(0) exchange were investigated at three lakes in China. Water-atmosphere exchange was overall characterized by net Hg(0) emissions, with lake-specific mean exchange fluxes ranging from 0.9 to 1.8 ng m-2 h-1, which produced negative δ202Hg (mean: -1.61 to -0.03‰) and Δ199Hg (-0.34 to -0.16‰) values. Emission-controlled experiments conducted using Hg-free air over the water surface at Hongfeng lake (HFL) showed negative δ202Hg and Δ199Hg in Hg(0) emitted from water, and similar values were observed between daytime (mean δ202Hg: -0.95‰, Δ199Hg: -0.25‰) and nighttime (δ202Hg: -1.00‰, Δ199Hg: -0.26‰). Results of the Hg isotope suggest that Hg(0) emission from water is mainly controlled by photochemical Hg(0) production in water. Deposition-controlled experiments at HFL showed that heavier Hg(0) isotopes (mean ε202Hg: -0.38‰) preferentially deposited to water, likely indicating an important role of aqueous Hg(0) oxidation played during the deposition process. A Δ200Hg mixing model showed that lake-specific mean emission fluxes from water surfaces were 2.1-4.1 ng m-2 h-1 and deposition fluxes to water surfaces were 1.2-2.3 ng m-2 h-1 at the three lakes. Results from the this study indicate that atmospheric Hg(0) deposition to water surfaces indeed plays an important role in Hg cycling between atmosphere and water bodies.

Defining upstream enhancing and inhibiting sequence patterns for plant peroxisome targeting signal type 1 using large-scale in silico and in vivo analyses.

Peroxisomes are universal eukaryotic organelles essential to plants and animals. Most peroxisomal matrix proteins carry peroxisome targeting signal type 1 (PTS1), a C-terminal tripeptide. Studies from various kingdoms have revealed influences from sequence upstream of the tripeptide on peroxisome targeting, supporting the view that positive charges in the upstream region are the major enhancing elements. However, a systematic approach to better define the upstream elements influencing PTS1 targeting capability is needed. Here, we used protein sequences from 177 plant genomes to perform large-scale and in-depth analysis of the PTS1 domain, which includes the PTS1 tripeptide and upstream sequence elements. We identified and verified 12 low-frequency PTS1 tripeptides and revealed upstream enhancing and inhibiting sequence patterns for peroxisome targeting, which were subsequently validated in vivo. Follow-up analysis revealed that nonpolar and acidic residues have relatively strong enhancing and inhibiting effects, respectively, on peroxisome targeting. However, in contrast to the previous understanding, positive charges alone do not show the anticipated enhancing effect and that both the position and property of the residues within these patterns are important for peroxisome targeting. We further demonstrated that the three residues immediately upstream of the tripeptide are the core influencers, with a 'basic-nonpolar-basic' pattern serving as a strong and universal enhancing pattern for peroxisome targeting. These findings have significantly advanced our knowledge of the PTS1 domain in plants and likely other eukaryotic species as well. The principles and strategies employed in the present study may also be applied to deciphering auxiliary targeting signals for other organelles.

Identification of Phosphorus Stress Related Proteins in the Seedlings of Dongxiang Wild Rice (Oryza Rufipogon Griff.) Using Label-Free Quantitative Proteomic Analysis.

Phosphorus (P) deficiency tolerance in rice is a complex character controlled by polygenes. Through proteomics analysis, we could find more low P tolerance related proteins in unique P-deficiency tolerance germplasm Dongxiang wild rice (Oryza Rufipogon, DXWR), which will provide the basis for the research of its regulation mechanism. In this study, a proteomic approach as well as joint analysis with transcriptome data were conducted to identify potential unique low P response genes in DXWR during seedlings. The results showed that 3589 significant differential accumulation proteins were identified between the low P and the normal P treated root samples of DXWR. The degree of change was more than 1.5 times, including 60 up-regulated and 15 downregulated proteins, 24 of which also detected expression changes of more than 1.5-fold in the transcriptome data. Through quantitative trait locus (QTLs) matching analysis, seven genes corresponding to the significantly different expression proteins identified in this study were found to be uncharacterized and distributed in the QTLs interval related to low P tolerance, two of which (LOC_Os12g09620 and LOC_Os03g40670) were detected at both transcriptome and proteome levels. Based on the comprehensive analysis, it was found that DXWR could increase the expression of purple acid phosphatases (PAPs), membrane location of P transporters (PTs), rhizosphere area, and alternative splicing, and it could decrease reactive oxygen species (ROS) activity to deal with low P stress. This study would provide some useful insights in cloning the P-deficiency tolerance genes from wild rice, as well as elucidating the molecular mechanism of low P resistance in DXWR.

