Effects of amino acid replacements around the reactive site of chicken ovomucoid domain 3 on the inhibitory activity toward chymotrypsin and trypsin.

We have previously shown that replacing the P1-site residue (Ala) of chicken ovomucoid domain 3 (OMCHI3) with a Met or Lys results in the acquisition of inhibitory activity toward chymotrypsin or trypsin, respectively. However, the inhibitory activities thus induced are not strong. In the present study, we introduced additional amino acid replacements around the reactive site to try to make the P1-site mutants more effective inhibitors of chymotrypsin or trypsin. The amino acid replacement Asp-->Tyr at the P2' site of OMCHI3(P1Met) resulted in conversion to a 35000-fold more effective inhibitor of chymotrypsin with an inhibitor constant (K(i)) of 1. 17x10(-11) M. The K(i) value of OMCHI3(P1Met, P2'Ala) indicated that the effect on the interaction with chymotrypsin of removing a negative charge from the P2' site was greater than that of introducing an aromatic ring. Similarly, enhanced inhibition of trypsin was observed when the Asp-->Tyr replacement was introduced into the P2' site of OMCHI3(P1Lys). Two additional replacements, Asp-->Ala at the P4 site and Arg-->Ala at the P3' site, made the mutant a more effective inhibitor of trypsin with a K(i) value of 1. 44x10(-9) M. By contrast, Arg-->Ala replacement at the P3' site of OMCHI3(P1Met, P2'Tyr) resulted in a greatly reduced inhibition of chymotrypsin, and Asp-->Ala replacement at the P4 site produced only a small change when compared with a natural variant of OMCHI3. These results clearly indicate that not only the P1-site residue but also the characteristics, particularly the electrostatic properties, of the amino acid residues around the reactive site of the protease inhibitor determine the strength of its interactions with proteases. Furthermore, amino acids with different characteristics are required around the reactive site for strong inhibition of chymotrypsin and trypsin.     

ATM regulates Cdt1 stability during the unperturbed S phase to prevent re-replication

Ataxia-telangiectasia mutated (ATM) plays crucial roles in DNA damage responses, especially with regard to DNA double-strand breaks (DSBs). However, it appears that ATM can be activated not only by DSB, but also by some changes in chromatin architecture, suggesting potential ATM function in cell cycle control. Here, we found that ATM is involved in timely degradation of Cdt1, a critical replication licensing factor, during the unperturbed S phase. At least in certain cell types, degradation of p27^Kip1 was also impaired by ATM inhibition. The novel ATM function for Cdt1 regulation was dependent on its kinase activity and NBS1. Indeed, we found that ATM is moderately phosphorylated at Ser1981 during the S phase. ATM silencing induced partial reduction in levels of Skp2, a component of SCF^Skp2 ubiquitin ligase that controls Cdt1 degradation. Furthermore, Skp2 silencing resulted in Cdt1 stabilization like ATM inhibition. In addition, as reported previously, ATM silencing partially prevented Akt phosphorylation at Ser473, indicative of its activation, and Akt inhibition led to modest stabilization of Cdt1. Therefore, the ATM-Akt-SCF^Skp2 pathway may partly contribute to the novel ATM function. Finally, ATM inhibition rendered cells hypersensitive to induction of re-replication, indicating importance for maintenance of genome stability.     

Aggregatibacter actinomycetemcomitans induces detachment and death of human gingival epithelial cells and fibroblasts via elastase release following leukotoxin‐dependent neutrophil lysis

Aggregatibacter actinomycetemcomitans is considered to be associated with periodontitis. Leukotoxin (LtxA), which destroys leukocytes in humans, is one of this bacterium's major virulence factors. Amounts of neutrophil elastase (NE), which is normally localized in the cytoplasm of neutrophils, are reportedly increased in the saliva of patients with periodontitis. However, the mechanism by which NE is released from human neutrophils and the role of NE in periodontitis is unclear. In the present study, it was hypothesized that LtxA induces NE release from human neutrophils, which subsequently causes the breakdown of periodontal tissues. LtxA‐treatment did not induce significant cytotoxicity against human gingival epithelial cells (HGECs) or human gingival fibroblasts (HGFs). However, it did induce significant cytotoxicity against human neutrophils, leading to NE release. Furthermore, NE and the supernatant from LtxA‐treated human neutrophils induced detachment and death of HGECs and HGFs, these effects being inhibited by administration of an NE inhibitor, sivelestat. The present results suggest that LtxA mediates human neutrophil lysis and induces the subsequent release of NE, which eventually results in detachment and death of HGECs and HGFs. Thus, LtxA‐induced release of NE could cause breakdown of periodontal tissue and thereby exacerbate periodontitis.     

A method for accurate analysis of intermembrane space in organelles enclosed by double envelope membranes.

