ConTIG: Continuous representation learning on temporal interaction graphs.

Representation learning on temporal interaction graphs (TIG) aims to model complex networks with the dynamic evolution of interactions on a wide range of web and social graph applications. However, most existing works on TIG either (a) rely on discretely updated node embeddings merely when an interaction occurs that fail to capture the continuous evolution of embedding trajectories of nodes, or (b) overlook the rich temporal patterns hidden in the ever-changing graph data that presumably lead to sub-optimal models. In this paper, we propose a two-module framework named ConTIG, a novel representation learning method on TIG that captures the continuous dynamic evolution of node embedding trajectories. With two essential modules, our model exploits three-fold factors in dynamic networks including latest interaction, neighbor features, and inherent characteristics. In the first update module, we employ a continuous inference block to learn the nodes' state trajectories from time-adjacent interaction patterns using ordinary differential equations. In the second transform module, we introduce a self-attention mechanism to predict future node embeddings by aggregating historical temporal interaction information. Experiment results demonstrate the superiority of ConTIG on temporal link prediction, temporal node recommendation, and dynamic node classification tasks of four datasets compared with a range of state-of-the-art baselines, especially for long-interval interaction prediction.

Investigation of CuCoFe-LDH as an efficient and stable catalyst for the degradation of acetaminophen in heterogeneous electro-Fenton system: Key operating parameters, mechanisms and pathways.

Pharmaceuticals, as anthropogenic pollutants in a wide range of water sources, generally require specific treatment methods for degradation. A trimetallic layered double hydroxide (CuCoFe-LDH) was successfully fabricated by coprecipitation and applied as a novel heterogeneous electro-Fenton (EF) catalyst for the degradation of acetaminophen (ACT) from aqueous environments. The EF experiments showed that the CuCoFe-LDH/EF process achieved 100% of ACT degradation efficiency within 60 min at pH = 5, catalyst dosage of 0.50 g/L, current density of 10 mA/cm2 and initial ACT concentration of 20 mg/L. An impressive (>80%) mineralization of ACT was obtained over a wide pH range (pH 3-9) after 180 min. Meanwhile, the role of ·OH and O2.- were certified by radical quenching experiments and electron paramagnetic resonance (EPR) analysis. Through mechanism exploration, the coexistence of Cu and Co on Fe-based LDHs can accelerate the interfacial electron transfer and promote the formation of the reactive oxygen species (ROS), thus facilitating the EF process. Furthermore, the degradation by-products and possible degradation pathways of ACT in the CuCoFe-LDH/EF process were proposed. The reusability test and the treatment of various typical organic pollutants experiments indicated that the CuCoFe-LDH/EF process has excellent stability and broad application prospects. This work provides a valuable reference for the treatment of pharmaceuticals by the heterogeneous EF process in a wide range of pH.

Performance and methane potential of up-flow anaerobic sludge blanket treating thermal hydrolyzed sludge dewatering liquor.

Thermal hydrolysis pretreatment could release organic sufficiently from solid into liquid phase to accelerate the high solid sludge anaerobic digestion. Thus, up-flow anaerobic sludge blanket (UASB) could be a promising energy recovery process to treat thermal hydrolyzed sludge dewatering liquor with significantly augmented the organic loading rate (OLR). In this study, its performance was investigated using a lab-scale UASB to treat sludge dewatering liquor after 165 °C, 30 min thermal hydrolysis pretreatment. The results show that 85.57% of the organic in thermal hydrolyzed sludge dewatering liquor could be converted to methane. The UASB adapts to high OLR stably, and the COD removal efficiency was 71.98 ± 1.95% at OLR of 18.35 ± 0.78 kgCOD·(m3·d)-1, and the gap between the maximum potential and experimental methane production yields could be observed during different OLRs. It could be explained as the methanogenesis rate decreased due to the shift of dominant pathway from acetoclastic methanogenesis to syntrophic acetate oxidation following hydrogenotrophic methanogenesis. Methanospirillum became the dominant methanogen with the increase of OLR. In addition, the methane production yield and rate would be hindered till the ammonia nitrogen concentration exceeds 4 g·L-1. Direct interspecies electron transfer could be promising methods to improve UASB performance treating thermal hydrolyzed dewatering liquor.

