In vitro spontaneous reorganization of Haloferax volcanii envelope material into geometrical forms

High concentrations of NaCl and divalent cations were required for the stabilization of Haloferax volcanii envelopes. When the divalent cation concentration was lowered, the envelopes lost their angular shape and rouded up and the S-layer detached. When the combination of salts was just below the minimum enabling the envelope stabilization, partial rounding up and loss of the S-layer were observed. After a few days, a spontaneous and continuous reorganization of the envelope material occurred leading to the formation of geometrical envelope-like structures. This process could be stopped by either lowering the divalent cation concentration or by cooling the preparation, and resumed by restoring the initial conditions.Deceased 1990     

ATP is required for K+ active transport in the archaebacterium Haloferax volcanii

The Archaebacterium Haloferax volcanii concentrates K⁺ up to 3.6 M. This creates a very large K⁺ ion gradient of between 500- to 1,000-fold across the cell membrane. H. volcanii cells can be partially depleted of their internal K⁺ but the residual K⁺ concentration cannot be lowered below 1.5 M. In these conditions, the cells retain the ability to take up potassium from the medium and to restore a high internal K⁺ concentration (3 to 3.2 M) via an energy dependent, active transport mechanism with a K _m of between 1 to 2 mM. The driving force for K⁺ transport has been explored. Internal K⁺ concentration is not in equilibrium with m suggesting that K⁺ transport cannot be accounted for by a passive uniport process. A requirement for ATP has been found. Indeed, the depletion of the ATP pool by arsenate or the inhibition of ATP synthesis by N,N-dicyclohexylcarbodiimide inhibits by 100% K⁺ transport even though membrane potential m is maintained under these conditions. By contrast, the necessity of a m for K⁺ accumulation has not yet been clearly demonstrated. K⁺ transport in H. volcanii can be compared with K⁺ transport via the Trk system in Escherichia coli.Abbreviations CCCP Carbonylcyanide m-chlorophenyl-hydrazone - DCCD N,N-dicyclohexylcarbodiimide - MES 2-[N-morpholino] ethane sulfonic acid - MOPS 3-[N-morpholino] propane sulfonic acid - TRIS Tris (hydroxymethyl) aminomethane - TPP tetraphenyl phosphonium     

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.     

Ultrastructural observations on the cuticular envelope in salt glands ofFrankenia pauciflora

Summary During five developmental stages in differentiation of salt glands in leaves ofFrankenia pauciflora, details of the deposition of incrusting material in the cuticular envelope,i.e., hydrophobic suberin and/or cutin, have been observed by means of transmission electron microscopy.Around each transfusion area in the cuticular envelope a conspicuous lamellate ring structure is found. Thin 3.5 nm lamellae associated with the plasmalemma around each ring structure appear to participate in the formation of tripartite structures showing a reversed contrast compared to the plasmalemma. Below the ring structure the cuticular envelope is divided into an outer fibrillar and an inner amorphous zone. A gradual transition between the tripartite lamellae of the ring structure and the amorphous material of the envelope is evident. Very dense material present between the lamellae appear to accumulate in the transition zone. The results are discussed in relation to basic structural features of various incrustations of lipid nature.     

Salt-dependent studies of NADP-dependent isocitrate dehydrogenase from the halophilic archaeon <Emphasis Type="Italic">Haloferax volcanii</Emphasis>

The salt-dependent stability of recombinant dimeric isocitrate dehydrogenase [ICDH; isocitrate: NADP oxidoreductase (decarboxylating), EC 1.1.1.42] from the halophilic archaeon Haloferax volcanii (Hv) was investigated in various conditions. Hv ICDH dissociation/deactivation was measured to probe the respective effect of anions and cations on stability. Surprisingly, enzyme stability was found to be mainly sensitive to cations and very little (or not) sensitive to anions. Divalent cations induced a strong shift of the active/inactive transition towards low salt concentration. A high resistance of Hv ICDH to chemical denaturation was also found. The data were analysed and are discussed in the framework of the solvation stability model for halophilic proteins.     