Identification and characterisation of cold stress-related proteins in Oryza rufipogon at the seedling stage using label-free quantitative proteomic analysis.

In this study, label-free quantitative proteomics were used to study cold stress-related proteins in Dongxiang wild rice (Oryza rufipogon Griff., DWR) and cold sensitive cultivated rice 'Xieqingzao B'(Oryza sativa L. ssp. indica cv., XB). The results demonstrated the presence of 101 and 216 differentially expressed proteins (DEPs) were detected in DWR and XB, respectively, after cold stress. Bioinformatics analysis showed that DWR and XB differed significantly in their ability to scavenge reactive oxygen species (ROS) and regulate energy metabolism. Of the 101 DEPs of DWR, 46 DEPs related to differential expressed genes were also detected by transcriptome analysis. And 13 out of 101 DEPs were located in previous cold related quantitative trait loci (QTL). Quantitative real-time PCR analysis indicated that protein expression and transcription patterns were not similar in XB and DWR. Protein-protein interaction (PPI) network was constituted using the DEPs of DWR and XB, and the following three centre proteins were identified: Q8H3I3, Q9LDN2, and Q2QXR8. Next, we selected a centre protein and two of the 37 DEPs with high levels of differential expression (fold change ≥ 2) were used for cloning and prokaryotic expression. We found that Q5Z9Q8 could significantly improve the cold tolerance of Escherichia coli.

Transcription Factors Rc and OsVP1 Coordinately Regulate Preharvest Sprouting Tolerance in Red Pericarp Rice.

Red pericarp associates with seed dormancy or preharvest sprouting (PHS) tolerance in crops. To identify this association's molecular mechanism, a PHS mutant Osviviparous1 (Osvp1) was characterized in rice and crossed with Kasalath, a red pericarp cultivar with Rc (red coleoptiles) genotype. Among the dehulled seeds of F2 progenies, RcRcvp1vp1 seeds performed a lower PHS rate than rcrcvp1vp1 seeds and showed shallower pigmentation than RcRcVP1VP1 seeds. Kasalath and SL9 (an RcRcVP1VP1 substitution line with Nipponbare background) showed more ABA sensitivity than the Nipponbare (rcrcVP1VP1) by the germination assay, and the transcriptional abundance of ABA signal genes OsABI2, OsSnRK2, OsVP1, ABI5, and especially OsVP1 increased in the red pericarp line SL9. Moreover, OsVP1 can directly bind Rc (bHLH) promoter by yeast one-hybrid, which activates Rc and OsLAR expression in red pericarp rice. Furthermore, a luciferase complementation imaging assay showed that OsVP1 interacts with transcriptions factors Rc and OsC1. These results indicate that OsVP1 promotes proanthocyanidin accumulation through the interaction among OsVP1, Rc, and OsC1 and then increases the plant's ABA sensitivity and PHS resistance.

Zn-Co Sulfide Microflowers Anchored on Three-Dimensional Graphene: A High-Capacitance and Long-Cycle-Life Electrode for Asymmetric Supercapacitors.

Zinc-cobalt double-metal sulfides (ZCS) as Faradic electrode materials with high energy density have great potential for supercapacitors, but their poor transfer efficiency for electrons and ions hinders their electrochemical response. Herein, ZnCo2 (CO3 )1.5 (OH)3 @ZCS microflower hybrid arrays consisting of thin nanolayer petals were anchored on three-dimensional graphene (ZnCo2 (CO3 )1.5 (OH)3 @ZCS/3DG) by a simple hydrothermal method and additional ion-exchange process. A ZnCo2 (CO3 )1.5 (OH)3 @ZCS/3DG electrode delivered high capacitance (2228 F g-1 at 1 A g-1 ) and long cycling life (85.7 % retention after 17 000 cycles), which are ascribed to the multicomponent structural design. The 3DG conductive substrate improves the electron-transfer dynamics of the electrode material. Meanwhile, the microflowers consisting of thin nanolayer petals could not only provide many active sites for ions to improve the capacitance, but also alleviate the volume expansion to ensure the structural stability. Furthermore, an all-solid-state asymmetric supercapacitor based on a ZnCo2 (CO3 )1.5 (OH)3 @ZCS/3DG electrode achieved a high energy density of 27 W h kg-1 at 528.3 W kg-1 and exhibits exceptional cyclic stability for 23 000 cycles. Its ability to light a blue LED for 9 min verified the feasibility of its application for energy storage devices.

Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.).

BACKGROUND: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. RESULTS: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response. The results indicated that 1184 transcripts were differentially expressed in the leaves (323 up-regulated and 861 down-regulated) and 986 transcripts were differentially expressed in the roots (756 up-regulated and 230 down-regulated). 43 genes were up-regulated both in leaves and roots, 38 genes were up-regulated in roots but down-regulated in leaves, and only 2 genes were down-regulated in roots but up-regulated in leaves. Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in phosphorus deficiency tolerance. Meanwhile, the differentially expressed genes were also annotated with gene ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most important candidate genes was then identified by combining the differentially expressed genes found in the present study with previously identified phosphorus deficiency tolerance quantitative trait loci. CONCLUSION: The present work provides abundant genomic information for functional dissection of the phosphorus deficiency resistance of Dongxiang wild rice, which will be help to understand the biological regulatory mechanisms of phosphorus deficiency tolerance in Dongxiang wild rice.

Transcriptome analysis of phosphorus stress responsiveness in the seedlings of Dongxiang wild rice (Oryza rufipogon Griff.)

Abstract Background: Low phosphorus availability is a major factor restricting rice growth. Dongxiang wild rice (Oryza rufipogon Griff.) has many useful genes lacking in cultivated rice, including stress resistance to phosphorus deficiency, cold, salt and drought, which is considered to be a precious germplasm resource for rice breeding. However, the molecular mechanism of regulation of phosphorus deficiency tolerance is not clear. Results: In this study, cDNA libraries were constructed from the leaf and root tissues of phosphorus stressed and untreated Dongxiang wild rice seedlings, and transcriptome sequencing was performed with the goal of elucidating the molecular mechanisms involved in phosphorus stress response. The results indicated that 1184 transcripts were differentially expressed in the leaves (323 up-regulated and 861 down-regulated) and 986 transcripts were differentially expressed in the roots (756 up-regulated and 230 down-regulated). 43 genes were up-regulated both in leaves and roots, 38 genes were up-regulated in roots but down-regulated in leaves, and only 2 genes were down-regulated in roots but up-regulated in leaves. Among these differentially expressed genes, the detection of many transcription factors and functional genes demonstrated that multiple regulatory pathways were involved in phosphorus deficiency tolerance. Meanwhile, the differentially expressed genes were also annotated with gene ontology terms and key pathways via functional classification and Kyoto Encyclopedia of Gene and Genomes pathway mapping, respectively. A set of the most important candidate genes was then identified by combining the differentially expressed genes found in the present study with previously identified phosphorus deficiency tolerance quantitative trait loci. Conclusion: The present work provides abundant genomic information for functional dissection of the phosphorus deficiency resistance of Dongxiang wild rice, which will be help to understand the biological regulatory mechanisms of phosphorus deficiency tolerance in Dongxiang wild rice.

Synthesis of magnetic Fe3O4-Au hybrids for sensitive SERS detection of cancer cells at low abundance.

This work reports a facile synthesis of magnetic hybrids (Fe3O4-Au hybrids) with high SERS activity for detecting a low abundance of cancer cells. We labeled Raman reporter molecule 4-aminothiophenol (4-ATP) and the antibody of CEA (anti-CEA) on Fe3O4-Au hybrid nanoparticles (anti-CEA/4-ATP/Fe3O4-Au) as SERS tags and anti-CEA-labeled Au NPs (anti-CEA/Au) as SERS-active substrates to improve detection sensitivity. In the presence of CEA positive-expressed cancer cells (such as non-small lung cancer cells, A549), sandwich structures were formed as both SERS tags and SERS-active substrates could be bound to CEA at cell surfaces, leading to the formation of SERS hot spots at the junction of SERS tags and SERS-active substrates. As a result, an enhanced SERS signal of 4-ATP arose, which could be used to detect CEA on cell surfaces. This assay can specifically detect CEA-expressed A549 cells at a very low abundance (∼10 cells mL-1) and can be used for evaluating CEA expression levels of different cancer cells line. This assay has the advantages of high sensitivity (because the SERS technique itself enables the detection of very low concentration analytes, even single molecules), high specificity (because of the enhanced SERS signal arising in sandwich configuration, which is formed in specific antigen-antibody interaction events), and high efficiency (because the magnetic SERS tags can concentrate the captured cells and separate them from the complex detection system without repetitive washing steps). These features make our developed assay a rapid and facile method to sensitively detect a low abundance of cancer cells.