N-doped carbon intercalated Fe-doped MoS2 nanosheets with widened interlayer spacing: An efficient peroxymonosulfate activator for high-salinity organic wastewater treatment.

Peroxymonosulfate (PMS) heterogeneous catalysis dominated by nonradical pathway showed excellent adaptability for pollutant removal in complex water matrixes. Herein, ultra-small Fe-doped MoS2 nanosheets with N-doped carbon intercalation (CF-MoS2) were synthesized via a one-step hydrothermal method to treat high salinity organic wastewater. CF-MoS2 exhibited an expanded interlayer spacing by 1.63 times and the specific surface area by 9 times compared with Fe-doped MoS2 (F-MoS2), substantially increasing the active sites. Homogeneous Fe2+ catalytic experiments confirmed that the promotion of carbon intercalated MoS2 (C-MoS2) on Fe3+/Fe2+ redox cycle was much higher than pure MoS2. Besides, the considerable removal of tetracycline (TC) under high salinity conditions (0-7.1%) was attributed to the dominant role of PMS nonradical oxidation pathways, including 1O2 and surface-bound radicals. The catalytic sites included Fe3+/Fe2+, Mo4+/Mo5+/Mo6+, C=O, pyridine N, pyrrolic N and hydroxyl groups. Finally, density functional theory (DFT) was employed to get the radical electrophilic attack sites and nucleophile attack sites of TC, and the results were consistent with the TC degradation products determined by HPLC-MS. This work would broaden the application of MoS2-based catalysts, especially for PMS catalytic removal of organic pollutants from high salinity wastewater.

Site-directed integration of exogenous DNA into the soybean genome by LbCas12a fused to a plant viral HUH endonuclease.

High efficiency site-directed chromosomal integration of exogenous DNA in plants remains a challenge despite recent advances in genome editing technologies. One approach to mitigate this problem is to increase the effective concentration of the donor DNA at the target site of interest. HUH endonucleases (ENs) coordinate rolling circle replication. In vitro, they can form stable covalent bonds with DNA that carries their recognition motifs. When fused to a CRISPR-associated endonuclease, HUH ENs may improve integration rates by increasing the local donor concentration through tethering of the donor to the CRISPR nuclease. We tested this hypothesis by using chimeric proteins between LbCas12a as a CRISPR-associated endonuclease and the HUH EN from Faba Bean Necrotic Yellow Virus in soybean (Glycine max). Two fusion protein configurations were tested to integrate a 70-nt oligonucleotide donor into a commercially important target site using protoplasts and in planta transformation. Site-directed integration rates of the donor DNA, when tethered to the fusion protein, reached about 26% in plants and were up to four-fold higher than in untethered controls. Integrations via canonical homology-directed repair or non-homologous end joining were promoted by tethering in a similar fashion. This study is the first demonstration of HUH EN-associated tethering to improve site-directed DNA integration in plants.

Low H2S content biogas biodesulfurization from high solid sludge anaerobic digestion using limited external aeration biotrickling filter: Effect of gas-liquid pattern on oxygen utilization performance.

An efficient and precise method is needed for low H2S content biogas biodesulfurization, produced during high solid sludge anaerobic digestion. Continuous experiments were conducted to evaluate the performance of a lab-scale biotrickling filter (BTF) in H2S removal and oxygen utilization. The results show that the sulfur loading rate decreased by 66% compared to conventional H2S content, thus achieving a sufficient removal efficiency (>0.9). With a limited external aeration (0.5-2.0 molO2·molS-1), the oxygen consumption (O/Sre) to its supplement (O/Sin) ratios increased from 50-71% (conventional H2S) to 83-92% (low H2S), indicating that low H2S flux promotes a sufficient oxygen utilization. Furthermore, the difference in oxygen utilization between co-current and counter-current flow patterns decreased under limited external aeration as the H2S content sharply decreased. These results indicate that a dynamic oxygen-sulfur (O-S) balanced multistage BTF is expected to achieve a more precise vertical O-S distribution for sulfur resource recovery.

Beyond identity: Understanding the contribution of the 5' nucleotide of the antisense strand to RNAi activity.

