Erythrobacter vulgaris sp. nov., a novel organism isolated from the marine invertebrates

Four yellow-pigmented, gram-negative, chemoorganotrophic aerobic bacteria were isolated from starfish Stellaster equestris (strains 022-2-10T, 022-2-9, and 022-2-12) and soft coral (unidentified species) (strain 022-4-7) collected in the South China Sea. 16S rRNA gene sequence-based analyses of the new organisms revealed that Erythrobacter spp. were the closest relatives and shared the highest similarity of 98.7% to E. citreus, 98.5% to E. flavus, 97.9% to E. litoralis and 97.6% to E. longus. The novel organisms were tolerant to 3-6% NaCl, grew between 10 degrees C and 40 degrees C, and were not able to degrade gelatin, casein, and agar, while degraded Tween 80. Two strains (022-2-9 and 022-2-12) could weakly degrade starch. All strains produced a large pool of carotenoids and did not have Bacteriochlorophyll a. Phosphatidylethanolamine (30-36%), phosphatidylglycerol (39-46%), and phosphatidylcholine (21-27%) were the predominant phospholipids. Sphingoglycolipid was not detected. The major fatty acids were 16:0 (6-11%), 16:1omega7 (12-15%), and 18:1omega7 (46-49%). The two-hydroxy fatty acids, 13:0-2OH, 14:0-2OH, 15:0-2OH, 16:0-2OH were also present. The G + C content of the DNAs ranged from 61 to 62 mol%. The level of DNA similarity among four strains was conspecific and ranged from 94% to 98%. Even though new strains and other species of the genus had rather high level of 16S rRNA gene sequence similarities, DNA-DNA hybridization experiments showed only 33-39% of binding with the DNA of the type strains. On the basis of these results and the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the new organisms be classified as a novel species; the name Erythrobacter vulgaris sp. nov. is proposed. The type strain is 022-2-10T (= KMM 3465T = CIP 107841T).     

Oceanimonas smirnovii sp. nov., a novel organism isolated from the Black Sea

A slightly creamy, melanogenic, gram-negative, aerobic bacterium was isolated from seawater sample collected in the Karadag Natural Reserve of the Eastern Crimea, the Black Sea. The novel organism was chemoorganotrophic, had no obligate requirement in NaCl, tolerated to 12% NaCl, grew between 10 and 45 degrees C, was slightly alkaliphilic, and was not able to degrade starch, gelatin, agar, and Tween 80. 16S rRNA gene sequence-based analyses of the new organism revealed that Oceanimonas doudoroffii ATCC 27123T, Oceanimonas baumanii ATCC 700832T, and Oceanisphaera litoralis DSM 15406T were the closest relatives (similarity around 97%-96%). The G + C content of the DNA of the strain 31-13T was 55.5mol%. Phosphatidylethanolamine (49.0%), phosphatidylglycerol (41.8%), and diphosphatidylglycerol (9.2%) were the predominant phospholipids. The major fatty acids were 16:0 (24.1%), 16:1omega7 (40.3%), and 18:1omega7 (29.2%). On the basis of the significant differences demonstrated in the phenotypic and chemotaxonomic characteristics, it is suggested that the bacterium be classified as a novel species; the name Oceanimonas smirnovii sp. nov. is proposed. The type strain is 31-13T (UCM B-11076T = LMG 22147T = ATCC BAA-899T).     

Diacylglycerols Activate Mitochondrial Cationic Channel(s) and Release Sequestered Ca<Superscript>2+</Superscript>

Mitochondria contribute to cytosolic Ca²⁺ homeostasis through several uptake and release pathways. Here we report that 1,2-sn-diacylglycerols (DAGs) induce Ca²⁺ release from Ca²⁺-loaded mammalian mitochondria. Release is not mediated by the uniporter or the Na⁺/Ca²⁺ exchanger, nor is it attributed to putative catabolites. DAGs-induced Ca²⁺ efflux is biphasic. Initial release is rapid and transient, insensitive to permeability transition inhibitors, and not accompanied by mitochondrial swelling. Following initial rapid release of Ca²⁺ and relatively slow reuptake, a secondary progressive release of Ca²⁺ occurs, associated with swelling, and mitigated by permeability transition inhibitors. The initial peak of DAGs-induced Ca²⁺ efflux is abolished by La³⁺ (1 mM) and potentiated by protein kinase C inhibitors. Phorbol esters, 1,3-diacylglycerols and 1-monoacylglycerols do not induce mitochondrial Ca²⁺ efflux. Ca²⁺-loaded mitoplasts devoid of outer mitochondrial membrane also exhibit DAGs-induced Ca²⁺ release, indicating that this mechanism resides at the inner mitochondrial membrane. Patch clamping brain mitoplasts reveal DAGs-induced slightly cation-selective channel activity that is insensitive to bongkrekic acid and abolished by La³⁺. The presence of a second messenger-sensitive Ca²⁺ release mechanism in mitochondria could have an important impact on intracellular Ca²⁺ homeostasis.     

Strain relief at the active site of phosphoserine aminotransferase induced by radiation damage

The X-ray susceptibility of the lysine-pyridoxal-5'-phosphate Schiff base in Bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 K to 1.3 A resolution, complemented by on-line spectroscopic studies. X-rays induce deprotonation of the internal aldimine, changes in the Schiff base conformation, displacement of the cofactor molecule, and disruption of the Schiff base linkage between pyridoxal-5'-phosphate and the Lys residue. Analysis of the "undamaged" structure reveals a significant chemical strain on the internal aldimine bond that leads to a pronounced geometrical distortion of the cofactor. However, upon crystal exposure to the X-rays, the strain and distortion are relaxed and eventually diminished when the total absorbed dose has exceeded 4.7 x 10(6) Ggamma. Our data provide new insights into the enzymatic activation of pyridoxal-5'-phosphate and suggest that special care should be taken while using macromolecular crystallography to study details in strained active sites.     

