Solution structure of a BolA-like protein from Mus musculus

The BolA-like proteins are widely conserved from prokaryotes to eukaryotes. The BolA-like proteins seem to be involved in cell proliferation or cell-cycle regulation, but the molecular function is still unknown. Here we determined the structure of a mouse BolA-like protein. The overall topology is alphabetabetaalphaalphabetaalpha, in which beta(1) and beta(2) are antiparallel, and beta(3) is parallel to beta(2). This fold is similar to the class II KH fold, except for the absence of the GXXG loop, which is well conserved in the KH fold. The conserved residues in the BolA-like proteins are assembled on the one side of the protein.     

Membrane translocation of lumenal domains of membrane proteins powered by downstream transmembrane sequences

Translocation of the N-terminus of a type I signal anchor (SA-I) sequence across the endoplasmic reticulum membrane can be arrested by tagging with a streptavidin-binding peptide tag (SBP tag) and trapping by streptavidin. In the present study, we first examine the affinity required for the translocation arrest. When the SBP tag is serially truncated, the ability for arrest gradually decreases. Surface plasmon resonance analysis shows that an interaction as strong as 10⁻⁸ M or a smaller dissociation constant is required for trapping the topogenesis of a natural SA-I sequence. Such truncated tags, however, become effective by mutating the SA-I sequence, suggesting that the translocation motivation is considerably influenced by the properties of the SA-I sequence. In addition, we introduce the SBP tag into lumenal loops of a multispanning membrane protein, human erythrocyte band 3. Among the tagged loops between transmembrane 1 (TM1) and TM8, three loops are trapped by cytosolic streptavidin. These loops are followed by TM sequences possessing topogenic properties, like the SA-I sequence, and translocation of one loop is diminished by insertion of a proline into the following TM sequence. These findings suggest that the translocation of lumenal loops by SA-I–like TM sequences has a crucial role in topogenesis of multispanning membrane proteins.     

Structural basis for the recognition of nucleophosmin-anaplastic lymphoma kinase oncoprotein by the phosphotyrosine binding domain of Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target-2

The nucleophosmin-anaplastic lymphoma kinase (NPM-ALK) fusion oncoprotein, formed by the t(2;5) chromosomal translocation in anaplastic large-cell lymphomas, has constitutive tyrosine kinase activity and interacts with a number of signaling molecules. One of the interacting partners of NPM-ALK is the adaptor protein, Suc1-associated neurotrophic factor-induced tyrosine-phosphorylated target (SNT), and mutations that deprive NPM-ALK of all three of the SNT-binding sites significantly reduced the transforming activity. In this study, the interactions of the three binding sites in NPM-ALK with the phosphotyrosine binding (PTB) domain of SNT-2 were analyzed. First, by isothermal titration calorimetry, we found that the phosphorylation-independent binding site in NPM-ALK interacts with the SNT-2 PTB domain more tightly than the phosphorylation-dependent binding sites. Second, the solution structure of the SNT-2 PTB domain in complex with the nonphosphorylated NPM-ALK peptide was determined by nuclear magnetic resonance spectroscopy. The NPM-ALK peptide interacts with the hydrophobic surface of the PTB domain and intermolecularly extends the PTB β-sheet. This interaction mode is much broader and more extensive than those of the phosphorylation-dependent binding sites. Our results indicate that the higher binding activity of the phosphorylation-independent binding site is caused by additional hydrophobic interactions.     

The variation of REE (rare earth elements) patterns in soil-grown plants: a new proxy for the source of rare earth elements and silicon in plants

