Sak serine-threonine kinase acts as an effector of Tec tyrosine kinase

The murine sak gene encodes a putative serine-threonine kinase which is homologous to the members of the Plk/Polo family. Although Sak protein is presumed to be involved in cell growth mechanism, efforts have failed to demonstrate its kinase activity. Little has been, therefore, elucidated how Sak is regulated and how Sak contributes to cell proliferation. Tec is a cytoplasmic protein-tyrosine kinase (PTK) which becomes activated by the stimulation of cytokine receptors, lymphocyte surface antigens, heterotrimeric G protein-linked receptors, and integrins. To clarify the in vivo function of Tec, we have tried to isolate the second messengers of Tec by using the yeast two-hybrid screening. One of such Tec-binding proteins turned out to be Sak. In human kidney 293 cells, Sak became tyrosine-phosphorylated by Tec, and the serine-threonine kinase activity of Sak was detected only under the presence of Tec, suggesting Sak to be an effector molecule of Tec. In addition, Tec activity efficiently protects Sak from the "PEST" sequence-dependent proteolysis. Internal deletion of the PEST sequences led to the stabilization of Sak proteins, and expression of these mutants acted suppressive to cell growth. Our data collectively supports a novel role of Sak acting in the PTK-mediated signaling pathway.     

Gene rearrangements in snake mitochondrial genomes: highly concerted evolution of control-region-like sequences duplicated and inserted into a tRNA gene cluster

Mitochondrial DNA (mtDNA) regions corresponding to two major tRNA gene clusters were amplified and sequenced for the Japanese pit viper, himehabu. In one of these clusters, which in most vertebrates characterized to date contains three tightly connected genes for tRNA(Ile), and tRNA(Gln), and tRNA(Met), a sequence of approximately 1.3 kb was found to be inserted between the genes for tRNA(Ile) and tRNA(Gln). The insert consists of a control-region-like sequence possessing some conserved sequence blocks, and short flanking sequences which may be folded into tRNA(Pro), tRNA(Phe), and tRNA(Leu) genes. Several other snakes belonging to different families were also found to possess a control-region-like sequence and tRNA(Leu) gene between the tRNA(Ile)and tRNA(Gln) genes. We also sequenced a region surrounded by genes for cytochrome b and 12S rRNA, where the control region and genes for tRNA(Pro) and tRNA(Phe) are normally located in the mtDNAs of most vertebrates. In this region of three examined snakes, a control-region- like sequence exists that is almost completely identical to the one found between the tRNA(Ile) and tRNA(Gln) genes. The mtDNAs of these snakes thus possess two nearly identical control-region-like sequences which are otherwise divergent to a large extent between the species. These results suggest that the duplicate state of the control-region- like sequences has long persisted in snake mtDNAs, possibly since the original insertion of the control-region-like sequence and tRNA(Leu) gene into the tRNA gene cluster, which occurred in the early stage of the divergence of snakes. It is also suggested that the duplicated control-region-like sequences at two distant locations of mtDNA have evolved concertedly by a mechanism such as frequent gene conversion. The secondary structures of the determined tRNA genes point to the operation of simplification pressure on the T psi C arm of snake mitochondrial tRNAs.      

GTOP: a database of protein structures predicted from genome sequences

Large-scale genome projects generate an unprecedented number of protein sequences, most of them are experimentally uncharacterized. Predicting the 3D structures of sequences provides important clues as to their functions. We constructed the Genomes TO Protein structures and functions (GTOP) database, containing protein fold predictions of a huge number of sequences. Predictions are mainly carried out with the homology search program PSI-BLAST, currently the most popular among high-sensitivity profile search methods. GTOP also includes the results of other analyses, e.g. homology and motif search, detection of transmembrane helices and repetitive sequences. We have completed analyzing the sequences of 41 organisms, with the number of proteins exceeding 120 000 in total. GTOP uses a graphical viewer to present the analytical results of each ORF in one page in a ‘color-bar’ format. The assigned 3D structures are presented by Chime plug-in or RasMol. The binding sites of ligands are also included, providing functional information. The GTOP server is available at http://spock.genes.nig.ac.jp/~genome/gtop.html.     

