NADP-dependent isocitrate dehydrogenase from the halophilic archaeon Haloferax volcanii: cloning,sequence determination and overexpression in Escherichia coli

A gene encoding NADP-dependent Ds-threo-isocitrate dehydrogenase was isolated from Haloferax volcanii genomic DNA by using a combination of polymerase chain reaction and screening of a lambda EMBL3 library. Analysis of the nucleotide sequence revealed an open reading frame of 1260 bp encoding a protein of 419 amino acids with 45837 Da molecular mass. This sequence is highly similar to previously sequenced isocitrate dehydrogenases. In the alignment of the amino acid sequences with those from several archaeal and mesophilic NADP-dependent isocitrate dehydrogenases, the residues involved in dinucleotide binding and isocitrate binding are well conserved. We have developed methods for the expression in Escherichia coli and purification of the enzyme from H. volcanii. This expression was carried out in E. coli as inclusion bodies using the cytoplasmic expression vector pET3a. The enzyme was refolded by solubilisation in 8 M urea followed by dilution into a buffer containing EDTA, MgCl(2) and 3 M NaCl. Maximal activity was obtained after several hours incubation at room temperature.     

NMR-derived folate-bound structure of dihydrofolate reductase 1 from the halophile Haloferax volcanii

Folate binds to dihydrofolate reductase (DHFR) to form a binary complex whose structure maintains the overall configuration of the enzyme; however, some significant changes are evident when a comparison is made to the enzyme. The structure of DHFR1 from the halophilic Halopherax volcanii was solved in its folate-bound form using nuclear magnetic resonance spectroscopy. NOE data obtained from the (15)N-NOESY-HSQC and (13)C-NOESY-HSQC experiments of the triply labeled ((1)H, (13)C, and (15)N) binary complex were used as input for the structure calculation with the Crystallography and Nuclear Magnetic Resonance System program. The resulting family of structures was compared with the enzyme solved by both nuclear magnetic resonance and X-ray crystallography and also to the mesophilic folate-bound enzyme from Escherichia coli. The binary complex exhibited less convergence of structure in the alpha2-helix and differences in the hinge residues D39 and A94. In comparison to the previously reported mesophilic binary complex solved by X-ray crystallography, the halophilic binary complex reported here does not agree with the convergence of the M20 loop to a single structure. The corresponding L21 loop of the halophilic binary complex family of structures solved by nuclear magnetic resonance indicates variability in this region.     

The proton gradient across the vacuo-lysosomal membrane of lutoids from the latex ofHevea brasiliensis. I. Further evidence for a proton-translocating ATPase on the vacuo-lysosomal membrane of intact lutoids

Summary Lutoids (vacuo-lysosomal particles) were isolated from the latex ofHevea brasiliensis. Using flow dialysis with¹⁴C-methylamine uptake as a pH probe and⁸⁶Rb rubidium+valinomycin distribution for estimations of transmembrane electrical potential, intact lutoids exhibited a pH of 1 unit (interior more acid) and a of –70 mV (interior negative), when suspended in an isotonic medium at physiological concentration of potassium (30mm) and pH 7.0, in the absence of ATP. In most cases, the Donnan potential was shown to fully account for pH in nonenergized lutoids. The addition of Mg-ATP (5mm) resulted in a marked acidification of the lutoidic internal space (0.7 to 1 pH unit) depending on the composition of the medium, and in a membrane depolarization by 60 mV (interior becoming less negative). The resulting electrochemical potential of protons ( ) increased by a hundred millivolts when lutoids were energized by ATP. These data strongly support an inward electrogenic proton translocating function for the ATPase of the vacuo-lysosomal membrane of lutoids. Results are discussed in terms of thein vivo maintenance of large lutoids/cytoplasm proton gradients, and of the rôle of these vacuo-lysosomes in the homeostasis of the cytoplasmic metabolism.     

