Biomedical subjects

Daisuke Sasaki

Publications and source records attributed to Daisuke Sasaki.

22 records · Page 2Linked to original sources

PubMed2003

Occurrence, horizontal transfer and degeneration of VDE intein family in Saccharomycete yeasts.

VDE is a homing endonuclease gene originally discovered as an intervening element in VMA1s of Saccharomyces cerevisiae. There have been two independent subfamilies of VDE, one from S. cerevisiae strain X2180-1A and the other from Saccharomyces sp. DH1-1A in the host VMA1 gene, and they share the identity of 96.3%. In order to search the occurrence, intra/interspecies transfer and molecular degeneration of VDE, complete sequences of VMA1 in 10 strains of S. cerevisiae, eight species of saccharomycete yeasts, Candida glabrata and Kluyveromyces lactis were determined. We found that six of 10 S. cerevisiae strains contain VDEs 99.7-100% identical to that of the strain X2180-1A, one has no VDE, whereas the other three harbour VDEs 100% identical to that of the strain DH1-1A. S. carlsbergensis has two VMA1s, one being 99.8% identical to that of the strain X2180-1A with VDE 100% identical to that of the strain DH1-1A and the other containing the same VMA1 in S. pastorianus with no VDE. This and other evidence indicates that intra/interspecies transmissions of VDEs have occurred among saccharomycete yeasts. Phylogenetic analyses of VMA1 and VDE suggest that the S. cerevisiae VDEs had branched earlier than other VDEs from an ancestral VDE and had invaded into the host loci as relatively late events. The two VDEs seemed to degenerate in individual host loci, retaining their splicing capacity intact. The degeneration of the endonuclease domains was distinct and, if compared, its apparent rate was much faster than that of the protein-splicing domains.

Amino Acid Substitution↗

PubMed2003

Targeting a complex transcriptome: the construction of the mouse full-length cDNA encyclopedia.

We report the construction of the mouse full-length cDNA encyclopedia,the most extensive view of a complex transcriptome,on the basis of preparing and sequencing 246 libraries. Before cloning,cDNAs were enriched in full-length by Cap-Trapper,and in most cases,aggressively subtracted/normalized. We have produced 1,442,236 successful 3'-end sequences clustered into 171,144 groups, from which 60,770 clones were fully sequenced cDNAs annotated in the FANTOM-2 annotation. We have also produced 547,149 5' end reads,which clustered into 124,258 groups. Altogether, these cDNAs were further grouped in 70,000 transcriptional units (TU),which represent the best coverage of a transcriptome so far. By monitoring the extent of normalization/subtraction, we define the tentative equivalent coverage (TEC),which was estimated to be equivalent to >12,000,000 ESTs derived from standard libraries. High coverage explains discrepancies between the very large numbers of clusters (and TUs) of this project,which also include non-protein-coding RNAs,and the lower gene number estimation of genome annotations. Altogether,5'-end clusters identify regions that are potential promoters for 8637 known genes and 5'-end clusters suggest the presence of almost 63,000 transcriptional starting points. An estimate of the frequency of polyadenylation signals suggests that at least half of the singletons in the EST set represent real mRNAs. Clones accounting for about half of the predicted TUs await further sequencing. The continued high-discovery rate suggests that the task of transcriptome discovery is not yet complete.

Animals↗

PubMed2002

Myosin light chain 2 modulates MgADP-induced contraction in rabbit skeletal and bovine cardiac skinned muscle.

Skinned skeletal and cardiac muscle fibres can be activated by MgADP in the presence of MgATP without Ca2+; the isometric tension is developed in a sigmoidal manner with the addition of MgADP under relaxing conditions. The critical concentrations of MgADP for this MgADP-induced contraction are about 7.5 and 2.6 mM for skeletal and cardiac muscle fibres, respectively. To investigate whether muscle regulatory proteins, myosin light chain 2 (LC2) and troponin C (TnC), play a part in the MgADP-induced contraction, these proteins were partly extracted by treatment with trans-1,2-cyclohexanediamine-N,N,N',N'-tetraacetic acid (CDTA), a chelater of divalent cations, and the MgADP-tension relationship was examined in rabbit psoas and bovine cardiac skinned fibres. We found that the sigmoidal MgADP-tension relationship became hyperbolic after a partial extraction of LC2 (about 30 %) and TnC (about 70 %). Reconstitution with LC2 restored the sigmoidal MgADP-tension relationship of control fibres almost fully in both skeletal and cardiac fibres, whereas reconstitution with TnC alone had no effect. Furthermore, cardiac fibres reconstituted with skeletal LC2 exhibited an MgADP-tension relationship intermediate between skeletal and cardiac fibres. The partial extraction of LC2 and TnC resulted in a reduction of the inhibitory effect of inorganic phosphate (P(i)) on the MgADP-activated tension. Reconstitution with LC2 restored the original P(i)-tension relationship, whereas reconstitution with TnC had no effect. In other words, extraction of LC2 apparently increased the affinity of myosin for MgADP but decreased the affinity for P(i). These results demonstrate that LC2 modulates MgADP-induced activation of actomyosin interaction.

Adenosine Diphosphate↗

PubMed2002

Elementary steps of the cross-bridge cycle in bovine myocardium with and without regulatory proteins.

The role of regulatory proteins in the elementary steps of the cross-bridge cycle in bovine myocardium was investigated. The thin filament was selectively removed by gelsolin and the actin filament was reconstituted without tropomyosin or troponin. Further reconstitution was achieved by adding tropomyosin and troponin. The effects of MgATP and phosphate (Pi) on the rate constants of exponential processes were studied in control, actin filament-reconstituted, and thin filament-reconstituted myocardium at pCa < or = 4.66, pH 7.00, 25 degrees C. In control myocardium, the MgATP association constant was 9.1 +/- 1.3 mM(-1), and the Pi association constant 0.14 +/- 0.04 mM(-1). The equilibrium constant of the cross-bridge detachment step was 2.6 +/- 0.4, and the equilibrium constant of the force generation step was 0.59 +/- 0.04. In actin filament-reconstituted myocardium without regulatory proteins, the MgATP association constant was approximately the same, and the Pi association constant increased to 2.8x. The equilibrium constant of cross-bridge detachment decreased to 0.2x, but the equilibrium constant of the force generation step increased to 4x. These kinetic constants regained control values after reconstitution of the thin filament. These results indicate that tension/cross-bridge in the presence of regulatory proteins is approximately 1.5-1.7x of that in the absence of regulatory proteins. These results further indicate that regulatory proteins promote detachment of cross-bridges.

Actins↗