Publications

structural and functional insights into aeropyrum pernix oppa, a member of a novel archaeal oppa subfamily.	in this study we gain insight into the structural and functional characterization of the aeropyrum pernix oligopeptide-binding protein (oppa(ap)) previously identified from the extracellular medium of an aeropyrum pernix cell culture at late stationary phase. oppa(ap) showed an n-terminal q32 in a pyroglutamate form and c-terminal processing at the level of a threonine-rich region probably involved in protein membrane anchoring. moreover, the oppa(ap) protein released into the medium was identif ...	2010	21097609
crystal structure of the cambialistic superoxide dismutase from aeropyrum pernix k1--insights into the enzyme mechanism and stability.	aeropyrum pernix k1, an aerobic hyperthermophilic archaeon, produces a cambialistic superoxide dismutase that is active in the presence of either of mn or fe. the crystal structures of the superoxide dismutase from a. pernix in the apo, mn-bound and fe-bound forms were determined at resolutions of 1.56, 1.35 and 1.48 å, respectively. the overall structure consisted of a compact homotetramer. analytical ultracentrifugation was used to confirm the tetrameric association in solution. in the mn-boun ...	2010	21182595
thermophilic archaeal enzymes and applications in biocatalysis.	thermophilic enzymes have advantages for their use in commercial applications and particularly for the production of chiral compounds to produce optically pure pharmaceuticals. they can be used as biocatalysts in the application of 'green chemistry'. the thermophilic archaea contain enzymes that have already been used in commercial applications such as the l-aminoacylase from thermococcus litoralis for the resolution of amino acids and amino acid analogues. this enzyme differs from bacterial l-a ...	2011	21265764
stability of diether c(25,25) liposomes from the hyperthermophilic archaeon aeropyrum pernix k1.	temperature and ph effects were studied for stability, structural organization, fluidity and permeability of vesicles from a polar lipid methanol fraction isolated from the aeropyrum pernix. we determined the permeability of c(25,25) liposomes using fluorescence intensity of released calcein. at ph 7.0 and 9.0, and from 85°c to 98°c, only 10% of entrapped calcein was released. after 10 h at 90°c, calcein release reached 27%, independent of ph. fluorescence anisotropy measurements of hydrophobic ...	2011	21295560
cooperativity of alpha- and beta-subunits of group ii chaperonin from the hyperthermophilic archaeum aeropyrum pernix k1.	alpha- and beta-subunits (apcpna and apcpnb) are group ii chaperonins from the hyperthermophilic archaeum aeropyrum pernix k1, specialized in preventing the aggregation and inactivation of substrate proteins under conditions of transient heat stress. in the present study, the cooperativity of alpha- and beta-subunits from the a. pernix k1 was investigated. the apcpna and apcpnb chaperonin genes were overexpressed in e. coli rosetta and codonplus (de3), respectively. each of the recombinant alpha ...	2011	21364306
purification and biochemical properties of a cytochrome bc complex from the aerobic hyperthermophilic archaeon aeropyrum pernix.	the bioenergetics of archaea with respect to the evolution of electron transfer systems is very interesting. in contrast to terminal oxidases, a canonical bc1 complex has not yet been isolated from archaea. in particular, c-type cytochromes have been reported only for a limited number of species.	2011	21396131
microbial community structure of hydrothermal deposits from geochemically different vent fields along the mid-atlantic ridge.	to evaluate the effects of local fluid geochemistry on microbial communities associated with active hydrothermal vent deposits, we examined the archaeal and bacterial communities of 12 samples collected from two very different vent fields: the basalt-hosted lucky strike (37°17'n, 32°16.3'w, depth 1600-1750 m) and the ultramafic-hosted rainbow (36°13'n, 33°54.1'w, depth 2270-2330 m) vent fields along the mid-atlantic ridge (mar). using multiplexed barcoded pyrosequencing of the variable region 4 ...	2011	21418499
