Structure and function of WD40 domain proteins

The WD40 domain exhibits a β-propeller architecture, often comprising seven blades. The WD40 domain is one of the most abundant domains and also among the top interacting domains in eukaryotic genomes. In this review, we will discuss the identification, definition and architecture of the WD40 domains. WD40 domain proteins are involved in a large variety of cellular processes, in which WD40 domains function as a protein-protein or protein-DNA interaction platform. WD40 domain mediates molecular recognition events mainly through the smaller top surface, but also through the bottom surface and sides. So far, no WD40 domain has been found to display enzymatic activity. We will also discuss the different binding modes exhibited by the large versatile family of WD40 domain proteins. In the last part of this review, we will discuss how post-translational modifications are recognized by WD40 domain proteins.

Examination of Geographical, Clinical and Intrahost Variations in the 3' Repeat Region of CagA Gene in Helicobacter pylori

The size variation of the cytoxin-associated protein (cagA), which is dependent on the 3' repeat region (3'RR) of the cagA gene, is known to play a crucial role in the pathogenesis of Helicobacter pylori infection. The present study evaluated the relationship between the 3'RR variation and the geographic distribution, clinical manifestations, and locations of colonization in the stomach. We evaluated the 3'RR of H. pylori isolates from 78 patients with gastric cancer, peptic ulcer, and non-ulcer dyspepsia from Japan, Hong Kong, India, and the United States and assessed the variations of 3'RR according to the geographical and clinical characteristics. Sixty eight (87.2%) patients had the same 650 bp band without geographical differences. The frequency of polymorphisms in the 3'RR did not differ when compared to the clinical manifestations (P=0.868). The length of 3'RR did not differ by location of colonization. In conclusion, the 3'RR variation of cagA gene is not associated with the geographical and clinical characteristics of the patients studied.

Evaluation of first and second Markov chains sensitivity and specificity as statistical approach for prediction of sequences of genes in virus double strand DNA genomes

Growing amount of information on biological sequences has made application of statistical approaches necessary for modeling and estimation of their functions. In this paper, sensitivity and specificity of the first and second Markov chains for prediction of genes was evaluated using the complete double stranded DNA virus. There were two approaches for prediction of each Markov Model parameter, initial probability and transition matrix, which together with the first and second Markov chains resulted in development of eight algorithms for gene prediction. In order to compare the algorithms, a sensitivity and specificity repeated measure with 3 factors [Markov model, type of selection and estimation of transition probabilities] were utilized. Results significantly revealed that the second order Markov chain had more sensitivity and specificity than the first order Markov chain, with p-Value < 0.001. By adding the covariates, the number of annotated genes per length of genome as well as the A and T and C and G contents of genomes in the repeated measure showed an insignificant difference between the sensitivities of the two Markov models [0.407, 0.071 and 0.120, respectively]. It was also proved that gene base-pairs per genome length and A and T contents of the genome, as model covariates, resulted in significant differences between the specificities of the Markov models

Identification and expression analysis of two Arabidopsis LRP-protein encoding genes responsive to some abiotic stresses

Two Arabidopsis thaliana genes, psr9.2 and psr 9.4 appeared to be highly similar to a phosphate-starved induced gene, psr9, isolated from Brassica nigra suspension cells. Sequence analysis classified the encoded polypeptides as members of leucine-rich repeat [LRR] proteins superfamily. The sequence of psr9 proteins comprise a unique N-terminal region encompassing a coiled-coil structure proceeding eleven LRRs along the C-terminal. Expression pattern analysis showed the responsiveness of these genes to various environmental conditions. Although both psr9 genes, psr9.2 and psr9.4, are expressed throughout the plant, the expression of psr9.2 was higher in the root whereas psr9.4 expression was prominent in the shoot. The expression levels were increased proportional to the duration of phosphate deprivation treatment. Plants exposed to cold temperature expressed both genes at high levels in both roots and shoots. In contrast, heat shock increased the expression levels of both genes in the shoots while reducing it in roots. High-salt treatment upregulated the expression of psr9 genes only in the roots. These data may suggest distinct roles for psr9 genes during plant response to various environmental conditions

Biological activity of the virulence factor cagA of Helicobacter pylori / 中华医学杂志(英文版)

<p><b>BACKGROUND</b>China is one of the countries with the highest incidence of H. pylori and more than 9090 isolates possessed the cagA gene. This study was to evaluate the biological activity of the H. pylori virulence factor cagA isolated from Chinese patients.</p><p><b>METHODS</b>cagA DNA fragments were amplified from the genomic DNA and subsequently cloned into the mammalian expression vector for cell transfection and DNA sequencing. cagA protein, phosphorylated-tyrosine cagA and the complex of cagA precipitated with SHP-2 were identified respectively by western blot in the crude cell lysate from conditionally immortalized gastric epithelial cells at 48 hours after transfection with cagA DNA. In addition, the ability of induction of scattering phenotype was examined after transient expression of cagA in AGS cells.</p><p><b>RESULTS</b>The C-terminal half of cagA contained only one repeated sequence and three tandem five-amino-acid motifs glutamic acid-proline-isoleucine-tyrosine-alanine (EPIYA). Moreover, the amino acid sequence of D2 region in repeated sequence was aspartic acid-phenylanaline-aspartic acid (D-F-D) which was significantly distinguished from the three repeated sequences and aspartic acid-aspartic adid-leucine (D-D-L) in the western standard strain NCTC11637. Western blot revealed that cagA became phosphorylated in tyrosine site and bound with SHP-2 after transient expression of cagA DNA in gastric epithelial cells. Transient expression of cagA in AGS cells showed that cagA was able to induce the elongation phenotype although to a lesser extent than western strains.</p><p><b>CONCLUSIONS</b>cagA perturbs cell signaling pathways by binding with SHP-2. However, significant difference exists in amino acid sequence and biological function of cagA in Chinese compared with those of western countries.</p>

Expression and purification of heptad repeat region of the mumps virus F protein and analysis of characteristics / 生物工程学报

Two Heptad repeat motifs (HR1 and HR2) from paramyxoviruses F protein could form thermostable heterodimers containing high alpha-helix while virus infected host cell. Following that the viral membrane and the host cell membrane were juxtaposed, which leads to membrane fusion. Mumps virus (MuV) is a member of the genus Rubulavirus in the family of Paramyxoviridae. MuV could use similar infection mechanism as well as other paramyxoviruses. In this study the HR1 and HR2 regions of MuV F protein were predicted by a computer program and expressed in E. coli with the GST fusion expression system. The GST fusion or GST-removed proteins were purified with Gluthathion Sepharose 4B Column. GST pull-down experiment suggested the interaction of HR1 and HR2 peptides, and analysis of gel filtration showed two peptides could form multimer, which indicates that the HR regions of MuV F protein may play an important role in virus fusion.