Exploring the potentials of halophilic prokaryotes from a solar saltern for synthesizing nanoparticles: The case of silver and selenium

Halophiles are the organisms that thrive in extreme high salt environments. Despite the extensive studies on their biotechnological potentials, the ability of halophilic prokaryotes for the synthesis of nanoparticles has remained understudied. In this study, the archaeal and bacterial halophiles from a solar saltern were investigated for the intracellular/extracellular synthesis of silver and selenium nanoparticles. Silver nanoparticles were produced by the archaeal Haloferax sp. (AgNP-A, intracellular) and the bacterial Halomonas sp. (AgNP-B, extracellular), while the intracellular selenium nanoparticles were produced by the archaeal Halogeometricum sp. (SeNP-A) and the bacterial Bacillus sp. (SeNP-B). The nanoparticles were characterized by various techniques including UV-Vis spectroscopy, XRD, DLS, ICP-OES, Zeta potentials, FTIR, EDX, SEM, and TEM. The average particle size of AgNP-A and AgNP-B was 26.34 nm and 22 nm based on TEM analysis. Also, the characteristic Bragg peaks of face-centered cubic with crystallite domain sizes of 13.01 nm and 6.13 nm were observed in XRD analysis, respectively. Crystallographic characterization of SeNP-A and SeNP-B strains showed a hexagonal crystallite structure with domain sizes of 30.63 nm and 29.48 nm and average sizes of 111.6 nm and 141.6 nm according to TEM analysis, respectively. The polydispersity index of AgNP-A, AgNP-B, SeNP-A, and SeNP-B was determined as 0.26, 0.28, 0.27, and 0.36 and revealed high uniformity of the nanoparticles. All of the synthesized nanoparticles were stable and their zeta potentials were calculated as (mV): -33.12, -35.9, -31.2, and -29.34 for AgNP-A, AgNP-B, SeNP-A, and SeNP-B, respectively. The nanoparticles showed the antibacterial activity against various bacterial pathogens. The results of this study suggested that the (extremely) halophilic prokaryotes have great potentials for the green synthesis of nanoparticles.

Production of Polyhydroxyalkanoates by Two Halophilic Archaeal Isolates from Chott El Jerid Using Inexpensive Carbon Sources

The large use of conventional plastics has resulted in serious environmental problems. Polyhydroxyalkanoates represent a potent replacement to synthetic plastics because of their biodegradable nature. This study aimed to screen bacteria and archaea isolated from an extreme environment, the salt lake Chott El Jerid for the accumulation of these inclusions. Among them, two archaeal strains showed positive results with phenotypic and genotypic methods. Phylogenetic analysis, based on the 16S rRNA gene, indicated that polyhydroxyalkanoate (PHA)-producing archaeal isolates CEJGTEA101 and CEJEA36 were related to Natrinema altunense and Haloterrigena jeotgali, respectively. Gas chromatography and UV-visible spectrophotometric analyses revealed that the PHA were identified as polyhydroxybutyrate and polyhydroxyvalerate, respectively. According to gas chromatography analysis, the strain CEJGTEA101 produced maximum yield of 7 wt % at 37 °C; pH 6.5; 20% NaCl and the strain CEJEA36 produced 3.6 wt % at 37 °C; pH 7; 25% NaCl in a medium supplemented with 2% glucose. Under nutritionally optimal cultivation conditions, polymers were extracted from these strains and were determined by gravimetric analysis yielding PHA production of 35% and 25% of cell dry weight. In conclusion, optimization of PHA production from inexpensive industrial wastes and carbon sources has considerable interest for reducing costs and obtaining high yield.