Complete Reversal of Coenzyme Specificity of Isocitrate Dehydrogenase from <Emphasis Type="Italic">Haloferax volcanii</Emphasis>

Haloferax volcanii Ds-threo-isocitrate dehydrogenase (ICDH) was highly expressed in bacteria as inclusion bodies. The recombinant enzyme was refolded, purified and characterized, and was found to be NADP-dependent like the wild-type protein. Sequence alignment of several isocitrate dehydrogenases from evolutionarily divergent organisms including H. volcanii revealed that the amino acid residues involved in coenzyme specificity are highly conserved. Our objective was to switch the coenzyme specificity of halophilic ICDH by altering these conserved amino acids. We were able to switch coenzyme specificity from NADP⁺ to NAD⁺ by changing five amino acids by site-directed mutagenesis (Arg291, Lys343, Tyr344, Val350 and Tyr390). The five mutants of ICDH were overexpressed in Escherichia coli as inclusion bodies and each recombinant ICDH protein was refolded and purified, and its kinetic parameters were determined. Coenzyme specificity did not switch until all five amino acids were substituted.     

NMR assignments of the binary hvDHFR1:folate complex

A better understanding of how salt affects enzyme activity can be gained via NMR studies of binary hvDHFR1:folate complex. Chemical shift assignments of the 17.9 kDa enzyme with bound substrate prepare the way for ongoing research of the effects of salt on enzyme flexibility through relaxation studies.     

Chemical analyses on cell envelope polymers of the halophilic,phototrophic Rhodospirillum salexigens

Whole cells of Rhodospirillum salexigens, an obligatory halophilic bacterium, have a very low peptidoglycan content (0.17 mol muramic acid/mg cell dry weight) which is not sufficient to form a sacculus structure. The isolated peptidoglycan contains glucosamine: muramic acid: diaminopimelic acid: alanine: glutamic acid in molar ratios of 1:1:1:2:3. The degree of cross linking is 30%. A polysaccharide consisting of glucosamine, an unknown compound X and a 2-amino-2-deoxy-pentose (relative molar ratios; 1:2:1) was extracted into the water phase of phenol water extracts of whole cells. The polysaccharide co-sedimented with peptidoglycan when cell homogenates were centrifuged in the presence of 4% NaCl (100,000xg, 4 h) or on a sucrose gradient (20–60% sucrose, 28,000xg, 16 h) in the presence or absence of NaCl and/or EDTA.Lack of -hydroxy fatty acids and of 2-keto-3-deoxyoctonate in all phenol-water extract fractions as well as in the whole cell hydrolysate indicates the absence of common outer membrane lipopolysaccharide in R. salexigens. Removal of the cell surface layer exposed six proteins to labeling with radioactive iodine catalyzed by lactoperoxidase. These proteins are suggested to be constituents of the outer membrane of R. salexigens.Abbreviations Ala alamine - A₂pm diaminopimelic acid - DDPT dimethyl-3,3-dithiobispropionimidate dihydrochloride - GlcN glucosamine - Glu glutamic acid - Gly glycine - His histidine - MurN muramic acid - SDS sodium dodecyl sulfate     

The 2-oxoacid dehydrogenase multienzyme complex of Haloferax volcanii

Those aerobic archaea whose genomes have been sequenced possess four adjacent genes that, by sequence comparisons with bacteria and eukarya, appear to encode the component enzymes of a 2-oxoacid dehydrogenase multienzyme complex. However, no catalytic activity of any such complex has ever been detected in the archaea. In Thermoplasma acidophilum, evidence has been presented that the heterologously expressed recombinant enzyme possesses activity with the branched chain 2-oxoacids and, to a lesser extent, with pyruvate. In the current paper, we demonstrate that in Haloferax volcanii the four genes are transcribed as an operon in vivo. However, no functional complex or individual enzyme, except for the dihydrolipoamide dehydrogenase component, could be detected in this halophile grown on a variety of carbon sources. Dihydrolipoamide dehydrogenase is present at low catalytic activities, the level of which is increased three to fourfold when Haloferax volcanii is grown on the branched-chain amino acids valine, leucine and isoleucine.     

