Queuosine is a structurally unique and functionally important tRNA modification, widely distributed in eukaryotes and bacteria. The final step of queuosine biosynthesis is the reduction/deoxygenation of epoxyqueuosine to form the cyclopentene motif of the nucleobase. The chemistry is performed by the structurally and functionally characterized cobalamin-dependent QueG. However, the queG gene is absent from several bacteria that otherwise retain queuosine biosynthesis machinery. Members of the IPR003828 family (previously known as DUF208) have been recently identified as nonorthologous replacements of QueG, and this family was renamed QueH. Here, we present the structural characterization of QueH from Thermotoga maritima. The structure reveals an unusual active site architecture with a [4Fe-4S] metallocluster along with an adjacent coordinated iron metal. The juxtaposition of the cofactor and coordinated metal ion predicts a unique mechanism for a two-electron reduction/deoxygenation of epoxyqueuosine. To support the structural characterization, in vitro biochemical and genomic analyses are presented. Overall, this work reveals new diversity in the chemistry of iron/sulfur- dependent enzymes and novel insight into the last step of this widely conserved tRNA modification.

Plant and fungal THI4 thiazole synthases produce the thiamin thiazole moiety in aerobic conditions via a single-turnover suicide reaction that uses an active-site Cys residue as sulfur donor. Multiple-turnover (i.e. catalytic) THI4s lacking an active-site Cys (non-Cys THI4s) that use sulfide as sulfur donor have been biochemically characterized -- but only from archaeal methanogens that are anaerobic, O2-sensitive hyperthermophiles from sulfide-rich habitats. These THI4s prefer iron as cofactor. A survey of prokaryote genomes uncovered non-Cys THI4s in aerobic mesophiles from sulfide-poor habitats, suggesting that multiple-turnover THI4 operation is possible in aerobic, mild, low-sulfide conditions. This was confirmed by testing 23 representative non-Cys THI4s for complementation of an Escherichia coli ΔthiG thiazole auxotroph in aerobic conditions. Sixteen were clearly active, and more so when intracellular sulfide level was raised by supplying Cys, demonstrating catalytic function in the presence of O2 at mild temperatures and indicating use of sulfide or a sulfide metabolite as sulfur donor. Comparative genomic evidence linked non-Cys THI4s with proteins from families that bind, transport, or metabolize cobalt or other heavy metals. The crystal structure of the aerotolerant bacterial Thermovibrio ammonificans THI4 was determined to probe the molecular basis of aerotolerance. The structure suggested no large deviations compared with the structures of THI4s from O2-sensitive methanogens, but is consistent with an alternative catalytic metal. Together with complementation data, use of cobalt rather than iron was supported. We conclude that catalytic THI4s can indeed operate aerobically and that the metal cofactor inserted is a likely natural determinant of aerotolerance.

Formaldehyde (HCHO) is a reactive carbonyl compound that formylates and cross-links proteins, DNA, and small molecules. It is of specific concern as a toxic intermediate in the design of engineered pathways involving methanol oxidation or formate reduction. The interest in engineering these pathways is not, however, matched by engineering-relevant information on precisely why HCHO is toxic or on what damage-control mechanisms cells deploy to manage HCHO toxicity. The only well-defined mechanism for managing HCHO toxicity is formaldehyde dehydrogenase-mediated oxidation to formate, which is counterproductive if HCHO is a desired pathway intermediate. We therefore sought alternative HCHO damage-control mechanisms via comparative genomic analysis. This analysis associated homologs of the Escherichia coli pepP gene with HCHO-related one-carbon metabolism. Furthermore, deleting pepP increased the sensitivity of E. coli to supplied HCHO but not other carbonyl compounds. PepP is a proline aminopeptidase that cleaves peptides of the general formula X-Pro-Y, yielding X + Pro-Y. HCHO is known to react spontaneously with cysteine to form the close proline analog thioproline (thiazolidine-4-carboxylate), which is incorporated into proteins and hence into proteolytic peptides. We therefore hypothesized that certain thioproline-containing peptides are toxic and that PepP cleaves these aberrant peptides. Supporting this hypothesis, PepP cleaved the model peptide Ala-thioproline-Ala as efficiently as Ala-Pro-Ala in vitro and in vivo, and deleting pepP increased sensitivity to supplied thioproline. Our data thus (i) provide biochemical genetic evidence that thioproline formation contributes substantially to HCHO toxicity and (ii) make PepP a candidate damage-control enzyme for engineered pathways having HCHO as an intermediate.