Characterisation of denatured states of sensory rhodopsin II by solution-state NMR

Sensory rhodopsin II (pSRII), a retinal-binding photophobic receptor from Natronomonas pharaonis, is a novel model system for membrane protein folding studies. Recently, the SDS-denatured states and the kinetics for reversible unfolding of pSRII have been investigated, opening the door to the first detailed characterisation of denatured states of a membrane protein by solution-state nuclear magnetic resonance (NMR) using uniformly 15N-labelled pSRII. SDS denaturation and acid denaturation of pSRII both lead to fraying of helix ends but otherwise small structural changes in the transmembrane domain, consistent with little changes in secondary structure and disruption of the retinal-binding pocket and tertiary structure. Widespread changes in the backbone amide dynamics are detected in the form of line broadening, indicative of μs-to-ms timescale conformational exchange in the transmembrane region. Detailed analysis of chemical shift and intensity changes lead to high-resolution molecular insights on structural and dynamics changes in SDS- and acid-denatured pSRII, thus highlighting differences in the unfolding pathways under the two different denaturing conditions. These results will form the foundation for furthering our understanding on the folding and unfolding pathways of retinal-binding proteins and membrane proteins in general, and also for investigating the importance of ligand-binding in the folding pathways of other ligand-binding membrane proteins, such as GPCRs.

Signaling and Adaptation Modulate the Dynamics of the Photosensoric Complex of Natronomonas pharaonis

Motile bacteria and archaea respond to chemical and physical stimuli seeking optimal conditions for survival. To this end transmembrane chemo- and photoreceptors organized in large arrays initiate signaling cascades and ultimately regulate the rotation of flagellar motors. To unravel the molecular mechanism of signaling in an archaeal phototaxis complex we performed coarse-grained molecular dynamics simulations of a trimer of receptor/transducer dimers, namely NpSRII/NpHtrII from Natronomonas pharaonis. Signaling is regulated by a reversible methylation mechanism called adaptation, which also influences the level of basal receptor activation. Mimicking two extreme methylation states in our simulations we found conformational changes for the transmembrane region of NpSRII/NpHtrII which resemble experimentally observed light-induced changes. Further downstream in the cytoplasmic domain of the transducer the signal propagates via distinct changes in the dynamics of HAMP1, HAMP2, the adaptation domain and the binding region for the kinase CheA, where conformational rearrangements were found to be subtle. Overall these observations suggest a signaling mechanism based on dynamic allostery resembling models previously proposed for E. coli chemoreceptors, indicating similar properties of signal transduction for archaeal photoreceptors and bacterial chemoreceptors.

Achaea and bacteria can “see” and “sniffle”, they have photo- and chemosensors that measure the environment. On the cell poles, these sensor proteins form large arrays built of several thousands of different receptors. The receptors comprise extracellular or transmembrane sensory domains and elongated homodimeric coiled-coil bundles, which transduce the signals from the membrane across ~20 nm to a conserved cytoplasmic signaling subdomain in an unknown manner. In our study we performed coarse-grained molecular dynamics simulations of the phototactic receptor/transducer complex from Natronomonas pharaonis. Comparing fully methylated and demethylated complexes reveals an interconversion between states of different dynamics along the coiled-coil bundle, which might represent the essential characteristics of the signal transfer from the membrane to the binding sites of the downstream kinase CheA.

Bacterioruberin and salinixanthin carotenoids of extremely halophilic Archaea and Bacteria: a Raman spectroscopic study

Laboratory cultures of a number of red extremely halophilic Archaea (Halobacterium salinarum strains NRC-1 and R1, Halorubrum sodomense, Haloarcula valismortis) and of Salinibacter ruber, a red extremely halophilic member of the Bacteria, have been investigated by Raman spectroscopy using 514.5nm excitation to characterize their carotenoids. The 50-carbon carotenoid α-bacterioruberin was detected as the major carotenoid in all archaeal strains. Raman spectroscopy also detected bacterioruberin as the main pigment in a red pellet of cells collected from a saltern crystallizer pond. Salinibacter contains the C40-carotenoid acyl glycoside salinixanthin (all-E, 2'S)-2'-hydroxy-1'-[6-O-(methyltetradecanoyl)-β-d-glycopyranosyloxy]-3',4'-didehydro-1',2'-dihydro-β,ψ-carotene-4-one), for which the Raman bands assignments of are given here for the first time.