Structural aspects of the adaptation of Nostoc muscorum to salt

The physiological and biochemical changes during the adaptation of Nostoc muscorum to salt are accompanied by specific structural changes. Cells of Nostoc muscorum exposed to saline medium vary in size and envelope organization. There are also drastic changes in the intracellular organization of the thylakoidal assembly. The heterocysts exhibit a preferential tolerance to NaCl rather than mannitol. These findings suggest that Nostoc muscorum is equipped with a specific physiological capacity for NaCl tolerance.     

Identification of several intracellular carbohydrate-degrading activities from the halophilic archaeon Haloferax mediterranei

Three different amylolytic activities, designated AMY1, AMY2, and AMY3 were detected in the cytoplasm of the extreme halophilic archaeon Haloferax mediterranei grown in a starch containing medium. This organism had also been reported to excrete an α-amylase into the external medium in such conditions. The presence of these different enzymes which are also able to degrade starch may be related to the use of the available carbohydrates and maltodextrins, including the products obtained by the action of the extracellular amylase on starch that may be transported to the cytoplasm of the organism. The behavior of these intracellular hydrolytic enzymes on starch is reported here and compared with their extracellular counterpart. Two of these glycosidic activities (AMY1, AMY3) have also been purified and further characterized. As with other halophilic enzymes, they were salt dependent and displayed maximal activity at 3 M NaCl, and 50°C. The purification steps and molecular masses have also been reported. The other activity (AMY2) was also detected in extracts from cells grown in media with glycerol instead of starch and in a yeast extract medium. This enzyme was able to degrade starch yielding small oligosaccharides and displayed similar halophilic behavior with salt requirement in the range 1.5–3 M NaCl. Electronic supplementary material  The online version of this article (doi:) contains supplementary material, which is available to authorized users.     

Dynamics of a bloom of halophilic archaea in the Dead Sea

After a period of more than ten years in which bacterial and algal community sizes were extremely small, a dense bloom of halophilic archaea developed in the upper 5–10 m of the Dead Sea water column in the summer of 1992. The development of this bloom followed a dilution of the upper water layer by winter rainfloods, which enabled the development of a short-lived dense bloom of the unicellular green alga Dunaliella parva. The dense archaeal community (up to 3.5 × 10⁷ cells m1^–1 in June 1992) imparted a red coloration to the Dead Sea, due to its high content of bacterioruberin. Bacteriorhodopsin was not detected. High levels of potential heterotrophic activity were associated with the bloom, as measured by the incorporation of labeled organic substrates. After the decline of the algal bloom, archaeal numbers in the lake decreased only little, and most of the community was still present at the end of 1993. The amount of carotenoid pigment per cell, however, decreased 2–3-fold between June 1992 and August 1993. No new algal and archaeal blooms developed after the winter floods of 1992–1993, in spite of the fact that salinity values in the surface layer were sufficiently low to support a new algal bloom. A remnant of the 1992 Dunaliella bloom maintained itself at the lower end of the pycnocline at depths between 7 and 13 m (September 1992–August 1993). Its photosynthetic activity was small, and very little stimulation of archaeal growth and activity was associated with this algal community.     

