Kinetic Analysis of Conformational Changes of GroEL Based on the Fluorescence of Tyrosine 506

The conformational changes of GroEL during the ATPase cycle in the presence of GroES were studied by measuring the fluorescence intensity time course of intrinsic tyrosine Y506, which is located near the nucleotide-binding site. A GroEL solution containing GroES was mixed with an ATP solution to initiate the reaction cycle. The tyrosine fluorescence intensity relative to that without the nucleotide reached 112% within the dead time of the apparatus (>15 s^?1) and further increased to 123% at 0.57 s^?1 followed by a decrease to 102% at 0.32 s^?1. An initial conformational change and a second intermediate state were expected to occur in ATP-bound GroEL because similar changes were observed for the ATPase-deficient D398A mutant. The conformational change to the third intermediate state corresponded to a process during or after ATP hydrolysis because D398A had no decreasing phase. The second intermediate state before ATP hydrolysis was characterized for the first time.     

Involvement of Two Plasmids in Fenitrothion Degradation by Burkholderia sp. Strain NF100

A bacterium capable of utilizing fenitrothion (O,O-dimethyl O-4-nitro-m-tolyl phosphorothioate) as a sole carbon source was isolated from fenitrothion-treated soil. This bacterium was characterized taxonomically as being a member of the genus Burkholderia and was designated strain NF100. NF100 first hydrolyzed an organophosphate bond of fenitrothion, forming 3-methyl-4-nitrophenol, which was further metabolized to methylhydroquinone. The ability to degrade fenitrothion was found to be encoded on two plasmids, pNF1 and pNF2.     

Soluble CD26/dipeptidyl peptidase IV induces T cell proliferation through CD86 up-regulation on APCs.

CD26 is a T cell costimulatory molecule with dipeptidyl peptidase IV enzyme activity in its extracellular region. We have previously reported that the addition of soluble CD26 (sCD26) resulted in enhanced proliferation of peripheral blood T lymphocytes induced by the recall Ag, tetanus toxoid (TT). However, the mechanism involved in this immune enhancement has not yet been elucidated. In this paper, we demonstrate that the enhancing effect of sCD26 on TT-induced T cell proliferation occurred in the early stages of immune response. The cells directly affected by exogenously added sCD26 are the CD14-positive monocytes in the peripheral blood. Mannose-6 phosphate interfered with the uptake of sCD26 into monocytes, suggesting that mannose-6 phosphate/insulin-like growth factor II receptor plays a role in the transportation of sCD26 into monocytes. When sCD26 was added after Ag presentation had taken place, enhancement in TT-induced T cell proliferation was not observed. In addition, enhancement of TT-mediated T cell proliferation by sCD26 does not result from trimming of the MHC-bound peptide on the surface of monocytes. Importantly, we also showed that exogenously added sCD26 up-regulated the expression of the costimulatory molecule CD86 on monocytes through its dipeptidyl peptidase IV activity, and that this increased expression of CD86 was observed at both protein and mRNA level. Therefore, our findings suggest that sCD26 enhances T cell immune response to recall Ag via its direct effect on APCs.     

Smc5/6-mediated regulation of replication progression contributes to chromosome assembly during mitosis in human cells

The structural maintenance of chromosomes (SMC) proteins constitute the core of critical complexes involved in structural organization of chromosomes. In yeast, the Smc5/6 complex is known to mediate repair of DNA breaks and replication of repetitive genomic regions, including ribosomal DNA loci and telomeres. In mammalian cells, which have diverse genome structure and scale from yeast, the Smc5/6 complex has also been implicated in DNA damage response, but its further function in unchallenged conditions remains elusive. In this study, we addressed the behavior and function of Smc5/6 during the cell cycle. Chromatin fractionation, immunofluorescence, and live-cell imaging analyses indicated that Smc5/6 associates with chromatin during interphase but largely dissociates from chromosomes when they condense in mitosis. Depletion of Smc5 and Smc6 resulted in aberrant mitotic chromosome phenotypes that were accompanied by the abnormal distribution of topoisomerase IIα (topo IIα) and condensins and by chromosome segregation errors. Importantly, interphase chromatin structure indicated by the premature chromosome condensation assay suggested that Smc5/6 is required for the on-time progression of DNA replication and subsequent binding of topo IIα on replicated chromatids. These results indicate an essential role of the Smc5/6 complex in processing DNA replication, which becomes indispensable for proper sister chromatid assembly in mitosis.     

A Dominant Trait Linked to Chromosome 1 in DBA/2 Mice for the Resistance to Autoimmune Gastritis Appears in Bone Marrow Cells