Development of antimicrobial thermoplastic material from archaeal poly-γ-L-glutamate and its nanofabrication

Here we describe a stoichiometric ion-complex of archaeal poly-γ-L-glutamate (L-PGA) and hexadecylpyridinium cation (HDP(+)), called PGAIC, which shows remarkable chemical resistance and potential as a novel functional thermoplastic. PGAIC films suppressed the proliferation of prokaryotic (Escherichia coli, Bacillus subtilis, Salmonella typhimurium, and Staphylococcus aureus) and eukaryotic (Saccharomyces cerevisiae) microorganisms. Moreover, its antifungal activity was demonstrated against a prevalent species of Candida (Candida albicans) and a filamentous fungus (Aspergillus niger). The minimal inhibitory concentrations were estimated as 0.25 mg mL(-1), and zones of growth inhibition appeared when PGAIC-coated polyethylene terephthalate (PET) films were placed in culture plates, whereas PET had very little effect on fungal growth. Soluble PGAIC thus shows promises as an antimicrobial and as a coating substrate. We also succeeded in synthesizing an L-PGA-based nanofiber using an ethanol solution of PGAIC.

Diketopiperazines produced by the halophilic archaeon, Haloterrigena hispanica, activate AHL bioreporters

The generic term "quorum sensing" has been adopted to describe the bacterial cell-to-cell communication mechanism which coordinates gene expression when the population has reached a high cell density. Quorum sensing depends on the synthesis of small molecules that diffuse in and out of bacterial cells. There are few reports about this mechanism in Archaea. We report the isolation and chemical characterization of small molecules belonging to class of diketopiperazines (DKPs) in Haloterrigena hispanica, an extremely halophilic archaeon. One of the DKPs isolated, the compound cyclo-(L-prolyl-L-valine) activated N-acyl homoserine lactone (AHL) bioreporters, indicating that Archaea may have the ability to interact with AHL-producing bacteria within mixed communities.

The Lon protease from the haloalkaliphilic archaeon Natrialba magadii is transcriptionally linked to a cluster of putative membrane proteases and displays DNA-binding activity

The ATP-dependent Lon protease is universally distributed in bacteria, eukaryotic organelles and archaea. In comparison with bacterial and eukaryal Lon proteases, the biology of the archaeal Lon has been studied to a limited extent. In this study, the gene encoding the Lon protease of the alkaliphilic haloarchaeon Natrialba magadii (Nmlon) was cloned and sequenced, and the genetic organization of Nmlon was examined at the transcriptional level. Nmlon encodes a 84 kDa polypeptide with a pI of 4.42 which contains the ATPase, protease and membrane targeting domains of the archaeal-type LonB proteases. Nmlon is part of an operon that encodes membrane proteases and it is transcribed as a polycistronic mRNA in N. magadii cells at different growth stages. Accordingly, NmLon was detected in cell membranes of N. magadii throughout growth by Western blot analysis using specific anti-NmLon antibodies. Interestingly, in electrophoretic mobility shift assays, purified NmLon bound double stranded as well as single stranded DNA in the presence of elevated salt concentrations. This finding shows that DNA-binding is conserved in the LonA and LonB subfamilies and suggests that Lon-DNA interaction may be relevant for its function in haloarchaea.

Extremolyte-like applicability of an archaeal exopolymer, poly-gamma-L-glutamate

An extremely halophilic archaeon Natrialba aegyptiaca produces extracellular poly-gamma-glutamate (PGA), in which only L-glutamate is polymerized via gamma-amide linkages. We examined the extremolyte-like applicability of archaeal PGA and found the ameliorating effects of L-PGA on the resistibility to freeze-thawing and proteolysis, thermostability, and alkalotolerance of a model enzyme, labile DNA ligase. For example, the coexistence of low (e.g. 0.01 mg mL(-1)) and high (e.g. 0.1 mg mL(-1)) concentrations of L-PGA with an average molecular mass of 1000 kDa increased the midpoint of thermal inactivation of DNA ligase by about 15 degrees C and 18 degrees C, respectively, and the model enzyme further remained active even under extremely alkaline conditions of pH 11.4 in the presence of the high concentration of L-PGA. This is the first characterization of the stereo-regular PGA molecules as atypical extremolytes. L-PGA from extremophiles has great potential as a bio-based protectant (or stabilizer) with industrial versatility.

