Autophosphorylation of heme-regulated eukaryotic initiation factor 2α kinase and the role of the modification in catalysis

Heme-regulated eukaryotic initiation factor 2α (eIF2α) kinase (HRI), functions in response to heme shortage in reticulocytes and aids in the maintenance of a heme:globin ratio of 1:1. Under normal conditions, heme binds to HRI and blocks its function. However, during heme shortage, heme dissociates from the protein and autophosphorylation subsequently occurs. Autophosphorylation comprises a preliminary critical step before the execution of the intrinsic function of HRI; specifically, phosphorylation of Ser-51 of eIF2α to inhibit translation of the globin protein. The present study indicates that dephosphorylated mouse HRI exhibits strong intramolecular interactions (between the N-terminal and C-terminal domains) compared to phosphorylated HRI. It is therefore suggested that autophosphorylation reduces the intramolecular interaction, which induces irreversible catalytic flow to the intrinsic eIF2α kinase activity after heme dissociates from the protein. With the aid of MS, we identified 33 phosphorylated sites in mouse HRI overexpressed in Escherichia coli. Phosphorylated sites at Ser, Thr and Tyr were predominantly localized within the kinase insertion region (16 sites) and kinase domain (12 sites), whereas the N-terminal domain contained five sites. We further generated 30 enzymes with mutations at the phosphorylated residues and examined their catalytic activities. The activities of Y193F, T485A and T490A mutants were significantly lower than that of wild-type protein, whereas the other mutant proteins displayed essentially similar activity. Accordingly, we suggest that Tyr193, Thr485 and Thr490 are essential residues in the catalysis.     

Fluvial transport of carbon along the river-to-ocean continuum and its potential impacts on a brackish water food web in the Iwaki River watershed, northern Japan

Riverine transport of dissolved inorganic carbon (DIC) from land to the ocean is an important carbon flux that influences the carbon budget at the watershed scale. However, the dynamics of DIC in an entire river network has remained unknown, especially in mountainous Japanese watersheds. We examined the effects of watershed land use and geology on the transports of inorganic carbon as well as weathered silica (Si) and calcium (Ca) in the Iwaki River system where agricultural and residential areas have developed in the middle and lower parts of the watershed. The concentration and stable carbon isotope ratios (δ¹³C) of DIC showed the longitudinal increase of ¹³C-depleted inorganic carbon along the river. As a result, most streams and rivers were supersaturated in dissolved CO₂ that will eventually be emitted to the atmosphere. The possible origin of ¹³C-depleted carbon is CO₂ derived from the decomposition of organic matter in agricultural and urban landscapes, as well as from in-stream respiration. In addition, agricultural and urban areas, respectively, exported the large amount of dissolved Si and Ca to the rivers, suggesting that CO₂ increased by respiration accelerates the chemical weathering of silicate and carbonate materials in soils, river sediments, and/or urban infrastructure. Furthermore, riverine bicarbonate flux is likely to enter shell carbonates of Corbicula japonica, an aragonitic bivalve, in the downstream brackish lake (Lake Jusan). These results revealed that the flux of DIC from the human-dominated watersheds is a key to understanding the carbon dynamics and food-web structure along the land-to-river-to-ocean continuum.     

Identification and functional and spectral characterization of a globin-coupled histidine kinase from Anaeromyxobacter sp. Fw109-5

Two-component signal transduction systems regulate numerous important physiological functions in bacteria. In this study we have identified, cloned, overexpressed, and characterized a dimeric full-length heme-bound (heme:protein, 1:1 stoichiometry) globin-coupled histidine kinase (AfGcHK) from Anaeromyxobacter sp. strain Fw109-5 for the first time. The Fe(III), Fe(II)-O(2), and Fe(II)-CO complexes of the protein displayed autophosphorylation activity, whereas the Fe(II) complex had no significant activity. A H99A mutant lost heme binding ability, suggesting that this residue is the heme proximal ligand. Moreover, His-183 was proposed as the autophosphorylation site based on the finding that the H183A mutant protein was not phosphorylated. The phosphate group of autophosphorylated AfGcHK was transferred to Asp-52 and Asp-169 of a response regulator, as confirmed from site-directed mutagenesis experiments. Based on the amino acid sequences and crystal structures of other globin-coupled oxygen sensor enzymes, Tyr-45 was assumed to be the O(2) binding site at the heme distal side. The O(2) dissociation rate constant, 0.10 s(-1), was substantially increased up to 8.0 s(-1) upon Y45L mutation. The resonance Raman frequencies representing ν(Fe-O2) (559 cm(-1)) and ν(O-O) (1149 cm(-1)) of the Fe(II)-O(2) complex of Y45F mutant AfGcHK were distinct from those of the wild-type protein (ν(Fe-O2), 557 cm(-1); ν(O-O), 1141 cm(-1)), supporting the proposal that Tyr-45 is located at the distal side and forms hydrogen bonds with the oxygen molecule bound to the Fe(II) complex. Thus, we have successfully identified and characterized a novel heme-based globin-coupled oxygen sensor histidine kinase, AfGcHK, in this study.     