Centrifugal filtration through a double layer of silicone oil was applied to determine the intermembrane space of organelles enclosed by double envelope membranes, i.e. proplastids, chloroplasts, mitochondria and amyloplasts. The organelles, capable of transporting adenylates by an adenylate translocator located in the inner envelope membrane, were incubated with increasing concentrations of adenylates while maintaining their specific radioactivities constant. Intermembrane spaces were estimated by extrapolation of radioactivities recovered after filtration of the organelles. The values estimated were compared to those obtained employing the classical method measuring the intake of [14C]-sucrose and [14C]-sorbitol which are impermeable to the inner membranes of organelles. The intermembrane space determined by the present method was shown to be uniformly smaller than the sucrose-permeable space which was always smaller than the sorbitol-permeable space.     

Mitochondrial DNA haplogrouping of the brown bear,Ursus arctos (Carnivora: Ursidae) in Asia,based on a newly developed APLP analysis

Sequence analyses of the complete brown bear, Ursus arctos, mitochondrial DNA (mtDNA) genome have detected scattered single nucleotide polymorphisms (SNPs) that define distinct mtDNA haplogroups in phylogeographical studies. The degraded DNA in historical samples, such as stuffed or excavated specimens, however, is often not suitable for sequence analyses. To address this problem, we developed an amplified product length polymorphism (APLP) analysis for mtDNA‐haplogrouping U. arctos specimens by detecting haplogroup‐specific SNPs. We verified the validity and utility of this method by analysing up to 170‐year‐old skin samples from U. arctos specimens collected widely across continental Eurasia. We detected some of the same haplogroups as those occurring in eastern Hokkaido (Japan) and eastern Alaska in continental Eurasia (the Altai and the Caucasus). Our results show that U. arctos in eastern Hokkaido and eastern Alaska descended from a common ancestor in continental Eurasia, and suggest that U. arctos occupied several refugia in southern Asia during the Last Glacial Maximum. © 2014 The Linnean Society of London, Biological Journal of the Linnean Society, 2014, 111 , 627–635.     

Phylogeography of the leaf beetle Chrysolina virgata in wetlands of Japan inferred from the distribution of mitochondrial haplotypes

The genetic differentiation among populations of the leaf beetle Chrysolina virgata living in wetlands of Japan was studied based on the sequence data of the mitochondrial cytochrome oxidase subunit I gene region (750 bp). Two distinct lineages of mitochondrial haplotypes were found: one (clade A) consisted of 26 haplotypes distributed over the distribution range of C. virgata between north‐east Honshu and Kyushu, whereas the other (clade B) was monotypic and confined to a small region in north‐east Honshu where it coexisted with clade A. Nested clade analysis for these haplotypes suggested that range expansion and following differentiation due to isolation by distance might have resulted in the present distribution pattern of the haplotypes in clade A. We discuss the evolutionary process leading to the occurrence of two distinct haplotype clades in Japan in terms of repeated colonization from the continent and range expansion and contraction during climatic changes.     

Differential Responsiveness in Zonal Growth of Cocklebur Seed Axes to CO2, C2H4, O2 and Respiration Inhibitors

The axial growth of de-coated cocklebur (Xanthium pennsylvanicumWallr.) seeds, whose axes were divided into 4 zones, was examinedin relation to the temperature-dependent shift of the effectof C₂H₄ on germination. At 23?C, where both C₂H₄ and CO₂ stimulatedgermination, CO₂ promoted the axial growth at the radicle tipzone, whereas C₂H₄ promoted growth in the proximal portion ofthe axis. At 33?C, C₂H₄ inhibited germination, and stronglysuppressed the growth at the radicle tip, whereas the effectof CO₂ did not change. The inhibition of growth at the radicletip zone was alleviated by O₂ enrichment, which also reversedthe inhibition of germination. It is thus apparent that thetemperature-dependent shift of the action of C₂H₄ is associatedwith a temperature-dependent responsiveness of the radicle tipzone to C₂H₄. Growth of the radicle tip zone was sensitive toNaN₃, whereas the proximal portion was sensitive to benzohydroxamicacid, an inhibitor of alternative respiration, suggesting thatthere may be an increase in the operation of the alternativerespiration path along a gradient of axial tissue from the tiptowards the cotyledonary side. The effects of CO₂ and C₂H₄ arediscussed in relation to the different respiratory activitiesin each axial zone of cocklebur seeds. (Received May 9, 1986; Accepted November 6, 1986)     

Changes in chromatin structure during aging of human skin fibroblasts

Human skin fibroblasts from embryo, 16-, 30- and 60-year-old adults were cultivated and passaged in vitro. Their chromatin structures were examined by the sensitivity to micrococcal nuclease and by electron microscopy. When the mode of DNA degradation by the nuclease was analysed during in vitro aging of the embryo skin fibroblasts, the discrete ladder of nucleosomal DNA became obscure in old cells. Analogous change of chromatin structure was also observed even in young cells as their donor ages increased. From the observation with electron microscopy, it became clear that chromatin of fibroblasts from 30-year-old adults does not have regularly spaced nucleosomes, compared with chromatin from embryo. These results suggest that the length of the linker DNA which connects core particles becomes to be heterogeneous by aging, both in vivo and in vitro in human skin fibroblasts.