In both the pharmaceutical and agricultural fields, RNA-based products have capitalized upon the mechanism of RNA interference for targeted reduction of gene expression to improve phenotypes and traits. Reduction in gene expression by RNAi is the result of a small interfering RNA (siRNA) molecule binding to an ARGONAUTE (AGO) protein and directing the effector complex to a homologous region of a target gene's mRNA. siRNAs properties that govern RNA-AGO association have been studied in detail. The siRNA 5' nucleotide (nt) identity has been demonstrated in plants to be an important property responsible for directing association of endogenous small RNAs with different AGO effector proteins. However, it has not been investigated whether the 5' nt identity is an efficacious determinant for topically-applied chemically synthesized siRNAs. In this study, we employed a sandpaper abrasion method to study the silencing efficacies of topically-applied 21 base-pair siRNA duplexes. The MAGNESIUM CHELATASE and GREEN FLUORESCENT PROTEIN genes were selected as endogenous and transgenic gene targets, respectively, to assess the molecular and phenotypic effects of gene silencing. Collections of siRNA variants with different 5' nt identities and different pairing states between the 5' antisense nt and its match in the sense strand of the siRNA duplex were tested for their silencing efficacy. Our results suggest a flexibility in the 5' nt requirement for topically applied siRNA duplexes in planta and highlight the similarity of 5' thermodynamic rules governing topical siRNA efficacy across plants and animals.

One-pot synthesis of N-doped carbon intercalated molybdenum disulfide nanohybrid for enhanced adsorption of tetracycline from aqueous solutions.

Nitrogen-doped carbon intercalated molybdenum disulfide nanohybrid (NC-MoS2) with well-interconnected nanosheets was successfully fabricated using a one-pot hydrothermal method and applied as a novel adsorbent to remove tetracycline (TC) from aqueous solutions. Series material characterizations indicated that the intercalation of nitrogen-doped carbon into MoS2 nanosheets could produce widened interlayer spacing, enlarge the specific surface area and create more extensive functional groups. The adsorption kinetics and isotherms investigations revealed that the pseudo-second-order model and Langmuir isotherm model could fit well the TC adsorption behavior of NC-MoS2. Particularly, NC-MoS2 possessed a high maximum adsorption capacity (1128.4 mg/g) that was approximately 2.8 times that of pristine MoS2 (409.84 mg/g) at 308 K and pH = 6.0 ± 0.1. Furthermore, the relevant thermodynamic parameters indicated that the adsorption process was spontaneous and endothermic. The adsorption process was dependent on multiple interactions including hydrophobicity, π-π stacking interaction and hydrogen bond. These findings demonstrated that NC-MoS2 had potential applications for treating TC-containing water and broadened the application of metal sulfides in the environmental field.

Upregulation of microRNA-141 suppresses epithelial-mesenchymal transition and lymph node metastasis in laryngeal cancer through HOXC6-dependent TGF-ß signaling pathway.

Laryngeal cancer is one of the most malignant cancers among the head and neck malignant tumors. Abnormal expression of microRNAs (miRNAs) contributes to cancer development through regulating proliferation and apoptosis of cancer cells. In this study, we aim to explore the roles of microRNA-141 (miR-141), Homeobox C6 (HOXC6) and TGF-ß signaling pathway in epithelial-mesenchymal transition (EMT) and lymph node metastasis in laryngeal cancer. Initially, we identified differentially expressed genes in laryngeal cancer, among which HOXC6 was identified. Then the target miRNA of HOXC6 was predicted and verified. Next, expression of miR-141, HOXC6, TGF-ß1, Smad3, Vimentin and Snail in cancer tissues was detected. Then, AMC-HN-8 cells were transfected with miR-141 mimic, miR-141 inhibitor and HOXC6-siRNA to investigate specific role of miR-141, HOXC6 and TGF-ß signaling pathway in laryngeal cancer in vivo and in vitro. Our results showed that HOXC6 was a target gene of miR-141, which was downregulated in laryngeal cancer. Besides, overexpression of miR-141 could downregulate HOXC6 and inhibit the TGF-ß signaling pathway. Upregulation of miR-141 or silencing of HOXC6 can repress EMT, viability, migration and invasion abilities of laryngeal cancer cells. In addition, upregulation of miR-141 inhibited the tumor growth and lymph node metastasis in vivo. In summary, our findings demonstrated that upregulated miR-141 decreased HOXC6 expression, and inhibited the TGF-ß signaling pathway, EMT and lymph node metastasis in laryngeal cancer, which is of clinical significance in the treatment of laryngeal cancer.