嗜盐古菌Haloferax sp. D1227中超氧化物歧化酶功能鉴定及其增强细菌耐盐性的研究

【背景】细菌、酵母或植物来源的超氧化物歧化酶(Superoxide dismutase,SOD)编码基因在异源宿主中表达并提高宿主耐盐性的研究已有一些报道,其异源宿主也多为植物,而古菌来源的超氧化物歧化酶编码基因在细菌中成功表达并提高其耐盐性的研究尚无报道。【目的】寻找嗜盐古菌Haloferax sp.D1227中的超氧化物歧化酶编码基因并鉴定其功能,将其在4-硝基苯酚降解细菌Burkholderia sp.SJ98中表达,研究该古菌的超氧化物歧化酶对菌株SJ98耐盐性和降解4-硝基苯酚功能的影响。【方法】通过生物信息学方法寻找嗜盐古菌D1227中潜在的超氧化物歧化酶编码基因,利用表达载体p ET-28a和广泛宿主载体p BBR1MCS-2将其分别在E.coli BL21(DE3)和4-硝基苯酚的降解菌株SJ98中异源表达,检测细胞抽提液和纯化蛋白的超氧化物歧化酶比活力。分别以葡萄糖和4-硝基苯酚为碳源,在M9培养基和添加500 mmol/L Na Cl(Na Cl含量约3%)的M9培养基中分别培养细菌SJ98的重组菌株和空载体重组菌株,利用全自动生长曲线分析仪和高效液相色谱等方法检测重组菌株的生长能力和对4-硝基苯酚的降解能力。【结果】通过生物信息学分析,在嗜盐古菌D1227基因组中发现了潜在的超氧化物歧化酶编码基因sod A,其在E.coli BL21(DE3)和菌株SJ98中分别异源表达均具有超氧化物歧化酶活力[细胞抽提液的比活力分别为21.07±0.02 U/mg和84.56±0.16 U/mg,从BL21(DE3)菌株纯化的蛋白Sod AD1227比活力为179.46±3.43 U/mg]。在添加500 mmol/L Na Cl的M9培养基中培养时,以葡萄糖为碳源,重组菌株SJ98[p BBR-sod A]仍可正常生长,而空载体对照菌株SJ98[p BBR1MCS-2]几乎丧失了生长能力;以4-硝基苯酚为碳源,菌株SJ98[p BBR-sod A]保持了利用底物生长和降解底物的能力,而菌株SJ98[p BBR1MCS-2]的生长和降解能力几乎丧失。用软件Phyre2模拟分析Sod AD1227的单体结构,该蛋白拥有Fe/Mn-SOD家族的典型结构特征,推测其属于Fe/Mn-SOD家族。【结论】本研究为利用古菌SOD对细菌进行改造以适应高盐环境中降解有机污染物的应用提供了潜在的可行性。     

Bacteriorhodopsin in a bloom of halobacteria in the Dead Sea

A dense bloom of red halobacteria developed in the Dead Sea in the summer 1980, bacterial densities of up to 1.9 x10⁷ cells ml^-1 were observed. The population consisted of two types: pleomorphic, cup-shaped cells and rod-shaped cells. A high content of bacteriorhodopsin was found in the bloom (up to 0.4 nmol per mg protein). The rod-shaped Halobacterium was isolated and was shown to contain bacteriorhodopsin.Abbreviations 20 specific gravity at 20°C - Tris Tris-(hydroxymethyl)-aminomethane     

Production of polyhydroxyalkanoates from inexpensive extruded rice bran and starch by Haloferax mediterranei

Low-cost raw materials can be used to reduce significantly the production cost of polyhydroxyalkanoates (PHA). In this study, extruded rice bran (ERB) and extruded cornstarch (ECS) were used as carbon sources to produce PHA by an archaea, Haloferax mediterranei, which cannot use native rice bran or cornstarch as a carbon source. By employing pH-stat control strategy to maintain pH at 6.9–7.1 in a 5-liter jar fermentor using ERB:ECS (1:8 g/g) as the major carbon source, we obtained a cell concentration of 140 g/L, PHA concentration of 77.8 g/L and PHA content of 55.6 wt.% in a repeated fed-batch fermentation. In contrast, when ECS was used as the major carbon source, we obtained 62.6 g/L cell concentration, 24.2 g/L PHA concentration and 38.7 wt.% PHA content. Under a hyper-saline condition and with no nitrogen-limitation restriction, the repeated fed-batch process can be sustained a long time for the mass production of PHA.     