Rare earth elements (REEs) in five species of soil-grown plants (Taxodium japonicum, Populus sieboldii, Sasa nipponica, Thea sinensis and Vicia villosa) and in the soil on which each plant grew were determined with an inductively coupled plasma mass spectrometer (ICP-MS) in order to observe the variation in the distribution of REEs and to elucidate their source in soil-grown plants. The plant samples were divided into root (secondary root and main root), trunk (stem) and leaf; the soils into water soluble (soil_{soluble fraction}), HCl and HNO₃ soluble (soil_{non-silicate fraction}) and HF soluble (soil_{silicate fraction}). The REE abundances of samples were compared using REE patterns where the abundances were normalized to those of a chondrite and plotted on a logarithmic scale against the atomic number. All the plants showed similar REE patterns independent of species and location, and a W-shape variation (W-type tetrad effect) and abundance depletion of cerium (negative Ce anomaly) were found in each REE patterns of plants, more conspicuous tetrad effect being observed in HREE (heavier rare earth elements) region than in LREE (lighter rare earth elements) region. The overall variation of REE patterns of each secondary root was not similar to that of soil_{soluble fraction}, but similar to that of soil_{silicate fraction} except for the tetrad effect and Ce anomaly. The REE patterns can be interpreted by the idea that plants of different species take in REEs and Si from different parts in the soil. The results of this study seem to imply that Sasa nipponica and Vicia villosa take in free REEs and Si rather directly from silicate in the soil, and that a majority of REEs and Si in Taxodium japonicum and Thea sinensis are originated from the soluble fraction in the soil.     

Life span and renal morphological characterization of the SAMP1//Ka mouse.

The senescence-accelerated-mouse prone 1 (SAMP1) is considered to be a model of accelerated senility and it also develops severe kidney damage. The SAMP1//Ka mouse is a specific pathogen free (SPF) subline of SAMP1. The present study examined the life span of the SAMP1//Ka mouse and morphologically investigated the kidneys of this animal at 3, 4, 5, 9, 12, 15, 18 and 24 months of age. Males survived for an average of 25 months and females for 28 months. The median lifespan was 18 months for males and 20 for females. Focal cell infiltration and thickening of the basement membrane in the glomerular capsules or tubules appeared from 4 months of age. At 12 months old, glomerular lesions with expansion of the mesangial matrix and thickening of the basement membrane as well as scar lesions in the outer cortex appeared, and amyloid was deposited in the interstitium or glomeruli from 18 months of age. Morphometrically, although the area of the kidney sections was increased at 24 months of age, the diameter of the renal corpuscles, the number of nuclei of the proximal convoluted tubules and the percentage of renal corpuscles with a cuboidal glomerular capsule did not change with age. The results of the present study indicate that the life span of the SAMP1//Ka is increased and that their age-related renal changes differ from those of the original SAMP1.     

Functional discrimination of membrane proteins using machine learning techniques

Background  

Discriminating membrane proteins based on their functions is an important task in genome annotation. In this work, we have analyzed the characteristic features of amino acid residues in membrane proteins that perform major functions, such as channels/pores, electrochemical potential-driven transporters and primary active transporters.     

Neuronal nitric oxide synthase and cyclooxygenase-2 in diabetic nephropathy of type 2 diabetic OLETF rats.

Neuronal nitric oxide synthase (nNOS) and cyclooxygenase-2 (COX-2) regulate the tubuloglomerular feedback (TGF) and renin-angiotensin system (RAS) in the kidney. In type 1 diabetic rats, renal overproduction of these enzymes and their relationship to the pathogenesis of diabetic nephropathy has been demonstrated. In the present study, we histologically and immunohistochemically investigated the kidneys of Otsuka Long-Evans Tokushima Fatty (OLETF) rats, as a model of type 2 diabetes, at 62 weeks of age (chronic phase of diabetes). The kidneys of OLETF rats showed typical diabetic nephropathy. Quantitative scores for glomerulosclerosis and interstitial fibrosis in OLETF rats were significantly higher than those of age-matched control Long-Evans Tokushima Otsuka (LETO) rats. nNOS- and COX-2-positive immunoreactions were observed in the distal tubules and collecting ducts. These reactions appeared to be more widely distributed in OLETF, and the number of nNOS-and COX-2-positive sites in the OLETF were significantly more than those in LETO rats. Expression of renin, angiotensin II, and inducible nitric oxide synthase (iNOS) were also examined immunohistochemically, and no differences between OLETF and LETO rats were observed in the distributions and the number of immunoreactive-sites. In conclusion, the overproduction of nNOS and COX-2 in the kidney of OLETF rats was confirmed, suggesting that the overproduction of nNOS and/or COX-2 does not affect the intrarenal RAS or iNOS production but does affect TGF.