Ubiquitin carboxyl-terminal hydrolases are required for period maintenance of the circadian clock at high temperature in Arabidopsis.

Protein ubiquitylation participates in a number of essential cellular processes including signal transduction and transcription, often by initiating the degradation of specific substrates through the 26S proteasome. Within the ubiquitin-proteasome system, deubiquitylating enzymes (DUBs) not only help generate and maintain the supply of free ubiquitin monomers, they also directly control functions and activities of specific target proteins by modulating the pool of ubiquitylated species. Ubiquitin carboxyl-terminal hydrolases (UCHs) belong to an enzymatic subclass of DUBs, and are represented by three members in Arabidopsis, UCH1, UCH2 and UCH3. UCH1 and UCH2 influence auxin-dependent developmental pathways in Arabidopsis through their deubiquitylation activities, whereas biological and enzymatic functions of UCH3 remain unclear. Here, we demonstrate that Arabidopsis UCH3 acts to maintain the period of the circadian clock at high temperatures redundantly with UCH1 and UCH2. Whereas single uch1, uch2 and uch3 mutants have weak circadian phenotypes, the triple uch mutant displays a drastic lengthening of period at high temperatures that is more extreme than the uch1 uch2 double mutant. UCH3 also possesses a broad deubiquitylation activity against a range of substrates that link ubiquitin via peptide and isopeptide linkages. While the protein target(s) of UCH1-3 are not yet known, we propose that these DUBs act on one or more factors that control period length of the circadian clock through removal of their bound ubiquitin moieties, thus ensuring that the clock oscillates with a proper period even at elevated temperatures.

Degradation of nitrobenzene wastewater in an acidic environment by Ti(IV)/H2O2/O3 in a rotating packed bed.

The rotating packed bed (RPB) as a continuous flow reactor performs very well in degradation of nitrobenzene wastewater. In this study, acidic nitrobenzene wastewater was degraded using ozone (O3) combined with hydrogen peroxide and titanium ions (Ti(IV)/H2O2/O3) or using only H2O2/O3 in a RPB. The degradation efficiency of nitrobenzene by Ti(IV)/H2O2/O3 is roughly 16.84% higher than that by H2O2/O3, and it reaches as high as 94.64% in 30 min at a H2O2/O3 molar ratio of 0.48. It is also found that the degradation efficiency of nitrobenzene is significantly affected by the high gravity factor, H2O2/O3 molar ratio, and Ti(IV) concentration, and it reaches a maximum at a high gravity factor of 40, a Ti(IV) concentration of 0.50 mmol/L, a pH of 4.0, a H2O2/O3 molar ratio of 0.48, a liquid flow rate of 120 L/h, and an initial nitrobenzene concentration of 1.22 mmol/L. Both direct ozonation and indirect ozonation are involved in the reaction of O3 with organic pollutants. The indirect ozonation due to the addition of different amounts of tert-butanol (·OH scavenger) in the system accounts for 84.31% of the degradation efficiency of nitrobenzene, indicating that the nitrobenzene is dominantly oxidized by ·OH generated in the RPB-Ti(IV)/H2O2/O3 process. Furthermore, the possible oxidative degradation mechanisms are also proposed to better understand the role of RPB in the removal of pollutants. Graphical abstract ᅟ.

Ailanthone Promotes Human Vestibular Schwannoma Cell Apoptosis and Autophagy by Downregulation of miR-21.