Chemically engineering endogenous amino acids with a molecular tag is one of the most common routes of artificially functionalizing proteins for identification or cellular delivery. However, it is challenging to make conjugation efficient, facile and productive as well as avoiding a high chance of deactivation of the functional proteins. Here we present a new and straightforward design to specifically tether the distinct six polyhistidine tag, terminally expressed on protein cargoes and cellular membrane proteins by using bispecific circular aptamers (bc-apts). The anti-His tag aptamer on one end of the bc-apt can easily recognize the biorthogonal six polyhistidine tag (His tag) on functional proteins like EGFP or RNase A. Meanwhile, a cell-specific aptamer, sgc8, on the other end efficiently facilitates the targeted delivery of functional proteins, improving their overall bioactivity in the cellular milieu by around 4 fold. Therefore, the nuclease-resistant bc-apt is a promising molecular tethering reagent to enable the noncovalent crosslink between live diseased cells and His tag protein cargoes.

Hepatocellular carcinoma is the most frequent primary liver cancer leading to a major health problem worldwide, with a lack of effective therapies after diagnosis. Paradol, a phenolic compound found in ginger, displayed bioactivities such as anti-oxidant, inhibition of promyelocytic leukemia cells and oral squamous carcinoma cells, while its effects on human hepatocellular carcinoma cells are unknown. Here, the cytotoxicity of paradol against hepatocellular carcinoma cell was investigated, as well as the underlying signaling pathways. By CCK-8 assay and transwell migration assay, paradol was found to reduce HepG2 cell viability and migration effectively, with IC50 of 35.87 mu M at 24 h. By cell cycle analysis and western blot, the accumulation of cells in G0/G1 phase and the downregulation of CCND1 and CCNE1 have proved the contribution of G0/G1 arrest for the cytotoxicity against HepG2 cells. Further, apoptotic death was demonstrated in HepG2 cells treated with paradol, by DAPI staining, Annexin-FITC/PI staining followed by flow cytometry and western blot for Bcl-2 and Bax. For signaling mechanism, the western blot data presented elevated p38 MAPK and JNK activation after paradol treatment. In summary, we have discovered paradol as a potential agent against hepatocellular carcinoma. It could inhibit proliferation and migration, partly through inducing apoptosis by G0/G1 phase arrest in hepatocellular carcinoma HepG2 cells, via MAPK signaling.

云作业的调度算法的优良对整个云系统的工作效率具有重要意义.首先,找出影响云作业调度的关键因素,建立资源约束模型;随后,通过植物生长规律的Logistic模型来改进现有的模拟植物生长算法,使其生长依据能量动力改变植物生长的方式;最后,通过4种不同的植物模型进行比较,分析其不同特点,并与6个典型的云作业调度算法比较,得出结论:基于Logistic模型改进的模拟植物生长算法具有更好的作业调度效率.

Flavins are notoriously photolabile, but while the photoproducts derived from the iso-alloxazine ring are well known the other photoproducts are not. In the case of FAD, typically the main cellular flavin, the other photoproducts are predicted to include four- and five-carbon sugars linked to ADP. These FAD photoproducts were shown to be potent glycating agents, more so than ADP-ribose. Such toxic compounds would require disposal via an ADP-sugar diphosphatase or other route. Comparative analysis of bacterial genomes uncovered a candidate disposal gene that is chromosomally clustered with genes for FAD synthesis or transport and is predicted to encode a protein of the PhnP cyclic phosphodiesterase family. The representative PhnP family enzyme from Koribacter versatilis (here named Fpd, FAD photoproduct diphosphatase) was found to have high, Mn2+-dependent diphosphatase activity against FAD photoproducts, FAD, and ADP-ribose, but almost no phosphodiesterase activity against riboflavin 4',5'-cyclic phosphate, a chemical breakdown product of FAD. To provide a structural basis of the unique Fpd activity, the crystal structure of K. versatilis Fpd was determined. The results place Fpd in the broad metallo-β-lactamase-like family of hydrolases, a diverse family commonly using two metals for hydrolytic catalysis. The active site of Fpd contains two Mn2+ ions and a bound phosphate, consistent with a diphosphatase mechanism. Our results characterize the first PhnP family member that is a diphosphatase rather than a cyclic phosphodiesterase and suggest its involvement in a cellular damage-control system that efficiently hydrolyzes the reactive, ADP-ribose-like products of FAD photodegradation.