Accurate Determination of S-Phase Fraction in Proliferative Cells by Dual Fluorescence and Peroxidase Immunohistochemistry with 5-Bromo-2��-Deoxyuridine (BrdU) and Ki67 Antibodies

To ensure the maintenance of tissues in mammals, cell loss must be balanced with cell production, the proliferative activity being different from tissue to tissue. In this article, the authors propose a new method for the quantification of the proliferative activity, defined as the S-phase fraction of actively cycling cells, by dual labeling with fluorescence and peroxidase immunohistochemistry using BrdU (marker of S-phase) and Ki67 antibodies (marker of G₁-, S-, G₂-, and M-phases) after a one-step antigen retrieval. In the generative cell zones of fundic and pyloric glandular stomachs, where the majority of cells were cycling, the authors measured a proliferative activity of 31%. In the epithelium of the forestomach and the skin, where cycling cells are intermingled with G₀ and differentiated cells, proliferative activities were 21% and 13%, respectively. In the adrenal cortex, in which cycling cells were sparsely distributed, the proliferative activity reached 32%. During the regenerative process in the skin after a lesion, the proliferative activity increased in proximity to the wound. The present one-step dual-labeling method has revealed that the proliferative activity is different between tissues and depends on the physiological or pathological state.     

Eukaryotic initiation factor 2alpha kinase is a nitric oxide-responsive mercury sensor enzyme: potent inhibition of catalysis by the mercury cation and reversal by nitric oxide

The activity of one of the eukaryotic initiation factor 2alpha kinases, heme-regulated inhibitor (HRI), is modulated by heme binding. Here, we demonstrate for the first time that Hg2+ strongly inhibits the function of HRI (IC50=0.6 microM), and nitric oxide fully reverses this inhibition. Other divalent metal cations, such as Fe2+, Cu2+, Cd2+, Zn2+ and Pb2+, also significantly inhibit kinase activity with IC50 values of 1.9-8.5 microM. Notably, inhibition by cations other than Hg2+ is not reversed by nitric oxide. Our present data support dual roles of Hg2+ and nitric oxide in the regulation of protein synthesis during cell emergency states.     

Across-population variation in sex ratio in invasive Japanese Potamopyrgus antipodarum (Caenogastropoda: Rissooidea: Hydrobiidae)

Potamopyrgus antipodarum, a well-known invasive species, has both sexual and asexual forms in its native area, and is generally asexual in exotic areas. Potamopyrgus antipodarum was sampled from ten locations in central and western Japan, and the sex distribution was analyzed. Males were found in two of the ten localities; the percentages of males in these localities were 7.2 and 7.3 %, which is within the range of that observed in asexual populations in native and introduced areas. A flow cytometry analysis showed that populations with a low percentage of males (Kanro) and populations consisting only of females (Banyu Park, Hadano and Yugawara) and perhaps the population reported as having a high male percentage in a previous study (Chiba; 29.8 %) were triploid. Males from Chiba and Kanro produced sperm. Most of the females from Chiba stored sperm in their seminal receptacle, showing that they had copulated, but no females from Kanro stored sperm. Fertilization by males, normal development of fertilized eggs, and the fecundity of juveniles should be evaluated in further studies to demonstrate the sexual reproduction of P. antipodarum in Japan. The risk of introduction of sexual P. antipodarum individuals is further discussed in the article.     