Characterization of the dominant halophilic archaea in a bacterial bloom in the dead sea

Abstract A mass bloom of halophilic archaea developed in the Dead Sea in the summer of 1992, with peak densities of more than 3 × 10⁷ cells/ml, imparting a red coloration to the water. Microscopical examination showed a numerical dominance of pleomorphic, flat cells. Attempts to identify the dominant type of halophilic archaea by means of growth experiments, both on agar plates and by dilution in liquid media, were unsuccessful, as viable counts obtained were two or more orders of magnitude lower than the total microscopic counts. Analysis of the polar lipids in the Dead Sea biomass during the bloom showed one major glycolipid to be present in the extracts, corresponding with the sulfated diglycosyl diether lipid (S-DGD-1) characteristic of the genus Haloferax . No indications were found for the presence of significant amounts of other glycolipids that indicate the presence of large numbers of Dead Sea archaea such as Halobacterium sodomense or Haloarcula marismortui , or Halobacterium species such as H. halobium, H. salinarium and H. saccharovorum . Thus, the numerically dominant organisms in the bloom is probably a difficult to culture, not yet isolated, representative of the genus Haloferax .     

Cytochrome c Oxidase (Heme aa 3) from Paracoccus denitrificans: Analysis of Mutations in Putative Proton Channels of Subunit I

One of the challenging features of energy-transducing terminal oxidases, like the aa ₃ cytochrome c oxidase of Paracoccus denitrificans, is the translocation of protons across the cytoplasmic membrane, which is coupled to the transfer of electrons to oxygen. As a prerequisite for a more advanced examination of the enzymatic properties, several amino acid residues, selected on the basis of recent three-dimensional structure determinations, were exchanged in subunit I of the Paracoccus enzyme by site-directed mutagenesis. The properties of the mutated oxidases were analyzed by different methods to elucidate whether they are involved in the coupled and coordinated transfer of protons via two different pathways either to the site of oxygen reduction or through the enzyme from the cytoplasm to the periplasmic side.     

The Prokaryote-to-Eukaryote Transition Reflected in the Evolution of the V/F/A-ATPase Catalytic and Proteolipid Subunits

Changes in the primary and quarternary structure of vacuolar and archaeal type ATPases that accompany the prokaryote-to-eukaryote transition are analyzed. The gene encoding the vacuolar-type proteolipid of the V-ATPase from Giardia lamblia is reported. Giardia has a typical vacuolar ATPase as observed from the common motifs shared between its proteolipid subunit and other eukaryotic vacuolar ATPases, suggesting that the former enzyme works as a hydrolase in this primitive eukaryote. The phylogenetic analyses of the V-ATPase catalytic subunit and the front and back halves of the proteolipid subunit placed Giardia as the deepest branch within the eukaryotes. Our phylogenetic analysis indicated that at least two independent duplication and fusion events gave rise to the larger proteolipid type found in eukaryotes and in Methanococcus. The spatial distribution of the conserved residues among the vacuolar-type proteolipids suggest a zipper-type interaction among the transmembrane helices and surrounding subunits of the V-ATPase complex. Important residues involved in the function of the F-ATP synthase proteolipid have been replaced during evolution in the V-proteolipid, but in some cases retained in the archaeal A-ATPase. Their possible implication in the evolution of V/F/A-ATPases is discussed. Received: 27 August 1997 / Accepted: 14 January 1998     

Presence of an extramitochondrial anion-stimulated ATPase in the rabbit kidney: Localization along the nephron and effect of corticosteroids