Identification of polyhydroxyalkanoates in Halococcus and other haloarchaeal species

Polyhydroxyalkanoates (PHAs) are accumulated in many prokaryotes. Several members of the Halobacteriaceae produce poly-3-hydroxybutyrate (PHB), but it is not known if this is a general property of the family. We evaluated identification methods for PHAs with 20 haloarchaeal species, three of them isolates from Permian salt. Staining with Sudan Black B, Nile Blue A, or Nile Red was applied to screen for the presence of PHAs. Transmission electron microscopy and (1)H-nuclear magnetic resonance spectroscopy were used for visualization of PHB granules and chemical confirmation of PHAs in cell extracts, respectively. We report for the first time the production of PHAs by Halococcus sp. (Halococcus morrhuae DSM 1307(T), Halococcus saccharolyticus DSM 5350(T), Halococcus salifodinae DSM 8989(T), Halococcus dombrowskii DSM 14522(T), Halococcus hamelinensis JCM 12892(T), Halococcus qingdaonensis JCM 13587(T)), Halorubrum sp. (Hrr. coriense DSM 10284(T), Halorubrum chaoviator DSM 19316(T), Hrr. chaoviator strains NaxosII and AUS-1), haloalkaliphiles (Natronobacterium gregoryi NCMB 2189(T), Natronococcus occultus DSM 3396(T)) and Halobacterium noricense DSM 9758(T). No PHB was detected in Halobacterium salinarum NRC-1 ATCC 700922, Hbt. salinarum R1 and Haloferax volcanii DSM 3757(T). Most species synthesized PHAs when growing in synthetic as well as in complex medium. The polyesters were generally composed of PHB and poly-ss-hydroxybutyrate-co-3-hydroxyvalerate (PHBV). Available genomic data suggest the absence of PHA synthesis in some haloarchaea and in all other Euryarchaeota and Crenarchaeota. Homologies between haloarchaeal and bacterial PHA synthesizing enzymes had indicated to some authors probable horizontal gene transfer, which, considering the data obtained in this study, may have occurred already before Permian times.

Isolation and functional expression of the bop gene from Halobiforma lacisalsi

A novel bop gene was described from Halobiforma lacisalsi strain AJ5(T), an extremely halophilic archaeon isolated from Ayakekum Lake, China. Following six rounds of PCR amplification based on the conserved fragment of the bop gene, the complete sequence of the bop gene, including the 5' and 3' flanking regions of the conserved fragment, was obtained by the ligation-mediated PCR amplification (LPA) approach. The data presented provide us with further insight into the distribution of bop-like genes in the family Halobacteriaceae. This is the first example of a bop-like gene in halophiles found in the high-pH environment. Alignment and hydropathy analysis of the deduced amino acid sequence identified the conserved functional sites as well as some variations compared with other bacterio-opsins. Molecular phylogenetic analysis revealed the position of the bacterio-opsin of strain AJ5, which is closest to that of Haloterrigena sp. arg-4 with 85% identity. In the presence of all-trans retinal, recombinant Escherichia coli cells expressing the gene turned dark purple. The purple membrane from the recombinant E. coli showed maximal absorption at 540 nm.