5-Deoxyribose is formed from 5′-deoxyadenosine, a toxic byproduct of radical S -adenosylmethionine (SAM) enzymes. The degradative fate of 5-deoxyribose is unknown. Here, we define a salvage pathway for 5-deoxyribose in bacteria, consisting of phosphorylation, isomerization, and aldol cleavage steps. Analysis of bacterial genomes uncovers widespread, unassigned three-gene clusters specifying a putative kinase, isomerase, and sugar phosphate aldolase. We show that the enzymes encoded by the Bacillus thuringiensis cluster, acting together in vitro, convert 5-deoxyribose successively to 5-deoxyribose 1-phosphate, 5-deoxyribulose 1-phosphate, and dihydroxyacetone phosphate plus acetaldehyde. Deleting the isomerase decreases the 5-deoxyribulose 1-phosphate pool size, and deleting either the isomerase or the aldolase increases susceptibility to 5-deoxyribose. The substrate preference of the aldolase is unique among family members, and the X-ray structure reveals an unusual manganese-dependent enzyme. This work defines a salvage pathway for 5-deoxyribose, a near-universal metabolite.

Focusing on the shortcoming of low storage efficiency and high recovery cost after copy failure of the current Hadoop,Hopfield Neural Network (HNN) was used to improve the overall performance.Firstly,the resource characteristics that affect the storage efficiency were analyzed.Secondly,the resource constraint model was established,the Hopfield energy function was designed and simplified.Finally,the average utilization rate of 8 nodes was analyzed by using the standard test case Wordcount,and the performance and resource utilization of the proposed strategy were compared with three typical algorithms including dynamic resource allocation algorithm,energy-efficient algorithm and Hadoop default storage strategy,and the comparison results showed that the average efficiency of the storage strategy based on HNN was promoted by 15.63％,32.92％ and 55.92％ respectively.The results indicate that the proposed algorithm can realize the resource load balancing,help to improve the storage capacity of Hadoop,and speed up the retrieval.

Human dihydroorotate dehydrogenase (HsDHODH) is a flavin-dependent mitochondrial enzyme that has been certified as a potential therapeutic target for the treatment of rheumatoid arthritis and other autoimmune diseases. On the basis of lead compound 4, which was previously identified as potential HsDHODH inhibitor, a novel series of thiazole derivatives were designed and synthesized. The X-ray complex structures of the promising analogues 12 and 33 confirmed that these inhibitors bind at the putative ubiquinone binding tunnel and guided us to explore more potent inhibitors, such as compounds 44, 46, and 47 which showed double digit nanomolar activities of 26, 18, and 29 nM, respectively. Moreover, 44 presented considerable anti-inflammation effect in vivo and significantly alleviated foot swelling in a dose-dependent manner, which disclosed that thiazole-scaffold analogues can be developed into the drug candidates for the treatment of rheumatoid arthritis by suppressing the bioactivity of HsDHODH.

A novel series of naphthalimide-cyclam conjugates were designed and synthesized. Among them, compounds 4c, 4d, 8c and 8d which bearing long lipophilic alkyl chains, displayed comparable or more potent cytotoxic activities against human tumor cell lines than amonafide. Furthermore, the four compounds were proved to possess strong inhibition against both topoisomerase I and II. The representative compound 8c exhibited moderate DNA intercalation activity. Molecular modeling studies identified the possible interaction of compound 8c with the molecular target by forming topoisomerase/DNA/drug ternary complex. Finally, derivatives with long lipophilic alkyl chains could efficiently induce apoptosis. (C) 2015 Published by Elsevier Ltd.

A novel series of metal complexes of naphthalimide-cyclam conjugates were synthesized and their in vitro antitumor activities were evaluated. The newly-synthesized compounds showed huge diversity of antiproliferative potency due to variety of metal ions and length of alkyl chains, among which the Zn(II) and Cr(III) complexes exhibited comparable antiproliferative activities with amonafide via multiple tyrosine kinase inhibition. Further research revealed that the representative compound 8a displayed broad-spectrum antiproliferative activity against 15 cancer cell lines with average IC50 value 10.18 +/- 3.25 mu M, and effective antiangiogenic activity on human microvascular endothelial cells (HMEC-1). In brief, metal complexes of naphthalimide-cyclam conjugates were firstly designed and synthesized as multi-target tyrosine kinase inhibitors and proved of their antitumor capacities. (C) 2014 Elsevier Masson SAS. All rights reserved.