Summary To determine whether kidney membrane fractions contain an extramitochondrial anion-stimulated ATPase, we compared the pharmacological and kinetic properties of HCO₃-ATPase activities in mitochondrial and microsomal fractions prepared from rabbit kidney cortex and outer medulla. The results indicated that this activity differed markedly in each type of fraction. Microsomal HCO₃-ATPase was less sensitive than mitochondrial ATPase to azide, oligomycin, DCCD and thiocyanate, but was more sensitive to filipin and displayed different dependency towards ATP, magnesium and pH. Microsomal ATPase activity was stimulated by sulfite much more strongly than by bicarbonate, whereas mitochondrial activity was stimulated by both these anions to a similar extent. These results demonstrate the presence of an extramitochondrial HCO₃-ATPase in kidney membrane fractions. HCO₃-ATPase was also measured in single microdissected segments of the rabbit nephron using a radiochemical microassay previously developed for tubular Na, K-ATPase activity. An enzyme with the pharmacological and kinetic properties of the microsomal enzyme was detected in both proximal tubule, distal convoluted tubule and collecting duct, but the thick ascending limb was devoid of any detectable activity. Long-term DOCA administration markedly increased HCO₃-ATPase activity in the distal convoluted and collecting tubule. The insensitivity of microsomal HCO₃-ATPase to vanadate indicates that it belongs to the F₀–F₁ class of ATPases, and might therefore be involved in proton transport. This hypothesis is also supported by the localization of tubular HCO₃-ATPase activity at the sites of urinary acidification.     

Vibrational spectroscopy of bacteriorhodopsin mutants: I. Tyrosine-185 protonates and deprotonates during the photocycle

The techniques of FTIR difference spectroscopy and site-directed mutagenesis have been combined to investigate the role of individual tyrosine side chains in the proton-pumping mechanism of bacteriorhodopsin (bR). For each of the 11 possible bR mutants containing a single Tyr----Phe substitution, difference spectra have been obtained for the bR----K and bR----M photoreactions. Only the Tyr-185----Phe mutation results in the disappearance of a set of bands that were previously shown to be due to the protonation of a tyrosinate during the bR----K photoreaction [Rothschild et al.: Proceedings of the National Academy of Sciences of the United States of America 83:347, (1986]). The Tyr-185----Phe mutation also eliminates a set of bands in the bR----M difference spectrum associated with deprotonation of a Tyr; most of these bands (e.g., positive 1272-cm-1 peak) are completely unaffected by the other ten Tyr----Phe mutations. Thus, tyrosinate-185 gains a proton during the bR----K reaction and loses it again when M is formed. Our FTIR spectra also provide evidence that Tyr-185 interacts with the protonated Schiff base linkage of the retinal chromophore, since the negative C = NH+ stretch band shifts from 1640 cm-1 in the wild type to 1636 cm-1 in the Tyr-185----Phe mutant. A model that is consistent with these results is that Tyr-185 is normally ionized and serves as a counter-ion to the protonated Schiff base. The primary photoisomerization of the chromophore translocates the Schiff base away from Tyr-185, which raises the pKa of the latter group and results in its protonation.     

Longitudinal component of trans-root electrical potential difference: evidence from application of metabolic inhibitors to the cut end of excised maize roots

Changes in trans-root electrical potential induced by application of metabolic inhibitors (carbonyl cyanide m-chlorophenylhydrazone, vanadate, diethylstilbestrol, N-ethyl maleimide, p-chloromercuribenzene sulfonic acid, KCN, salicylhydroxamic acid) and electron acceptors (hexachloroiridate IV and hexacyanoferrate III) to the cut end of excised roots of maize demonstrated existence of a longitudinal component of trans-root electrical potential. It was probably associated with redox plasma membrane bound system(s) and coupled to the cyanide sensitive and alternative respiration pathways. This revised version was published online in July 2006 with corrections to the Cover Date.     

The cell membrane plays a crucial role in survival of bacteria and archaea in extreme environments