Ailanthone (AIL) is a quassinoid isolated from the traditional Chinese medicinal herb Ailanthus altissima. The antitumor activities of AIL have been reported in several cancers. The purpose of the present study was to explore the effect of AIL on vestibular schwannomas (VSs). Various concentrations of AIL (0-1 µM) were used to treat human primary VS cells, and then cell viability, proliferation, apoptosis, and autophagy were assessed. Expression of miR-21 in VS cells was altered by miRNA transfection. The functional actions of AIL on miR-21 dysregulated cells were also assessed. AIL significantly reduced the viability of VS cells, and the IC50 value was 0.48 ± 0.023 µM. In response to 0.6 µM AIL, BrdU+ cell rate and cyclin D1 expression were reduced, apoptotic cell rate was increased, caspase 3 and caspase 9 were cleaved, Beclin-1 and LC3-II were accumulated, and p62 was downregulated. miR-21 was lowly expressed in AIL-treated cells, and AIL-induced apoptosis and autophagy were attenuated by miR-21 overexpression. In addition, AIL downregulated Ras and Raf and deactivated MEK, ERK, mTOR, and p70S6K, while the downregulation and deactivation induced by AIL were reversed by miR-21 overexpression. To conclude, AIL inhibited VS cell proliferation and induced apoptosis and autophagy. The antitumor activities of AIL in VS cells were realized possibly via downregulation of miR-21 and blocking the Ras/Raf/MEK/ERK and mTOR pathways.

Functional polymorphisms in the IL-10 gene with susceptibility to esophageal, nasopharyngeal, and oral cancers.

Emerging evidence showed that functional polymorphisms in the IL-10 gene may have effects on individuals' susceptibility to nasopharyngeal, oral and esophageal cancers, yet individually published findings are inconsistent. We therefore designed the meta-analysis to investigate the correlations of IL-10 genetic polymorphisms with susceptibility to nasopharyngeal, oral and esophageal cancers. The EMBASE, MEDLINE, CINAHL, Web of Science and the Chinese Biomedical Database (CBM) databases were searched with no language restrictions. We use Comprehensive Meta-analysis 2.0 software to carry out statistical analysis. Ten case-control studies with a number of 1,883 patients and 2,857 healthy subjects were enrolled. Our results revealed that IL-10 rs1800872 T>G and rs1800896 A>G polymorphisms has a significantly association with the increased risk of esophageal cancer under the allele and dominant models; rs1800871 T>G, rs1800872 T>G and rs1800896 A>G under allele and dominant models could increase the risk of nasopharyngeal cancer; rs1800871T>G, rs1800872T>G and rs1800896 A>G SNPs under allele model were closely related to the susceptibility to oral cancer. Our findings support the point that IL-10 genetic polymorphisms may play essential role in identifying esophageal cancer, nasopharyngeal cancer and oral cancer at early stage.

The Prevention Effect of Selenium on Prevalence of Children Kaschin-Beck Disease in Active Endemic Areas in Qinghai Plateau.

Selenium deficiency is an important environmental risk factor of Kaschin-Beck disease (KBD), and appropriate selenium supplement can reduce the prevalence of KBD. Guide and Xinghai counties, active endemic areas of KBD in Qinghai Plateau, are characteristic with low level of selenium. The aim of this article was to explore the relationship between selenium content and prevalence of children KBD in some active endemic areas from Guide and Xinghai counties. The historical data of KBD were collected, including the detectable rates of KBD and selenium contents of the hair of children, and then the relationship between the prevalence of KBD and selenium contents of hair was analyzed. In KBD endemic areas of Guide County, the detectable rates of X-ray and metaphysic lesion were declined from 25.00 and 16.96% in 2000 to 13.75 and 13.75% in 2010, respectively. Similarly, in KBD endemic areas of Xinghai County, the detectable rates of X-ray and metaphysic lesion were declined from 46.51 and 40.31% in 2000 to 10.64 and 8.51% in 2010, respectively. The selenium contents of hair in Xinghai county were increased from 130.01 ± 48.08 µg/kg in 2003 to 211.8 ± 86.64 µg/kg in 2010(t = 2.98, P < 0.05); the selenium content of hair in Guide County were increased from 142.30 ± 62.02 µg/kg in 2003 to 182.09 ± 78.46 µg/kg in 2010 (t = 3.12, P < 0.05). There was a negative correlation between the prevalence of KBD and selenium contents of hair (r = -0.785). There was a close relationship between selenium content and prevalence of KBD. Selenium could reduce the prevalence of KBD, so it is very necessary to supplement selenium appropriately for KBD prevention.

Selenium: a protective factor for Kaschin-Beck disease in Qing-Tibet Plateau.

There is a close relationship between selenium deficiency and Kaschin-Beck disease (KBD). Although the etiology of KBD is not known and selenium deficiency is not its actual cause, it is an important environmental risk factor. In particular, in the Qing-Tibet Plateau, a selenium-deficient region, the prevalence of KBD is serious and still increasing and continues to damage public health. By providing selenium to the population in appropriate amounts, and especially to children, KBD can be effectively controlled and prevented.