Songbird tap dancing produces non-vocal sounds*

Vocalizations have been elucidated in previous songbird studies, whereas less attention has been paid to non-vocal sounds. In the blue-capped cordon-bleu (Uraeginthus cyanocephalus), both sexes perform courtship displays that are accompanied by singing and distinct body movements (i.e. dance). Our previous study revealed that their courtship bobbing includes multiple rapid steps. This behaviour is quite similar to human tap dancing, because it can function as both visual and acoustic signals. To examine the acoustic signal value of such steps, we tested if their high-speed step movements produce non-vocal sounds that have amplitudes similar to vocal sounds. We found that step behaviour affected step sound amplitude. Additionally, the dancing step sounds were substantially louder than feet movement sounds in a non-courtship context, and the amplitude range overlapped with that of song notes. These results support the idea that in addition to song cordon-bleus produce acoustic signals with their feet.     

Membrane integration of the second transmembrane segment of band 3 requires a closely apposed preceding signal-anchor sequence

We have investigated the topogenic rules of multispanning membrane proteins using erythrocyte band 3. Here, the fine structural requirements for the correct disposition of its second transmembrane segment (TM2) were assessed. We made fusion proteins where TM1 and the loop sequence preceding TM2 were changed and fused to prolactin. They were expressed in a cell-free system supplemented with rough microsomal membrane, and their topologies on the membrane were assessed by protease sensitivity and N-glycosylation. TM1 was demonstrated to be a signal-anchor sequence that mediates translocation of the downstream portion, and thus TM2 should be responsible to halt the translocation to acquire TM topology. When the loop between TM1 and TM2 was elongated, however, TM2 was readily translocated through the membrane and not integrated. For the membrane integration of TM2, TM2 must be in close proximity to TM1. The TM1 can be replaced with another signal-anchor sequence with a long hydrophobic segment but not with a signal sequence with shorter hydrophobic stretch. The length of the hydrophobic segment affected final topology of TM2. We concluded that the two TM segments work synergistically within the translocon to acquire the correct topology and that the length of the preceding signal sequence is critical for stable transmembrane assembly of TM2. We propose that direct interaction among the TM segments is one of the critical factors for the transmembrane topogenesis of multispanning membrane proteins.     

Dual effects of (D-Ala2,Met5)-enkephalinamide on CRF and ACTH secretion

An intra-third ventricular administration of (D-Ala2,Met5)-enkephalinamide (DALA) did not elevate plasma ACTH and corticosterone levels in unanesthetized freely moving rats, but intra-third ventricular administration of DALA and methionine (Met)-enkephalin potentiated a mild stress (hanging for 10 or 30 sec)-induced plasma ACTH and corticosterone elevations in unanesthetized freely moving rats. DALA and Met-enkephalin seemed to stimulate CRF release from the median eminence to increase plasma ACTH, as the CRF concentration in the median eminence area was reduced after injection in these stressed rats. When hypothalamic tissues were perifused in vitro, DALA (1-100 ng/ml) reduced the release of CRF. These results suggest that the opiates seem to have a dual effect on the CRF-ACTH system depending on which action overrides the other.     

Development of Serum Glycoproteomic Profiling Technique; Simultaneous Identification of Glycosylation Sites and Site-Specific Quantification of Glycan Structure Changes