The cytoplasmic membrane of bacteria and archaea determine to a large extent the composition of the cytoplasm. Since the ion and in particular the proton and/or the sodium ion electrochemical gradients across the membranes are crucial for the bioenergetic conditions of these microorganisms, strategies are needed to restrict the permeation of these ions across their cytoplasmic membrane. The proton and sodium permeabilities of all biological membranes increase with the temperature. Psychrophilic and mesophilic bacteria, and mesophilic, (hyper)thermophilic and halophilic archaea are capable of adjusting the lipid composition of their membranes in such a way that the proton permeability at the respective growth temperature remains low and constant (homeo-proton permeability). Thermophilic bacteria, however, have more difficulties to restrict the proton permeation across their membrane at high temperatures and these organisms have to rely on the less permeable sodium ions for maintaining a high sodium-motive force for driving their energy requiring membrane-bound processes. Transport of solutes across the bacterial and archaeal membrane is mainly catalyzed by primary ATP driven transport systems or by proton or sodium motive force driven secondary transport systems. Unlike most bacteria, hyperthermophilic bacteria and archaea prefer primary ATP-driven uptake systems for their carbon and energy sources. Several high-affinity ABC transporters for sugars from hyperthermophiles have been identified and characterized. The activities of these ABC transporters allow these organisms to thrive in their nutrient-poor environments. This revised version was published online in August 2006 with corrections to the Cover Date.     

tRNA 3' end maturation in archaea has eukaryotic features: the RNase Z from Haloferax volcanii

Here, we report the first characterization and partial purification of an archaeal tRNA 3' processing activity, the RNase Z from Haloferax volcanii. The activity identified here is an endonuclease, which cleaves tRNA precursors 3' to the discriminator. Thus tRNA 3' processing in archaea resembles the eukaryotic 3' processing pathway. The archaeal RNase Z has a KCl optimum at 5mM, which is in contrast to the intracellular KCl concentration being as high as 4M KCl.The archaeal RNase Z does process 5' extended and intron-containing pretRNAs but with a much lower efficiency than 5' matured, intronless pretRNAs. At least in vitro there is thus no defined order for 5' and 3' processing and splicing. A heterologous precursor tRNA is cleaved efficiently by the archaeal RNase Z. Experiments with precursors containing mutated tRNAs revealed that removal of the anticodon arm reduces cleavage efficiency only slightly, while removal of D and T arm reduces processing effciency drastically, even down to complete inhibition. Comparison with its nuclear and mitochondrial homologs revealed that the substrate specificity of the archaeal RNase Z is narrower than that of the nuclear RNase Z but broader than that of the mitochondrial RNase Z.     

Function, structure and regulation of cyanobacterial and chloroplast ATP synthase

The proton-translocating ATP synthase from chloroplasts and cyanobacteria forms ATP upon photosynthetic electron transport by using the proton gradient across the thylakoid membrane. Both enzymes contain nine different subunits and from the similarity in gene organisation and the high degree of amino acid sequence homology of the subunits it appears that these ATP synthases might have a common ancestor. Both enzymes need to be activated by membrane energisation in order to perform catalytic activity but, in contrast to the chloroplast ATP synthase, that from the studied cyanobacteria (with the exception of Spirulina platensis ) shows no effect of the redox state on activation. Functionally, the cyanobacterial enzyme corresponds to the reduced form of the chloroplast ATP synthase. In the chloroplast enzyme a stretch of 9 amino acids, including two cysteines in the γ-subunit, is involved in this redox effect and this stretch is absent in cyanobacteria. With γ-mutants from the cyanobacterium Synechocystis 6803 the role of this stretch is studied. When active, both the cyanobacterial and the reduced chloroplast ATP synthase transport 4 protons per ATP synthesised and hydrolysed. This ratio may depend on the environment of the enzyme such as protein and lipid composition and pH.     

向日葵V-ATPasea3亚基基因的克隆及表达分析

采用RACE技术,从向日葵P50中克隆V-ATPase a3亚基基因c DNA全长,并进行生物信息学分析;利用实时荧光定量PCR分析不同浓度、不同时间的Na Cl、ABA和PEG模拟干旱胁迫条件下V-ATPase a3亚基基因的表达特征,以及相同胁迫条件下该基因在向日葵不同器官的表达特征。序列分析表明,该基因c DNA全长2 873bp,含5'-UTR 109bp、3'-UTR 295bp及编码区2 469bp,编码822个氨基酸,其编码蛋白质的理论分子质量为204.55k Da,等电点为6.29,Gen Bank登录号为KU315054。该基因编码的蛋白质为疏水性的跨膜蛋白,亚细胞定位预测其在质膜上。向日葵V-ATPase a3亚基与已报道的10种植物的V-ATPase a3亚基的同源蛋白有高度相似的保守区域,在进化上与朝鲜蓟的亲缘关系最近。实时荧光定量PCR结果表明,向日葵受到Na Cl、ABA和PEG模拟干旱三种非生物胁迫后,V-ATPase a3亚基基因均上调表达,但表达模式不同,不同器官存在特异性表达差异。研究认为,V-ATPase a3亚基基因响应了向日葵非生物胁迫的应答,为加强对V-ATPase基因的利用奠定基础。     