Mining the bitter melon (momordica charantia l.) seed transcriptome by 454 analysis of non-normalized and normalized cDNA populations for conjugated fatty acid metabolism-related genes.

BACKGROUND: Seeds of Momordica charantia (bitter melon) produce high levels of eleostearic acid, an unusual conjugated fatty acid with industrial value. Deep sequencing of non-normalized and normalized cDNAs from developing bitter melon seeds was conducted to uncover key genes required for biotechnological transfer of conjugated fatty acid production to existing oilseed crops. It is expected that these studies will also provide basic information regarding the metabolism of other high-value novel fatty acids. RESULTS: Deep sequencing using 454 technology with non-normalized and normalized cDNA libraries prepared from bitter melon seeds at 18 DAP resulted in the identification of transcripts for the vast majority of known genes involved in fatty acid and triacylglycerol biosynthesis. The non-normalized library provided a transcriptome profile of the early stage in seed development that highlighted the abundance of transcripts for genes encoding seed storage proteins as well as for a number of genes for lipid metabolism-associated polypeptides, including Δ12 oleic acid desaturases and fatty acid conjugases, class 3 lipases, acyl-carrier protein, and acyl-CoA binding protein. Normalization of cDNA by use of a duplex-specific nuclease method not only increased the overall discovery of genes from developing bitter melon seeds, but also resulted in the identification of 345 contigs with homology to 189 known lipid genes in Arabidopsis. These included candidate genes for eleostearic acid metabolism such as diacylglycerol acyltransferase 1 and 2, and a phospholipid:diacylglycerol acyltransferase 1-related enzyme. Transcripts were also identified for a novel FAD2 gene encoding a functional Δ12 oleic acid desaturase with potential implications for eleostearic acid biosynthesis. CONCLUSIONS: 454 deep sequencing, particularly with normalized cDNA populations, was an effective method for mining of genes associated with eleostearic acid metabolism in developing bitter melon seeds. The transcriptomic data presented provide a resource for the study of novel fatty acid metabolism and for the biotechnological production of conjugated fatty acids and possibly other novel fatty acids in established oilseed crops.

The RPN5 subunit of the 26s proteasome is essential for gametogenesis, sporophyte development, and complex assembly in Arabidopsis.

The 26S proteasome is an essential multicatalytic protease complex that degrades a wide range of intracellular proteins, especially those modified with ubiquitin. Arabidopsis thaliana and other plants use pairs of genes to encode most of the core subunits, with both of the isoforms often incorporated into the mature complex. Here, we show that the gene pair encoding the regulatory particle non-ATPase subunit (RPN5) has a unique role in proteasome function and Arabidopsis development. Homozygous rpn5a rpn5b mutants could not be generated due to a defect in male gametogenesis. While single rpn5b mutants appear wild-type, single rpn5a mutants display a host of morphogenic defects, including abnormal embryogenesis, partially deetiolated development in the dark, a severely dwarfed phenotype when grown in the light, and infertility. Proteasome complexes missing RPN5a are less stable in vitro, suggesting that some of the rpn5a defects are caused by altered complex integrity. The rpn5a phenotype could be rescued by expression of either RPN5a or RPN5b, indicating functional redundancy. However, abnormal phenotypes generated by overexpression implied that paralog-specific functions also exist. Collectively, the data point to a specific role for RPN5 in the plant 26S proteasome and suggest that its two paralogous genes in Arabidopsis have both redundant and unique roles in development.

Ubiquitin C-terminal hydrolases 1 and 2 affect shoot architecture in Arabidopsis.