Characterization and interpretation of disease-associated alterations of protein glycosylation are the central aims of the emerging glycoproteomics projects, which are expected to lead to more sensitive and specific diagnosis and improve therapeutic outcomes for various diseases. Here we report a new approach to identify carbohydrate-targeting serum biomarkers, termed isotopic glycosidase elution and labeling on lectin-column chromatography (IGEL). This technology is based on glycan structure-specific enrichment of glycopeptides by lectin-column chromatography and site-directed tagging of N-glycosylation sites by ¹⁸O during the elution with N-glycosidase. The combination of IGEL with 8-plex isobaric tag for relative and absolute quantitation (iTRAQ) stable isotope labeling enabled us not only to identify N-glycosylation sites effectively but also to compare glycan structures on each glycosylation site quantitatively in a single LC/MS/MS analysis. We applied this method to eight sera from lung cancer patients and controls, and finally identified 107 glycopeptides in their sera, including A2GL_Asn151, A2GL_Asn290, CD14_Asn132, CO8A_Asn417, C163A_Asn64, TIMP1_Asn30, and TSP1_Asn1049 which showed the significant change of the affinity to Concanavalin A (ConA) lectin between the lung cancer samples and the controls (p < 0.05 and more than twofold change). These screening results were further confirmed by the conventional lectin-column chromatography and immunoblot analysis using additional serum samples. Our novel methodology, which should be valuable for diverse biomarker discoveries, can provide high-throughput and quantitative profiling of glycan structure alterations.Glycan structure variations often show highly organ-specific manners (1, 2), as well as those manners that correlate with diverse disease states, (3, 4) e.g., cancer and inflammation. Thus, the carbohydrates are currently attracting a great deal of attention as specific targets of cancer biomarkers and therapy (5). In fact, certain changes of glycan structures are already in clinical use as serum biomarkers, such as AFP-L3 (6), and glycosylation at the specific site of therapeutic antibody proved to be essential for its therapeutic effect (7). Advances in proteomic technologies and analysis have stimulated a great interest in application of MS to identify glycosylation sites (8, 9) or analyze glycan structures (10, 11) from various biological specimens, but the comprehensive techniques which allow quantitative profiling of glycan structures on each glycosylation site have not been developed.The two major issues facing recent glycoproteomic studies are the difficulties in glycopeptide-specific enrichment tools involving lectin-column chromatography and the detection of glycopeptides in mass spectrometers. In the conventional lectin-column chromatography experiments, glycoprotein enrichment from complicated protein mixtures, such as human sera, resulted in a heavy contamination of hapten sugar, salts, and nonspecific proteins caused by protein-protein interactions of serum proteins (12). Even when the digested peptide mixture was subjected to the lectin-column chromatography, salt contamination and the eluting sugar-dependent biases of elution efficiency were inevitable. Moreover, the straightforward analysis of the eluted glycopeptides by MS was hardly possible without further deglycosylation and desalting steps.In this study we report our new approach for the identification of carbohydrate-targeting biomarkers, termed isotopic glycosidase elution and labeling on lectin-column chromatography (IGEL),¹ which is based on glycan structure-specific enrichment of glycopeptides by lectin- column chromatography and site-directed labeling of N-glycosylation sites by water-¹⁸O during the elution with N-glycosidase. We combined this method with 8-plex isotobaric tag for relative and absolute quantitation (iTRAQ) labeling for relative quantification of glycopeptides and applied them to search for carbohydrate-targeting serum biomarkers in lung cancer patient sera.     

The basis of the alkalophilic property of a species of bacillus.

An alkalophilic bacterium belonging to the genus Bacillus was isolated from an indigo ball. The bacterium exhibited a maximum growth rate at pH 10-0 TO 10-5. The incorporation of 14C-labelled amino acids or [14C]uracil, uptake of 14C-labelled alpha-amino isobutyric acid into the bacterium and oxygen consumption of the bacterium with amino acids as substrates were all maximum at pH 9-0 to 10-5. The uptake of [U-14C]glucose into the organism and oxygen consumption with carbohydrates, on the other hand, showed little variation of rate in the pH 8 to 10 region. The oxygen consumption of intact bacteria or protoplasts in culture medium was maximum at pH 10. The membrane of the bacterium oxidized NADH maximally at pH 7-5, and ATPase bound to the membrane exhibited maximum activity at pH 7.L-Lactate, L-alanine and malate dehydrogenases in the soluble fraction exhibited maximum activities at pH 7-4 to 8-4. The alkalophilic property of the bacterium may be due to the behaviour of the membrane towards charged substances admitted into the organisms.