Conversion of energy in halobacteria: ATP synthesis and phototaxis

Halobacteria are aerobic chemo-organotroph archaea that grow optimally between pH 8 and 9 using a wide range of carbon sources. These archaea have developed alternative processes of energy provision for conditions of high cell densities and the reduced solubility of molecular oxygen in concentrated brines. The halobacteria can switch to anaerobic metabolism by using an alternative final acceptor in the respiratory chain or by fermentation, or alternatively, they can employ photophosphorylation. Light energy is converted by several retinal-containing membrane proteins that, in addition to generating a proton gradient across the cell membrane, also make phototaxis possible in order to approach optimal light conditions. The structural and functional features of ATP synthesis in archaea are discussed, and similarities to F-ATPases (functional aspects) or vacuolar ATPases (structural aspects) are presented. Received: 18 December 1995 / Accepted: 3 April 1996     

Effects of longitudinal variations in stream habitat structure on fish abundance: an analysis based on subunit-scale habitat classification

SUMMARY 1. Stream reaches contain assortments of various habitat types that can be defined at different spatial scales, such as channel unit (e.g. pools, riffles) and subunit (patches within channel units). We described longitudinal (upstream–downstream) patterns of stream habitat structure by considering subunits as structural elements, and examined their effects on the abundance of masu salmon ( Oncorhynchus masou ) and rosyface dace ( Leuciscus ezoe ) in a third-order tributary of the Teshio River in northern Hokkaido, Japan.
2. Nine subunit types were determined on the basis of water depth, current velocity and substrate, using 0.5 × 0.5 m grids. Although both masu salmon and rosyface dace used pools as a major habitat, the former preferred a subunit type occurring at pool heads (PH subunit) while the latter preferred a slow-current edge type (SE-2 subunit).
3. Along the course of the stream, slow-edge subunits (SE-1, 2 and 3) increased in frequency downstream while fast-edge subunits (FE-1 and 2) decreased, suggesting a downstream development of slow-current edges. Regression analyses indicated that longitudinal variation in masu salmon abundance was explained by the area of PH, rather than pools. Masu salmon density increased with the area of PH. Rosyface dace abundance was explained by a combination of water depth and the area of SE-2, both effects being positive.
4. Longitudinal variations in the abundance of both species were related to the abundance of their preferred habitat at the subunit scale, rather than channel-unit scale. The results emphasise the importance of fine-scale patchiness when examining stream fish habitats.     

Structure-function analysis of the NB-ARC domain of plant disease resistance proteins

Resistance (R) proteins in plants are involved in pathogen recognitionand subsequent activation of innate immune responses. Most resistanceproteins contain a central nucleotide-binding domain. This so-calledNB-ARC domain consists of three subdomains: NB, ARC1, and ARC2.The NB-ARC domain is a functional ATPase domain, and its nucleotide-bindingstate is proposed to regulate activity of the R protein. A highlyconserved methionine–histidine–aspartate (MHD) motifis present at the carboxy-terminus of ARC2. An extensive mutationalanalysis of the MHD motif in the R proteins I-2 and Mi-1 isreported. Several novel autoactivating mutations of the MHDinvariant histidine and conserved aspartate were identified.The combination of MHD mutants with autoactivating hydrolysismutants in the NB subdomain showed that the autoactivation phenotypesare not additive. This finding indicates an important regulatoryrole for the MHD motif in the control of R protein activity.To explain these observations, a three-dimensional model ofthe NB-ARC domain of I-2 was built, based on the APAF-1 templatestructure. The model was used to identify residues importantfor I-2 function. Substitution of the selected residues resultedin the expected distinct phenotypes. Based on the model, itis proposed that the MHD motif fulfils the same function asthe sensor II motif found in AAA+ proteins (ATPases associatedwith diverse cellular activities)—co-ordination of thenucleotide and control of subdomain interactions. The presented3D model provides a framework for the formulation of hypotheseson how mutations in the NB-ARC exert their effects. Key words: Intramolecular interactions, MHD motif, NB-ARC domain, plant disease resistance, protein structure, R proteins, signal transduction, site-directed mutagenesis     