lipid-dependent gating of a voltage-gated potassium channel.	recent studies hypothesized that phospholipids stabilize two voltage-sensing arginine residues of certain voltage-gated potassium channels in activated conformations. it remains unclear how lipids directly affect these channels. here, by examining the conformations of the kvap in different lipids, we showed that without voltage change, the voltage-sensor domains switched from the activated to the resting state when their surrounding lipids were changed from phospholipids to nonphospholipids. suc ...	2011	21427721
stability of heterochiral hybrid membrane made of bacterial sn-g3p lipids and archaeal sn-g1p lipids.	the structure of membrane lipids in archaea is different from those of bacteria and eucarya in many ways including the chirality of the glycerol backbone. until now, heterochiral membranes were believed to be unstable; thus, no cellular organism could have existed before the separation of the groups of life. in this study, we tested the formation of heterochiral hybrid membrane made of bacterial sn-glycerol-3-phosphate-type polar lipid and archaeal sn-glycerol-1-phosphate-type polar lipid using ...	2011	21473653
discovery of permuted and recently split transfer rnas in archaea.	abstract: background: as in eukaryotes, precursor transfer rnas in archaea often contain introns that are removed in trna maturation. two unrelated archaeal species display unique pre-trna processing complexity in the form of split trna genes, in which 2-3 segments of trnas are transcribed from different loci, then trans-spliced to form a mature trna. another rare type of pre-trna, found only in eukaryotic algae, is permuted, where the 3' half is encoded upstream of the 5' half, and must be proc ...	2011	21489296
artificial modulation of the gating behavior of a k channel in a kvap-dna chimera.	we present experiments where the gating behavior of a voltage-gated ion channel is modulated by artificial ligand binding. we construct a channel-dna chimera with the kvap potassium channel reconstituted in an artificial membrane. the channel is functional and the single channel ion conductivity unperturbed by the presence of the dna. however, the channel opening probability vs. bias voltage, i.e., the gating, can be shifted considerably by the electrostatic force between the charges on the dna ...	2011	21526187
a synthetic s6 segment derived from kvap channel self-assembles, permeabilizes lipid vesicles and also exhibits ion channel activity in bilayer lipid membrane.	kvap is a voltage gated tetrameric potassium channel with six transmembrane (tm) (s1-s6) segments in each monomer from an archaeon, aeropyrum pernix. the objective of the present investigation was to understand the plausible role of the s6 segment, which has been proposed to form the inner lining of the pore, in the membrane assembly and functional properties of kvap channel. for this purpose a 22-residue peptide, corresponding to the s6 tm segment of kvap (amino acid 218-239) and a scrambled pe ...	2011	21592970
enhanced activity and enantioselectivity of a hyperthermophilic esterase from archaeon aeropyrum pernix k1 by acetone treatment.	to improve the activity and enantioselectivity of hyperthermophilic archaeon aeropyrum pernix k1 esterase (ape1547) and its mutants, they were purified by acetone-treated method. it was found that the acetone treatment not only caused ape1547 and its mutants to display higher activity and enantioselectivity but also saved more than 90% of time spent in purifying them by ni-chelating column. in hydrolysis of p-nitrophenyl caprylate, the acetone-treated ape1547 and mutant a containing the followin ...	2011	21643808
provirus induction in hyperthermophilic archaea: characterization of aeropyrum pernix spindle-shaped virus 1, apsv1, and aeropyrum pernix ovoid virus 1, apov1.	by in silico analysis we have identified two putative proviruses in the genome of the hyperthermophilic archaeaon aeropyrum pernix and in special conditions of a. pernix growth we were able to induce their replication. both viruses were isolated and characterized. negatively stained virions of one virus appeared as pleomorphic spindle-shaped particles, 180-210 nm × 40-55 nm, with tails of heterogeneous length, in the range of 0-300 nm. this virus was named aeropyrum pernix spindle-shaped virus 1 ...	2011	21784945