Kinetic folding of Haloferax volcanii and Escherichia coli dihydrofolate reductases: haloadaptation by unfolded state destabilization at high ionic strength

Salts affect protein stability by multiple mechanisms (e.g., the Hofmeister effect, preferential hydration, electrostatic effects and weak ion binding). These mechanisms can affect the stability of both the native state and the unfolded state. Previous equilibrium stability studies demonstrated that KCl stabilizes dihydrofolate reductases (DHFRs) from Escherichia coli (ecDHFR, E. coli DHFR) and Haloferax volcanii (hvDHFR1, H. volcanii DHFR encoded by the hdrA gene) with similar efficacies, despite adaptation to disparate physiological ionic strengths (0.2 M versus 2 M). Kinetic studies can provide insights on whether equilibrium effects reflect native state stabilization or unfolded state destabilization. Similar kinetic mechanisms describe the folding of urea-denatured ecDHFR and hvDHFR1: a 5-ms stopped-flow burst-phase species that folds to the native state through two sequential intermediates with relaxation times of 0.1-3 s and 25-100 s. The latter kinetic step is very similar to that observed for the refolding of hvDHFR1 from low ionic strength. The unfolding of hvDHFR1 at low ionic strength is relatively slow, suggesting kinetic stabilization as observed for some thermophilic enzymes. Increased KCl concentrations slow the urea-induced unfolding of ecDHFR and hvDHFR1, but much less than expected from equilibrium studies. Unfolding rates extrapolated to 0 M denaturant, k_unf(H₂O), are relatively independent of ionic strength, demonstrating that the KCl-induced stabilization of ecDHFR and hvDHFR1 results predominantly from destabilization of the unfolded state. This supports the hypothesis from previous equilibrium studies that haloadaptation harnesses the effects of elevated salt concentrations on the properties of the aqueous solvent to enhance protein stability.     

Structure, organization, and expression of genes coding for envelope components in the archaeon Methanosarcina mazei S-6

The antigenic mosaics of archaeal species are complex and lead to the distinction of different immunotypes. We began the dissection of the antigenic mosaic of the methanogen Methanosarcina mazei S-6 by gene cloning and sequencing. The analysis of the sequence, organization, and in vitro (heterologous) and in vivo expression of two three-gene clusters that encode proteins localized to the cell envelope and that are recognized by antibodies for surface structures is presented in this report. The amino acid sequences and compositions share characteristics with S-layer proteins and, most notably, have repeats of conserved sequences and secondary structures. Expressed genes produced proteins with a tendency to oligomerize, and one of these proteins was susceptible to breakdown at regular intervals. Altogether, the data reveal a modular system (clusters of homologous genes, proteins of similar sequences with conserved repeats) seemingly suitable for assembling an enormous variety of final molecular structures by rearranging and combining genes, proteins, and repeats, and thus generate the observed wide spectrum of antigenic diversity. Received: 26 June 1997 / Accepted: 5 November 1997     

Localization of chlorophyllase in the chloroplast envelope

Chlorophyllase catalyzes the first step in the catabolic pathway of chlorophyll. It is a constitutive enzyme located in chloroplast membranes. In isolated plastids the hydrolysis of the endogenous chlorophyll does not take place unless the membranes are solubilized in the presence of detergent. The structural latency of chlorophyllase activity appears to be due to the differential locations of substrate and enzyme within the plastids. Envelope membranes prepared from both chloroplasts and gerontoplasts contain chlorophyllase activity. The isolation of envelopes is associated with a marked increase in chlorophyllase activity per unit of protein. Yields of chlorophyllase and of specific envelope markers in the final preparations are similar, suggesting that the enzyme may be located in the envelope. It is hypothesized that the breakdown of chlorophyll during leaf senescence requires a mechanism that mediates the transfer of chlorophyll from the thylakoidal pigment-protein complexes to the sites of catabolic reactions in the envelope.Abbreviations ACT acyl CoA thioesterase - Chl chlorophyll - Chlide chlorophyllide - PC phosphatidylcholine