Tryptophan 171 in Pharaonis phoborhodopsin (sensory rhodopsin II) interacts with the chromophore retinal and its substitution with alanine or threonine slowed down the decay of M- and O-intermediate

Pharaonis phoborhodopsin (ppR), also called pharaonis sensory rhodopsin II, NpSRII, is a photoreceptor for the photophobic response of Natronomonas pharaonis. Tryptophan 182 (W182) of bacteriorhodopsin (bR) is near the chromophore retinal and has been suggested to interact with retinal during the photoreaction and also to be involved in the hydrogen-bonding network around the retinal. W182 of bR is conserved in ppR as tryptophan 171 (W171). To elucidate whether W171 of ppR interacts with retinal during the photoreaction and/or is involved in the hydrogen-bonding network as in bR, we formed W171-substituted mutants of ppR, W171A and W171T. Our low-temperature spectroscopic study has revealed that the substitution of W171 to Ala or Thr resulted in the stabilization of M- and O-intermediates. The stability of M and absorption spectral changes during the M-decay were different depending on the substituted residue. These findings suggest that W171 in ppR interacts with retinal and the degree of the interaction depends on the substituted residues, which might be rate determining in the M-decay. In addition, the involvement of W171 in the hydrogen-bonding network is suggested by the O-decay. We also found that glycerol slowed the decay of M and not of O.

Application of fluorescence resonance energy transfer (FRET) to investigation of light-induced conformational changes of the phoborhodopsin/transducer complex

The photoreceptor phoborhodopsin (ppR; also called sensory rhodopsin II) forms a complex with its cognate the Halobacterial transducer II (pHtrII) in the membrane, through which changes in the environmental light conditions are transmitted to the cytoplasm in Natronomonas pharaonis to evoke negative phototaxis. We have applied a fluorescence resonance energy transfer (FRET)-based method for investigation of the light-induced conformational changes of the ppR/pHtrII complex. Several far-red dyes were examined as possible fluorescence donors or acceptors because of the absence of the spectral overlap of these dyes with all the photointermediates of ppR. The flash-induced changes of distances between the donor and an acceptor linked to cysteine residues which were genetically introduced at given positions in pHtrII(1-159) and ppR were determined from FRET efficiency changes. The dye-labeled complex was studied as solubilized in 0.1% n-dodecyl-beta-D-maltoside (DDM). The FRET-derived changes in distances from V78 and A79 in pHtrII to V185 in ppR were consistent with the crystal structure data (Moukhametzianov, R. et al. [2006] Nature, 440, 115-119). The distance from D102 in pHtrII linker region to V185 in ppR increased by 0.33 angstroms upon the flash excitation. These changes arose within 70 ms (the dead time of instrument) and decayed with a rate of 1.1 +/- 0.2 s. Thus, sub-angstrom-scale distance changes in the ppR/pHtrII complex were detected with this FRET-based method using far-red fluorescent dyes; this method should be a valuable tool to investigate conformation changes in the transducer, in particular its dynamics.

Participation of the surface structure of Pharaonis phoborhodopsin, ppR and its A149S and A149V mutants, consisting of the C-terminal alpha-helix and E-F loop, in the complex-formation with the cognate transducer pHtrII, as revealed by site-directed 13C solid-state NMR

We have recorded 13C solid state NMR spectra of [3-13C]Ala-labeled pharaonis phoborhodopsin (ppR) and its mutants, A149S and A149V, complexed with the cognate transducer pharaonis halobacterial transducer II protein (pHtrII) (1-159), to gain insight into a possible role of their cytoplasmic surface structure including the C-terminal alpha-helix and E-F loop for stabilization of the 2:2 complex, by both cross-polarization magic angle spinning (CP-MAS) and dipolar decoupled (DD)-MAS NMR techniques. We found that 13C CP-MAS NMR spectra of [3-13C]Ala-ppR, A149S and A149V complexed with the transducer pHtrII are very similar, reflecting their conformation and dynamics changes caused by mutual interactions through the transmembrane alpha-helical surfaces. In contrast, their DD-MAS NMR spectral features are quite different between [3-13C]Ala-A149S and A149V in the complexes with pHtrII: 13C DD-MAS NMR spectrum of [3-13C]Ala-A149S complex is rather similar to that of the uncomplexed form, while the corresponding spectral feature of A149V complex is similar to that of ppR complex in the C-terminal tip region. This is because more flexible surface structure detected by the DD-MAS NMR spectra are more directly influenced by the dynamics changes than the CP-MAS NMR. It turned out, therefore, that an altered surface structure of A149S resulted in destabilized complex as viewed from the 13C NMR spectrum of the surface areas, probably because of modified conformation at the corner of the helix E in addition to the change of hydropathy. It is, therefore, concluded that the surface structure of ppR including the C-terminal alpha-helix and the E-F loops is directly involved in the stabilization of the complex through conformational stability of the helix E.