switch of substrate specificity of hyperthermophilic acylaminoacyl peptidase by combination of protein and solvent engineering.	the inherent evolvability of promiscuous enzymes endows them with great potential to be artificially evolved for novel functions. previously, we succeeded in transforming a promiscuous acylaminoacyl peptidase (apaap) from the hyperthermophilic archaeon aeropyrum pernix k1 into a specific carboxylesterase by making a single mutation. in order to fulfill the urgent requirement of thermostable lipolytic enzymes, in this paper we describe how the substrate preference of apaap can be further changed ...	2011	21748600
Crystallization and preliminary X-ray analysis of a dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix.	A dye-linked D-lactate dehydrogenase from the aerobic hyperthermophilic archaeon Aeropyrum pernix was crystallized using the hanging-drop vapour-diffusion method with polyethylene glycol 8000 as the precipitant. The crystals belonged to the monoclinic space group P2(1), with unit-cell parameters a = 63.4, b = 119.4, c = 70.2 Å, ß = 112.0°, and diffracted to 2.0 Å resolution on the BL26B1 beamline at SPring-8. The overall R(merge) was 4.5% and the completeness was 99.8%.	2011	22102248
cleavage of intron from the standard or non-standard position of the precursor trna by the splicing endonuclease of aeropyrum pernix, a hyper-thermophilic crenarchaeon, involves a novel rna recognition site in the crenarchaea specific loop.	in crenarchaea, several trna genes are predicted to express precursor-trnas (pre-trnas) with canonical or non-canonical introns at various positions. we initially focused on the trna(thr) species of hyperthermophilic crenarchaeon, aeropyrum pernix (ape) and found that in the living ape cells three trna(thr) species were transcribed and subsequently matured to functional trnas. during maturation, introns in two of them were cleaved from standard and non-standard positions. biochemical studies rev ...	2011	21846775
characterization of family iv udg from aeropyrum pernix and its application in hot-start pcr by family b dna polymerase.	recombinant uracil-dna glycosylase (udg) from aeropyrum pernix (a. pernix) was expressed in e. coli. the biochemical characteristics of a. pernix udg (apeudg) were studied using oligonucleotides carrying a deoxyuracil (du) base. the optimal temperature range and ph value for du removal by apeudg were 55-65°c and ph 9.0, respectively. the removal of du was inhibited by the divalent ions of zn, cu, co, ni, and mn, as well as a high concentration of nacl. the opposite base in the complementary stra ...	2011	22087273
structure and characterization of the 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase from aeropyrum pernix.	the first enzyme in the shikimic acid biosynthetic pathway, 3-deoxy-d-arabino-heptulosonate 7-phosphate synthase (dah7ps), varies significantly in size and complexity in the bacteria and plants that express it. the dah7ps from the archaebacterium aeropyrum pernix (dah7ps(ap)) is among the smallest and least complex of the dah7ps enzymes, leading to the hypothesis that dah7ps(ap) would not be subject to feedback regulation by shikimic acid pathway products. we overexpressed dah7ps(ap) in escheric ...	2011	22035970
profile structures of the voltage-sensor domain and the voltage-gated k^{+}-channel vectorially oriented in a single phospholipid bilayer membrane at the solid-vapor and solid-liquid interfaces determined by x-ray interferometry.	one subunit of the prokaryotic voltage-gated potassium ion channel from aeropyrum pernix (kvap) is comprised of six transmembrane α helices, of which s1-s4 form the voltage-sensor domain (vsd) and s5 and s6 contribute to the pore domain (pd) of the functional homotetramer. however, the mechanism of electromechanical coupling interconverting the closed-to-open (i.e., nonconducting-to-k^{+}-conducting) states remains undetermined. here, we have vectorially oriented the detergent (og)-solubilized v ...	2011	22060407
In vitro folding of K(v)AP, a voltage-gated K(+) channel.	In this contribution, we report in vitro folding of the archaebacterial voltage-gated K(+) channel, K(v)AP. We show that in vitro folding of the K(v)AP channel from the extensively unfolded state requires lipid vesicles and that the refolded channel is biochemically and functionally similar to the native channel. The in vitro folding process is slow at room temperature, and the folding yield depends on the composition of the lipid bilayer. The major factor influencing refolding is temperature, a ...	2011	22044112