Ric-3 promotes functional expression of the nicotinic acetylcholine receptor alpha7 subunit in mammalian cells

Expression of functional, recombinant alpha7 nicotinic acetylcholine receptors in several mammalian cell types, including HEK293 cells, has been problematic. We have isolated the recently described human ric-3 cDNA and co-expressed it in Xenopus oocytes and HEK293 cells with the human nicotinic acetylcholine receptor alpha7 subunit. In addition to confirming the previously reported effect on alpha7 receptor expression in Xenopus oocytes we demonstrate that ric-3 promotes the formation of functional alpha7 receptors in mammalian cells, as determined by whole cell patch clamp recording and surface alpha-bungarotoxin binding. Upon application of 1 mm nicotine, currents were undetectable in HEK293 cells expressing only the alpha7 subunit. In contrast, co-expression of alpha7 and ric-3 cDNAs resulted in currents that averaged 42 pA/pF with kinetics similar to those observed in cells expressing endogenous alpha7 receptors. Immunoprecipitation studies demonstrate that alpha7 and ric-3 proteins co-associate. Additionally, cell surface labeling with biotin revealed the presence of alpha7 protein on the plasma membrane of cells lacking ric-3, but surface alpha-bungarotoxin staining was only observed in cells co-expressing ric-3. Thus, ric-3 appears to be necessary for proper folding and/or assembly of alpha7 receptors in HEK293 cells.     

S3-12, Adipophilin, and TIP47 package lipid in adipocytes

Animals have evolved mechanisms to maintain circulating nutrient levels when energy demands exceed feeding opportunities. Mammals store most of their energy as triacylglycerol in the perilipin-coated lipid droplets of adipocytes. How newly synthesized triacylglycerol is delivered to perilipin-coated lipid droplets is poorly understood. Perilipin is a member of the evolutionarily related family of PAT proteins (Perilipin, Adipophilin, TIP47), which is defined by sequence similarity and association with lipid droplets. We previously showed that S3-12, which is also a member of this family, associates with a separate pool of lipid droplets that emerge when triacylglycerol storage is driven by adding oleate to the culture medium of adipocytes. Our current data extend these findings to demonstrate that nascent lipid droplets emerge with a coat composed of S3-12, TIP47, and adipophilin. After 100 min of oleate treatment, the nascent lipid droplets are more heterogeneous: S3-12 and TIP47 coat smaller, peripheral droplets and adipophilin coats a more medial population of droplets. Fractionation of untreated and oleate-treated adipocytes shows oleate-dependent redistribution of TIP47 and adipophilin from cytosolic fractions to the lipid droplet fraction. Inhibition of protein synthesis with cycloheximide does not block the oleate-induced formation of the nascent lipid droplets, nor does it prevent TAG accumulation. We suggest that the non-lipid droplet pools of S3-12, adipophilin, and TIP47 constitute a ready reservoir of coat proteins to permit rapid packaging of newly synthesized triacylglycerol and to maximize energy storage during nutrient excess.     

Stability and DNA binding ability of the DNA binding domains of interferon regulatory factors 1 and 3

The thermodynamic properties and DNA binding ability of the N-terminal DNA binding domains of interferon regulatory factors IRF-1 (DBD1) and IRF-3 (DBD3) were studied using microcalorimetric and optical methods. DBD3 is significantly more stable than DBD1: at 20 degrees C the Gibbs energy of unfolding of DBD3 is -28.6 kJ/mol, which is 2 times larger than that of DBD1, -14.9 kJ/mol. Fluorescence anisotropy titration experiments showed that at this temperature the association constants with the PRDI binding site are 1.1 x 10(6) M(-)(1) for DBD1 and 3.6 x 10(6) M(-)(1) for DBD3, corresponding to Gibbs energies of association of -34 and -37 kJ/mol, respectively. However, the larger binding energy of DBD3 is due to its larger electrostatic component, while its nonelectrostatic component is smaller than that of DBD1. Therefore, DBD1 appears to have more sequence specificity than DBD3. Binding of DBD1 to target DNA is characterized by a substantially larger negative enthalpy than binding of DBD3, implying that the more flexible structure of DBD1 forms tighter contacts with DNA than the more rigid structure of DBD3. Thus, the strength of the DBDs' specific association with DNA is inversely related to the stability of the free DBDs.     

Selection of control genes for quantitative RT-PCR based on microarray data

Use of internal reference gene(s) is necessary for adequate quantification of target gene expression by RT-PCR. Herein, we elaborated a strategy of control gene selection based on microarray data and illustrated it by analyzing endomyocardial biopsies with acute cardiac rejection and infection. Using order statistics and binomial distribution we evaluated the probability of finding low-varying genes by chance. For analysis, the microarray data were divided into two sample subsets. Among the first 10% of genes with the lowest standard deviations, we found 14 genes common to both subsets. After normalization using two selected genes, high correlation was observed between expression of target genes evaluated by microarray and RT-PCR, and in independent dataset by RT-PCR (r = 0.9, p < 0.001). In conclusion, we showed a simple and reliable strategy of selection and validation of control genes for RT-PCR from microarray data that can be easily applied for different experimental designs and tissues.