Characterization of heme-regulated eIF2alpha kinase: roles of the N-terminal domain in the oligomeric state, heme binding, catalysis, and inhibition

Heme-regulated eIF2alpha kinase [heme-regulated inhibitor (HRI)] plays a critical role in the regulation of protein synthesis by heme iron. The kinase active site is located in the C-terminal domain, whereas the N-terminal domain is suggested to regulate catalysis in response to heme binding. Here, we found that the rate of dissociation for Fe(III)-protoporphyrin IX was much higher for full-length HRI (1.5 x 10(-)(3) s(-)(1)) than for myoglobin (8.4 x 10(-)(7) s(-)(1)) or the alpha-subunit of hemoglobin (7.1 x 10(-)(6) s(-)(1)), demonstrating the heme-sensing character of HRI. Because the role of the N-terminal domain in the structure and catalysis of HRI has not been clear, we generated N-terminal truncated mutants of HRI and examined their oligomeric state, heme binding, axial ligands, substrate interactions, and inhibition by heme derivatives. Multiangle light scattering indicated that the full-length enzyme is a hexamer, whereas truncated mutants (truncations of residues 1-127 and 1-145) are mainly trimers. In addition, we found that one molecule of heme is bound to the full-length and truncated mutant proteins. Optical absorption and electron spin resonance spectra suggested that Cys and water/OH(-) are the heme axial ligands in the N-terminal domain-truncated mutant complex. We also found that HRI has a moderate affinity for heme, allowing it to sense the heme concentration in the cell. Study of the kinetics showed that the HRI kinase reaction follows classical Michaelis-Menten kinetics with respect to ATP but sigmoidal kinetics and positive cooperativity between subunits with respect to the protein substrate (eIF2alpha). Removal of the N-terminal domain decreased this cooperativity between subunits and affected the other kinetic parameters including inhibition by Fe(III)-protoporphyrin IX, Fe(II)-protoporphyrin IX, and protoporphyrin IX. Finally, we found that HRI is inhibited by bilirubin at physiological/pathological levels (IC(50) = 20 microM). The roles of the N-terminal domain and the binding of heme in the structural and functional properties of HRI are discussed.     

Activation of heme-regulated eukaryotic initiation factor 2alpha kinase by nitric oxide is induced by the formation of a five-coordinate NO-heme complex: optical absorption, electron spin resonance, and resonance raman spectral studies

Heme-regulated eukaryotic initiation factor 2alpha kinase (HRI) regulates the synthesis of hemoglobin in reticulocytes in response to heme availability. HRI contains a tightly bound heme at the N-terminal domain. Earlier reports show that nitric oxide (NO) regulates HRI catalysis. However, the mechanism of this process remains unclear. In the present study, we utilize in vitro kinase assays, optical absorption, electron spin resonance (ESR), and resonance Raman spectra of purified full-length HRI for the first time to elucidate the regulation mechanism of NO. HRI was activated via heme upon NO binding, and the Fe(II)-HRI(NO) complex displayed 5-fold greater eukaryotic initiation factor 2alpha kinase activity than the Fe(III)-HRI complex. The Fe(III)-HRI complex exhibited a Soret peak at 418 nm and a rhombic ESR signal with g values of 2.49, 2.28, and 1.87, suggesting coordination with Cys as an axial ligand. Interestingly, optical absorption, ESR, and resonance Raman spectra of the Fe(II)-NO complex were characteristic of five-coordinate NO-heme. Spectral findings on the coordination structure of full-length HRI were distinct from those obtained for the isolated N-terminal heme-binding domain. Specifically, six-coordinate NO-Fe(II)-His was observed but not Cys-Fe(III) coordination. It is suggested that significant conformational change(s) in the protein induced by NO binding to the heme lead to HRI activation. We discuss the role of NO and heme in catalysis by HRI, focusing on heme-based sensor proteins.     

Assessment of ‘top-down’ and ‘bottom-up’ forces as determinants of rotifer distribution among lakes in Ontario,Canada

Predation and food supply are generally perceived as important determinants of spatial and temporal variations of populations. The population dynamics of freshwater rotifers have been well researched in this aspect. However, their spatial variations have attracted less attention and have not been studied by simultaneously considering both predation and food supply. We studied spatial variations of rotifer abundance among 34 Canadian boreal lakes. A large part of the variance of rotifer abundance was associated with variables related to trophic status including chlorophyll a and total phosphorus. However, abundances of mesozooplankton such as potential predators and competitors did not correlate with rotifer abundance and did not explain the residual of the regression between rotifer abundance and chlorophyll a. The results of the present study indicated that variation in rotifer abundance among lakes was caused by bottom-up forces related to food supply and not by top-down predatory interactions. This provides a contrast to previous empiric and experimental studies that reported that temporal variations of rotifer abundance were mainly regulated by top-down interactions. This discrepancy suggests that overall differences in rotifer abundance among lakes are mainly determined by bottom-up forces while temporal changes in single lakes are shaped by top-down forces. Meanwhile, the composition of rotifer species was correlated with mesozooplankton abundance as well as trophic status. Rotifer species with long spines or rigid loricae were found in the lakes where mesozooplankton were abundant, which suggests that defensive morphology could have affected the rotifer species distribution among the study lakes.     

Evidence of phosphorus-limited individual and population growth of Daphnia in a Canadian Shield lake

We performed bag experiments in a Canadian Shield lake with generally high seston (suspended food particles mainly composed of algae) carbon (C):phosphorus (P) ratios, and investigated the responses of individual and population growth of herbivorous Daphnia dentifera on their abundance with (+P) and without (−P) a phosphorus enrichment to lake water. In both treatments, increased abundance of D. dentifera reduced seston C concentration and was accompanied by decreases in population and individual growth rates. However, P-enrichment increased seston P concentration and then reduced seston C:P ratio from 400–700 to ca 100 (by atoms). As a result, both individual and population growth rates were significantly higher in the +P treatment at all animal abundances even though seston C concentrations were similar between the treatments. The magnitude of the growth enhancement by the P-enrichment was independent of animal abundance. Stepwise regression analyses revealed that 71 and 90% of the variance in the population and individual growth rates, respectively, were explained by seston C and P concentrations, and that the contribution of the seston P concentration was roughly the same as that of seston C. Such joint effects of seston C and P indicate that food quality (P content) as well as food quantity (C concentration) can influence Daphnia not only at the level of individual growth but also at the level of population dynamics in P-limited lakes. Our results thus strongly corroborate the hypothesis that the population development of a key herbivore Daphnia in P-limited Canadian Shield lakes is inhibited by the direct effects of P-limited food on individual growth, which weaken the strength of trophic cascading interactions starting from piscivorous fish through planktivorous fish and zooplankton to algae.     

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.     

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.     

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.