Ubiquitin C-terminal hydrolases (UCHs) are a subset of de-ubiquitinating proteases that release covalently linked ubiquitin (Ub), and as such play essential roles in recycling Ub and reversing the action of Ub conjugation. We show here that two related Arabidopsis UCHs, UCH1, and UCH2, are important for shoot development. The UCH1 and 2 genes are ubiquitously expressed, with the corresponding proteins present in both the cytoplasm and nucleus. Unlike their animal and fungal counterparts, we found no evidence that the Arabidopsis UCH1 and 2 proteins stably associate with the 26S proteasome. Altering the levels of UCH1 and 2 has substantial effects on Arabidopsis shoot development, especially with respect to inflorescence architecture, with over-expression and double mutants enhancing and suppressing the outgrowth of cauline branches, respectively. Neither UCH1-over-expressing nor uch1-1 uch2-1 plants have detectably altered sensitivity to cytokinins or auxins individually, but exhibit an altered sensitivity to the ratio of the two hormones. UCH1-over-expressing plants show dramatically enhanced phenotypes when combined with auxin-insensitive mutants axr1-3 and axr2-1, suggesting that one or more aspects of auxin signaling are affected by this enzyme pair. Previous studies revealed that the ubiquitination and degradation of the AUX/IAA family of repressors is a key step in auxin signaling. Here, we show that turnover of a reporter fused to a representative AUX/IAA protein AXR3 is faster in the uch1-1 uch2-1 double mutant but slower in the UCH1 over-expression backgrounds. Taken together, our results indicate that de-ubiquitination helps to modify plant shoot architecture, possibly via its ability to directly or indirectly protect upstream target proteins involved in auxin/cytokinin signaling from Ub-mediated degradation.

The specialized cytosolic J-protein, Jjj1, functions in 60S ribosomal subunit biogenesis.

J-proteins and Hsp70 chaperones function together in diverse cellular processes. We identified a cytosolic J-protein, Jjj1, of Saccharomyces cerevisiae that is associated with 60S ribosomal particles. Unlike Zuo1, a 60S subunit-associated J-protein that is a component of the chaperone machinery that binds nascent polypeptide chains upon their exit from the ribosome, Jjj1 plays a role in ribosome biogenesis. Cells lacking Jjj1 have phenotypes very similar to those lacking Rei1, a ribosome biogenesis factor associated with pre-60S ribosomal particles in the cytosol. Jjj1 stimulated the ATPase activity of the general cytosolic Hsp70 Ssa, but not Ssb, Zuo1's ribosome-associated Hsp70 partner. Overexpression of Jjj1, which is normally approximately 40-fold less abundant than Zuo1, can partially rescue the phenotypes of cells lacking Zuo1 as well as cells lacking Ssb. Together, these results are consistent with the idea that Jjj1 normally functions with Ssa in a late, cytosolic step of the biogenesis of 60S ribosomal subunits. In addition, because of its ability to bind 60S subunits, we hypothesize that Jjj1, when overexpressed, is able to partially substitute for the Zuo1:Ssb chaperone machinery by recruiting Ssa to the ribosome, facilitating its interaction with nascent polypeptide chains.

Tripeptidyl peptidase II. An oligomeric protease complex from Arabidopsis.

The breakdown of most nuclear and cytoplasmic proteins involves their partial cleavage by the 26S proteasome followed by further disassembly to free amino acids by the combined action of endo- and exopeptidases. In animals, one important intermediate exopeptidase is tripeptidyl peptidase (TPP)II, which digests peptide products of the 26S proteasome and other endopeptidases into tripeptides. Here, we describe the purification and characterization of TPPII from Arabidopsis (Arabidopsis thaliana). Like its animal counterparts, Arabidopsis TPPII exists as a soluble, approximately 5- to 9-MD complex. Two related species of 153 and 142 kD are present in the purified preparations that are derived from a single TPP2 gene. Sequencing by Edman degradation of the intact polypeptides and mass spectrometry of proteolytic fragments demonstrated that the 142-kD form mainly differs from the 153-kD form by a truncation at the C-terminal end. This serine protease is a member of the subtilisin superfamily and is sensitive to the inhibitors alanine-alanine-phenylalanine-chloromethylketone and butabindide, which are diagnostic for the TPPII subfamily. The Arabidopsis TPP2 gene is widely expressed in many tissue types with related genes evident in other plant genomes. Whereas the 26S proteasome is essential, TPPII appears not as important for plant physiology. An Arabidopsis T-DNA mutant defective in TPP2 expression displays no phenotypic abnormalities and is not hypersensitive to either amino acid analogs or the 26S proteasome inhibitor MG132. As a consequence, plants likely contain other intermediate exopeptidases that assist in amino acid recycling.