A Complex of Cas Proteins 5, 6, and 7 Is Required for the Biogenesis and Stability of Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR)-derived RNAs (crRNAs) in Haloferax volcanii

The clustered regularly interspaced short palindromic repeats/CRISPR-associated (CRISPR-Cas) system is a prokaryotic defense mechanism against foreign genetic elements. A plethora of CRISPR-Cas versions exist, with more than 40 different Cas protein families and several different molecular approaches to fight the invading DNA. One of the key players in the system is the CRISPR-derived RNA (crRNA), which directs the invader-degrading Cas protein complex to the invader. The CRISPR-Cas types I and III use the Cas6 protein to generate mature crRNAs. Here, we show that the Cas6 protein is necessary for crRNA production but that additional Cas proteins that form a CRISPR-associated complex for antiviral defense (Cascade)-like complex are needed for crRNA stability in the CRISPR-Cas type I-B system in Haloferax volcanii in vivo. Deletion of the cas6 gene results in the loss of mature crRNAs and interference. However, cells that have the complete cas gene cluster (cas1–8b) removed and are transformed with the cas6 gene are not able to produce and stably maintain mature crRNAs. crRNA production and stability is rescued only if cas5, -6, and -7 are present. Mutational analysis of the cas6 gene reveals three amino acids (His-41, Gly-256, and Gly-258) that are essential for pre-crRNA cleavage, whereas the mutation of two amino acids (Ser-115 and Ser-224) leads to an increase of crRNA amounts. This is the first systematic in vivo analysis of Cas6 protein variants. In addition, we show that the H. volcanii I-B system contains a Cascade-like complex with a Cas7, Cas5, and Cas6 core that protects the crRNA.     

Affinity Purification and Structural Features of the Yeast Vacuolar ATPase Vo Membrane Sector

The membrane sector (V_o) of the proton pumping vacuolar ATPase (V-ATPase, V₁V_o-ATPase) from Saccharomyces cerevisiae was purified to homogeneity, and its structure was characterized by EM of single molecules and two-dimensional crystals. Projection images of negatively stained V_o two-dimensional crystals showed a ring-like structure with a large asymmetric mass at the periphery of the ring. A cryo-EM reconstruction of V_o from single-particle images showed subunits a and d in close contact on the cytoplasmic side of the proton channel. A comparison of three-dimensional reconstructions of free V_o and V_o as part of holo V₁V_o revealed that the cytoplasmic N-terminal domain of subunit a (a_NT) must undergo a large conformational change upon enzyme disassembly or (re)assembly from V_o, V₁, and subunit C. Isothermal titration calorimetry using recombinant subunit d and a_NT revealed that the two proteins bind each other with a K_d of ∼5 μm. Treatment of the purified V_o sector with 1-palmitoyl-2-hydroxy-sn-glycero-3-[phospho-rac-(1-glycerol)] resulted in selective release of subunit d, allowing purification of a V_oΔd complex. Passive proton translocation assays revealed that both V_o and V_oΔd are impermeable to protons. We speculate that the structural change in subunit a upon release of V₁ from V_o during reversible enzyme dissociation plays a role in blocking passive proton translocation across free V_o and that the interaction between a_NT and d seen in free V_o functions to stabilize the V_o sector for efficient reassembly of V₁V_o.