Trematode fauna of prosobranch snails of the genus Semisulcospira in Lake Biwa and the connected drainage system

The parasite fauna of prosobranch snails of the genus Semisulcospira was surveyed in Lake Biwa and the adjacent water system. One aspidogastrean and 28 digenetic trematode taxa were detected in 19209 snails consisting of 10 morphological species. There was no trematode species peculiar to members of the subgenus Biwamelania that is endemic to the Lake Biwa water system. However, one species, Notocotylus magniovatus, was found only in the non-endemic subgenus Semisulcospira. Of 23 digenean taxa detected in more than one host, 13 were distributed in both the lake and the tributaries. Seven of these had host taxa, more than 1% of which were infected with the parasite in both the lake and the tributaries, four had such hosts only in the tributaries, and two had no such hosts. Three species detected only in Lake Biwa were previously reported from other rivers in Japan. In the seven species detected only in the tributaries, two species had life cycles that could be maintained only in rivers. These results indicate that the core areas for the distribution of parasites of Semisulcospira are tributaries, and the lake is a sink for these species. These results contradict the expectation that the parasite fauna should be richer in the lake than in tributaries because the lake is a stable habitat over a geological time scale and has more divergent freshwater animals than the adjacent water system.     

Soluble MICA and a MICA Variation as Possible Prognostic Biomarkers for HBV-Induced Hepatocellular Carcinoma

MHC class I polypeptide-related chain A (MICA) molecule is induced in response to viral infection and various types of stress. We recently reported that a single nucleotide polymorphism (SNP) rs2596542 located in the MICA promoter region was significantly associated with the risk for hepatitis C virus (HCV)-induced hepatocellular carcinoma (HCC) and also with serum levels of soluble MICA (sMICA). In this study, we focused on the possible involvement of MICA in liver carcinogenesis related to hepatitis B virus (HBV) infection and examined correlation between the MICA polymorphism and the serum sMICA levels in HBV-induced HCC patients. The genetic association analysis revealed a nominal association with an SNP rs2596542; a G allele was considered to increase the risk of HBV-induced HCC (P = 0.029 with odds ratio of 1.19). We also found a significant elevation of sMICA in HBV-induced HCC cases. Moreover, a G allele of SNP rs2596542 was significantly associated with increased sMICA levels (P = 0.009). Interestingly, HCC patients with the high serum level of sMICA (>5 pg/ml) exhibited poorer prognosis than those with the low serum level of sMICA (≤5 pg/ml) (P = 0.008). Thus, our results highlight the importance of MICA genetic variations and the significance of sMICA as a predictive biomarker for HBV-induced HCC.     

Heavy-ion beam irradiation is an effective technique for reducing major allergens in peanut seeds

Heavy-ion beam irradiation is an effective technique for mutation breeding to produce new cultivars. Heavy-ion beams have high linear energy transfer capable of breaking the double-stranded DNA molecules, thus inducing stable knockout mutants. Here, we report the first application of this technology to produce hypoallergenic peanut lacking major allergens, Ara h 2 and 3, from the Japanese Nakateyutaka variety. After irradiation with either N or C heavy-ion beams at a dose of 100?Gy, seventeen knockout mutants from 11,335 screened M2 seeds were obtained, eight of which lacked either one of the two isoforms of Ara h 2, and the other nine lacked one of the isoforms of Ara h 3. This result indicates that heavy-ion beam irradiation is a powerful means of producing knockout hypoallergenic peanuts.     

DNA extraction and amplification methods for ephippial cases of Daphnia resting eggs in lake sediments: a novel approach for reconstructing zooplankton population structure from the past

This study describes a method of DNA extraction and amplification for ephippial cases of Daphnia resting eggs from lake sediment. Recent studies have reconstructed succession records of Daphnia species by genetically analyzing Daphnia resting eggs stored in lake sediments and revealed changes in dominant Daphnia species that correspond well with environmental changes. However, this approach is not applicable to lakes where most of the resting eggs in the sediment have already hatched out. We modified conventional methods for DNA extraction and amplification to enable genetic analyses of the ephippial case that envelops and protects the resting eggs, and we compared the performance of the modified method to the conventional one. We confirmed that we could efficiently analyze the sequences of the ephippial cases collected in a sediment core using our modified method. It enables us to reconstruct changes in genetic structure of Daphnia populations regardless of hatching rates of the resting eggs.