Structural basis for the function of DCN-1 in protein Neddylation

Covalent modification by Nedd8 (neddylation) stimulates the ubiquitin-protein isopeptide ligase (E3) activities of Cullins. DCN-1, an evolutionarily conserved protein, promotes neddylation of Cullins in vivo, binds directly to Nedd8, and associates with Cdc53 in the budding yeast Saccharomyces cerevisiae. The 1.9A resolution structure of yeast DCN-1 shows that the region encompassing residues 66-269 has a rectangular parallelepiped-like all alpha-helical structures, consisting of an EF-hand motif N-terminal domain and a closely juxtaposed C-terminal domain with six alpha-helices. The EF-hand motif structure is highly similar to that of the c-Cbl ubiquitin E3 ligase. We also demonstrate that DCN-1 directly binds to Rbx-1, a factor important for protein neddylation. The structural and biochemical results are consistent with the role of DCN-1 as a scaffold protein in a multisubunit neddylation E3 ligase complex.     

Electron transport pathway for a Streptomyces cytochrome P450: cytochrome P450 105D5-catalyzed fatty acid hydroxylation in Streptomyces coelicolor A3(2)

Streptomyces and other bacterial actinomycete species produce many important natural products, including the majority of known antibiotics, and cytochrome P450 (P450) enzymes catalyze important biosynthetic steps. Relatively few electron transport pathways to P450s have been characterized in bacteria, particularly streptomycete species. One of the 18 P450s in Streptomyces coelicolor A3(2), P450 105D5, was found to bind fatty acids tightly and form hydroxylated products when electrons were delivered from heterologous systems. The six ferredoxin (Fdx) and four flavoprotein Fdx reductase (FDR) proteins coded by genes in S. coelicolor were expressed in Escherichia coli, purified, and used to characterize the electron transfer pathway. Of the many possibilities, the primary pathway was NADH --> FDR1 --> Fdx4 --> P450 105D5. The genes coding for FDR1, Fdx4, and P450 105D5 are located close together in the S. coelicolor genome. Several fatty acids examined were substrates, including those found in S. coelicolor extracts, and all yielded several products. Mass spectra of the products of lauric acid imply the 8-, 9-, 10-, and 11-hydroxy derivatives. Hydroxylated fatty acids were also detected in vivo in S. coelicolor. Rates of electron transfer between the proteins were measured; all steps were faster than overall hydroxylation and consistent with rates of NADH oxidation. Substrate binding, product release, and oxygen binding were relatively fast in the catalytic cycle; high kinetic deuterium isotope effects for all four lauric acid hydroxylations indicated that the rate of C-H bond breaking is rate-limiting in every case. Thus, an electron transfer pathway to a functional Streptomyces P450 has been established.     

Reproduction strategy of Trias verrucosa (Orchidaceae) from China

Trias, an orchid genus, was reported in this paper from China as a newly recorded genus for the first time. The genus and its new species, T. verrucosa Z. J. Liu, L. J. Chen et S. P. Lei, were described and discussed. Trias consists of 19 species ranging from Assam of India to Indonesia and Australia in the southeast via Myanmar to Deccan of India in the southwest. Its occurrence in West Yunnan of China is a further indication of phytogeographical relations between this region and the tropical Asia. This new species grows on shady rocks in forests. By observing of its biological characteristics such as phenology and blooming biology, lots of cloned ramets of generation overlap were found, but there were no fruited plants, and that clonal reproduction could repeat had nothing to do with whether the ramet bloomed or not. The flowering season of this species is from early April to early May. The opening of flowers on plants or inflorescence was irregular and the florescence of single flowers was rather short, only lasting 4–5 d, and no fruited flowers were found. Based on the detection of mating systems, no flowers of artificial self-pollination and artificial cross-pollination have fruited. Since the flowering period is just before the rainy season in this region, the ecological conditions of dryness, strong wind, low temperature and weak light during that period of time are evidently unfavorable to plant blooming, pollinating and fruiting. Apparently, the short duration and sterility of each flower would avoid the invalid energy waste in unfavorable circumstances and save the limited energy for more valid asexual reproduction so that the opportunity of multiplication in an uncertain environment would be increased to ensure the progenitive success. The P/O value of T. verrucosa is 187.4 ± 22.4, which is obviously related with the highly valid usage of its conglutinated and hard tuberous pollinarium during pollination, indicating that this species could hold the characteristic of sexual reproduction. This is an adaptation of this type of plants to the rather atrocious ecological circumstance there by its reproduction strategy of strengthening asexual reproduction and weakening sexual reproduction, and so it enables the plants to survive in this region, long-distanced from the places where its relatives dwell.     

PCR-DGGE detection of the bacterial community structure in the Inner Mongolia steppe with two different DNA extraction methods

Compared with conventional methods, molecular biological technique, such as PCR-DGGE (denaturing gradient gel electrophoresis), is informative in examining the structure of the soil bacterial community through the extraction of microbial DNA from soil and generation of bacterial community profiles by PCR amplification of 16S rRNA genes. Extraction efficiency of soil microbial DNA is the most important step in these methods. At present, the frozen-thawing method and bead-beating method are most widely used in genomic extraction. Nevertheless, comparison of these two methods has not been conducted in different soil types, especially in humus-rich soil. In this study, extraction efficiencies of the two methods were compared in humus-rich steppe soil in Inner Mongolia based on the PCR-DGGE analysis of bacterial community structure. The results indicated that the bead-beating method is better than the frozen-thawing method in genomic DNA extraction efficiency. In addition, 21 bands in the DGGE pattern with the bead-beating method were further selected, cloned and sequenced. Based on similarity matching, all the sequences formed five major clusters: Actinobacteria; α-, β-, γ-, Proteobacteria ; Bacteriodetes ; Gemmatimonadetes and Acidobacteria . Of the 21 clones obtained from DGGE patterns, YC4 showed 99.7% similarity to Pseudomonas sp. (DQ339153); YC5, YC18 and YC19 showed 99.9 % similarity to Gram-positive bacterium (AB008510), Virgisporangium ochraceum (AB006162) and Micromonospora chalcea (X92613), respectively.     