Neonatal thymectomy (NTx) induces autoimmune gastritis (AIG) in BALB/c mice, a model for human type A chronic atrophic gastritis, but not in DBA/2 mice and rarely in CDF1 mice (a hybrid of BALB/c and DBA/2 mice). The aim of this study was to clarify the mechanisms of AIG-resistance in mice bearing the dominant trait of DBA/2. Linkage groups associated with, and cells related to AIG resistance were examined with CDF1-BALB/c backcrosses. Intracellular staining and flow-cytometric bead array for several cytokines were performed on NTx BALB/c mice and NTx DBA/2-chimeric BALB/c mice receiving DBA/2-bone marrow cells. In NTx BALB/c mice, IFN-γ-secreting CD4⁺ T cells were increased, but not in NTx DBA/2 mice. Because Vβ6⁺ T cell-bearing mice of half of their backcrosses developed AIG, but the other half of Vβ6⁺ T cell-negative mice developed scarcely, resistance for AIG generation is associated with the presence of the Mls-1a locus on chromosome 1 in DBA/2 mice, which deletes Vβ6⁺ T cells. NTx DBA/2-chimera BALB/c mice showed dominant production of IL-10 and resistance for AIG, although the deletion of Vβ6⁺ T cells was found not to be a cause of AIG-resistance from Mls-1a locus segregation experiments. Although NTx DBA/2-chimeric BALB/c mice did not suffer from AIG, they brought immediate precursors of T cells for AIG. It is concluded that DBA/2 mice generate bone marrow-derived cells that produce anti-inflammatory cytokines to prevent the activation of AIG-T cells.     

Identification and characterization of a novel gene family YPEL in a wide spectrum of eukaryotic species

During comprehensive sequence analysis of human chromosome 22, we identified a novel gene family consisting of five members (YPEL1 through YPEL5) which has high homology with Drosophila yippee gene. We cloned and sequenced cDNAs for all five genes and determined their exon/intron organization. These YPEL genes showed high homology (43.8-96.6%) at amino acid sequence level among them. Mouse counterparts (Ypel1 through Ypel5) were also identified in the syntenic region of mouse chromosomes and their cDNAs were cloned and sequenced. Each of five pairs of human/mouse orthologs revealed extremely high homology. Thus, we named these genes as members of YPEL gene family. We searched YPEL family genes from the public databases, and found 100 genes from 68 species including animals, plants and fungi. Amino acid sequences of these 100 YPEL proteins were extremely similar and a consensus sequence of C-X(2)-C-X(19)-G-X(3)-L-X(5)-N-X(13)-G-X(8)-C-X(2)-C-X(4)-GWXY-X(10)-K-X(6)-E was established for all the YPEL family proteins without exception. Interestingly, the indirect immunofluorescent staining indicated that YPEL1-4 proteins are localized to the centrosome and nucleolus during interphase and at several dot-like structures around the mitotic apparatus during mitotic phase of COS-7 cells. YPEL5 protein is localized to the centrosome and nucleus during interphase and at the mitotic spindle during mitosis of the same cell line. Thus, the YPEL family proteins were found in essentially all the eukaryotes and hence they must play important roles in the maintenance of life. The subcellular localization of YPEL proteins in association with centrosome or mitotic spindle suggests a novel function involved in the cell division.     

Antigen-specific CD4 effector T cells: Analysis of factors regulating clonal expansion and cytokine production: Clonal expansion and cytokine production by CD4 effector T cells

In order to fully understand T cell-mediated immunity, the mechanisms that regulate clonal expansion and cytokine production by CD4⁺ antigen-specific effector T cells in response to a wide range of antigenic stimulation needs clarification. For this purpose, panels of antigen-specific CD4⁺ T cell clones with different thresholds for antigen-induced proliferation were generated by repeated stimulation with high- or low-dose antigen. Differences in antigen sensitivities did not correlate with expression of TCR, CD4, adhesion or costimulatory molecules. There was no significant difference in antigen-dependent cytokine production by TG40 cells transfected with TCR obtained from either high- or low-dose-responding T cell clones, suggesting that the affinity of TCRs for their ligands is not primary determinant of T cell antigen reactivity. The proliferative responses of all T cell clones to both peptide stimulation and to TCRβ crosslinking revealed parallel dose-response curves. These results suggest that the TCR signal strength of effector T cells and threshold of antigen reactivity is determined by an intrinsic property, such as the TCR signalosome and/or intracellular signaling machinery. Finally, the antigen responses of high- and low-peptide-responding T cell clones reveal that clonal expansion and cytokine production of effector T cells occur independently of antigen concentration. Based on these results, the mechanisms underlying selection of high “avidity” effector and memory T cells in response to pathogen are discussed.     

Rheo-NMR Studies of an Enzymatic Reaction: Evidence of a Shear-Stable Macromolecular System

Understanding the effects of shear forces on biopolymers is key to understanding how biological systems function. Although currently there is good agreement between theoretical predictions and experimental measurements of the behavior of DNA and large multimeric proteins under shear flow, applying the same arguments to globular proteins leads to the prediction that they should only exhibit shear-induced conformational changes at extremely large shear rates. Nevertheless, contradictory experimental evidence continues to appear, and the effect of shear on these biopolymers remains contentious. Here, a custom-built rheo-NMR cell was used to investigate whether shear flow modifies enzyme action compared with that observed quiescently. Specifically, ¹H NMR was used to follow the kinetics of the liberation of methanol from the methylesterified polysaccharide pectin by pectinmethylesterase enzymes. Two different demethylesterifying enzymes, known to have different action patterns, were used. In all experiments performed, Couette flows with shear rates of up to 1570 s⁻¹ did not generate detectable differences in the rate of methanol liberation compared to unsheared samples. This study provides evidence for a shear-stable macromolecular system consisting of a largely β-sheet protein and a polysaccharide, in line with current theoretical predictions, but in contrast to some other experimental work on other proteins.