Halorubrum litoreum sp. nov., an extremely halophilic archaeon from a solar saltern

An extremely halophilic archaeon, strain Fa-1T, was isolated from a marine solar saltern in Fujian, China. Strain Fa-1T required Mg2+ and at least 2.0 M NaCl for growth. It was able to grow at pH 6.5–9.0 (optimally at pH 7.0–7.5) and at 20–55 °C (optimally at 37–42 °C). The major polar lipids of strain Fa-1T were phosphatidylglycerol, phosphatidylglycerol phosphate methyl ester, phosphatidylglycerol sulfate and a sulfated diglycosyl diether. On the basis of a 16S rRNA gene sequence analysis, strain Fa-1T was closely related to nine species of the genus Halorubrum, showing sequence similarities of 97.4–98.4 %. The G+C content of the DNA of strain Fa-1T is 64.9 mol% (T m). DNA–DNA hybridization values between strain Fa-1T and the most closely related members of the genus Halorubrum were below 51 %. On the basis of the data from this study, strain Fa-1T represents a novel species of the genus Halorubrum, for which the name Halorubrum litoreum sp. nov. is proposed. The type strain is Fa-1T (=CGMCC 1.5336T =JCM 13561T).

Halopiger xanaduensis gen. nov., sp. nov., an extremely halophilic archaeon isolated from saline Lake Shangmatala in Inner Mongolia, China

Strain SH-6(T) was isolated from the sediment of Lake Shangmatala, a saline lake in Inner Mongolia (China). Cells were pleomorphic. The organism was neutrophilic and required at least 2.5 M (15 %) NaCl, but not MgCl(2), for growth; optimal growth occurred at 4.3 M (25 %) NaCl. The G+C content of its DNA was 63.1 mol%. 16S rRNA gene sequence analysis revealed that strain SH-6(T) is a member of the family Halobacteriaceae, but there was a low level of similarity with other members of this family. Highest sequence similarity (94.6 %) was obtained with the 16S rRNA genes of the type strains of Natronolimnobius innermongolicus and Natronolimnobius baerhuensis. Polar lipid analyses revealed that strain SH-6(T) contains phosphatidylglycerol and phosphatidylglyceromethylphosphate, derived from both C(20)C(20) and C(20)C(25) glycerol diethers together with the glycolipid S(2)-DGD-1. On the basis of the data obtained, the new isolate could not be classified in any recognized genus. Strain SH-6(T) is thus considered to represent a novel species in a new genus within the family Halobacteriaceae, order Halobacteriales, for which the name Halopiger xanaduensis gen. nov., sp. nov. is proposed. The type strain of Halopiger xanaduensis is SH-6(T) (=CECT 7173(T)=CGMCC 1.6379(T)=JCM 14033(T)).

Halovivax ruber sp. nov., an extremely halophilic archaeon isolated from Lake Xilinhot, Inner Mongolia, China

A Gram-negative, pleomorphic, extremely halophilic archaeon, designated strain XH-70(T), was isolated from the saline Lake Xilinhot, in Inner Mongolia, China. It formed small (0.9-1.5 mm), red-pigmented, elevated colonies on agar medium. The strain required at least 2.5 M NaCl and 5 mM Mg(2+) for growth. The 16S rRNA gene sequence analysis indicated that strain XH-70(T) belongs to the family Halobacteriaceae, showing 99.5 % similarity to the type strain of Halovivax asiaticus and 94.7 and 94.6 % similarity, respectively, to the type strains of Natronococcus amylolyticus and Natronococcus occultus. Polar lipid analysis supported the placement of strain XH-70(T) in the genus Halovivax. DNA-DNA hybridization studies (32 % with Halovivax asiaticus CGMCC 1.4248(T)), as well as biochemical and physiological characterization, allowed strain XH-70(T) to be differentiated from Halovivax asiaticus. A novel species, Halovivax ruber sp. nov., is therefore proposed to accommodate this strain. The type strain is XH-70(T) (=CGMCC 1.6204(T)=DSM 18193(T)=JCM 13892(T)).