Complete genomic characterization of a pathogenic A.II strain of Francisella tularensis subspecies tularensis

Francisella tularensis is the causative agent of tularemia, which is a highly lethal disease from nature and potentially from a biological weapon. This species contains four recognized subspecies including the North American endemic F. tularensis subsp. tularensis (type A), whose genetic diversity is correlated with its geographic distribution including a major population subdivision referred to as A.I and A.II. The biological significance of the A.I - A.II genetic differentiation is unknown, though there are suggestive ecological and epidemiological correlations. In order to understand the differentiation at the genomic level, we have determined the complete sequence of an A.II strain (WY96-3418) and compared it to the genome of Schu S4 from the A.I population. We find that this A.II genome is 1,898,476 bp in size with 1,820 genes, 1,303 of which code for proteins. While extensive genomic variation exists between "WY96" and Schu S4, there is only one whole gene difference. This one gene difference is a hypothetical protein of unknown function. In contrast, there are numerous SNPs (3,367), small indels (1,015), IS element differences (7) and large chromosomal rearrangements (31), including both inversions and translocations. The rearrangement borders are frequently associated with IS elements, which would facilitate intragenomic recombination events. The pathogenicity island duplicated regions (DR1 and DR2) are essentially identical in WY96 but vary relative to Schu S4 at 60 nucleotide positions. Other potential virulence-associated genes (231) varied at 559 nucleotide positions, including 357 non-synonymous changes. Molecular clock estimates for the divergence time between A.I and A.II genomes for different chromosomal regions ranged from 866 to 2131 years before present. This paper is the first complete genomic characterization of a member of the A.II clade of Francisella tularensis subsp. tularensis.     

5'-单磷酸腺苷在水和乙醇/水体系中的溶解度模型

以固-液平衡理论溶解度模型、适用于非理想体系的λh方程为理论基础,结合本实验结晶条件,采用静态法测定了5’-单磷酸核苷(5’-AMP)在纯水以及不同配比乙醇/水体系中的溶解度,建立了5’-AMP水和乙醇/水体系的结晶热力学模型。显示该体系属于缔合引起的非理想溶液,并计算水及乙醇/水体系的溶解热和结晶热,为5’-单磷酸腺苷的工业结晶生产提供了热力学数据。     

Na^＋ and Water Uptake in Relation to the Radial Reflection Coefficient of Root in Arrowleaf Saltbush Under Salt Stress

The response of halophyte arrowleaf saltbush (Atriplex triangularis Willd) plants to a gradient of salt stress were investigated with hydroponically cultured seedlings. Under salt stress, both the Na+ uptake into root xylem and negative pressures in xylem vessels increased with the elevation of salinity (up to 500 mol/m3) in the root environment. However, the increment in negative pressures in root xylem far from matches the decrease in the osmotic potential of the root bathing solutions, even when the osmotic potential of xylem sap is taken into consideration. The total water potential of xylem sap in arrowleaf saltbush roots was close to the osmotic potential of root bathing solutions when the salt stress was low, but a progressively increased gap between the water potential of xylem sap and the osmotic potential of root bathing solutions was observed when the salinity in the root environment was enhanced. The maximum gap was 1.4 MPa at a salinity level of 500 mol/m3 without apparent dehydration of the tested plants. This discrepancy could not be explained with the current theories in plant physiology. The radial reflection coefficient of root in arrowleaf saltbush decreased with the enhanced salt stress was and accompanied by an increase in the Na+ uptake into xylem sap. However, the relative Na+ in xylem exudates based on the corresponding NaCl concentration in the root bathing solutions showed a tendency of decrease. The results showed that the reduction in the radial reflection coefficient of roots in the arrowleaf saltbush did not lead to a mass influx of NaCl into xylem when the radial reflection coefficient of the root was considerably small; and that arrowleaf saltbush could use small xylem pressures to counterbalance the salt stresses, either with the uptake of large amounts of salt, or with the development of xylem pressures dangerously negative. This strategy could be one of the mechanisms behind the high resistance of arrowleaf saltbush plants to salt stress.     

Cloning, sequence analysis and identification of a nonsense mutation-mediated mRNA decay of porcine GSTM2 gene

The glutathione S-transferase mu 2 gene （GSTM2） encodes a GST functioning in the elimination of electrophilic compounds and the regulation of cell growth. In this study, the sequence of porcine GSTM2 gene that contains the complete sequence encoding a protein of 218 amino acids was cloned. The deduced amino acid sequence shared 76%, 78% and 76% identity with that of human, mouse and rat, respectively, mRNA expression analysis showed that the porcine GSTM2 gene was expressed at a high level in liver and testis, at a medium level in longissimus dorsi muscle, adipose tissue, spleen and lung, at a low level in kidney, and at a very low level in heart and embryo. A nonsense mutation （CGA→TGA） resulted from C27T substitution in the fifth exon to produce a premature translation termination codon was identified, and it was discovered that nonsense-mediated mRNA decay might have an effect on the regulation of porcine GSTM2 gene expression. This polymorphism was analyzed in Large White, Landrace, Meishan and Qingping pig populations using the Taq I-polymerase chain reaction-restriction fragment length polymorphism method. The result showed that allele C had a higher frequency than allele T in each population.