Haloterrigena hispanica sp. nov., an extremely halophilic archaeon from Fuente de Piedra, southern Spain

An extremely halophilic archaeon belonging to the order Halobacteriales was isolated from Fuente de Piedra salt lake, Spain. This strain, designated FP1T, was a pleomorphic coccoid, neutrophilic and required at least 15 % (w/v) NaCl for growth. Strain FP1T grew at 37–60 °C, with optimal growth at 50 °C. Mg2+ was not required, but growth was observed with up to 10 % (w/v) MgSO4. Polar lipid analysis revealed the presence of mannose-6-sulfate(1-2)-glucose glycerol diether as a major glycolipid. Both C20C20 and C20C25 core lipids were present. The genomic DNA G+C content was 62.0 mol%. Phylogenetic analysis based on comparison of 16S rRNA gene sequences demonstrated that the isolate was most closely related to species of the genus Haloterrigena. DNA–DNA reassociation values between strain FP1T and the most closely related species of the genus Haloterrigena (Haloterrigena thermotolerans, Haloterrigena saccharevitans and Haloterrigena limicola) were lower than 29 %. It is therefore considered that strain FP1T represents a novel species of the genus Haloterrigena, for which the name Haloterrigena hispanica sp. nov. is proposed. The type strain is FP1T (=DSM 18328T=ATCC BAA-1310T).

Large-scale identification of N-terminal peptides in the halophilic archaea Halobacterium salinarum and Natronomonas pharaonis

Characterization of protein N-terminal peptides supports the quality assessment of data derived from genomic sequences (e.g., the correct assignment of start codons) and hints to in vivo N-terminal modifications such as N-terminal acetylation and removal of the initiator methionine. The current work represents the first large-scale identification of N-terminal peptides from prokaryotes, of the two halophilic euryarchaeota Halobacterium salinarum and Natronomonas pharaonis. Two methods were used that specifically allow the characterization of protein N-terminal peptides: combined fractional diagonal chromatography (COFRADIC) and strong cation exchange chromatography (SCX), both known to enrich for N-terminally blocked peptides. In addition to these specific methods, N-terminal peptide identifications were extracted from our previous genome-wide proteomic data. Combining all data, 606 N-terminal peptides from Hbt. salinarum and 328 from Nmn. pharaonis were reliably identified. These results constitute the largest available dataset holding identified and characterized protein N-termini for prokaryotes (archaea and bacteria). They allowed the validation/improvement of start codon assignments as automatic gene finders tend to misassign start codons for GC-rich genomes. In addition, the dataset allowed unravelling N-terminal protein maturation in archaea, showing that 60% of the proteins undergo methionine cleavage and that-in contrast to current knowledge-Nalpha-acetylation is common in the archaeal domain of life with 13-18% of the proteins being Nalpha-acetylated. The protein sets described in this paper are available by FTP and might be used as reference sets to test the performance of new gene finders.

Analysis of Light-Induced Conformational Changes of Natronomonas pharaonis Sensory Rhodopsin II by Time Resolved Electron Paramagnetic Resonance Spectroscopy†

The nature and kinetics of the conformational changes leading to the activated state of NpSRII/NpHtrII157 were investigated by time-resolved electron paramagnetic resonance (TR-EPR) spectroscopy in combination with site-directed spin labeling (SDSL) on a series of spin labeled mutants of NpSRII. A structural rearrangement of the cytoplasmic moiety of NpSRII upon light activation was detected (helices B, C, F and G). The increase in distance between helices C and F in the M-trapped state of the complex observed in one double mutant is in line with the notion that an outward movement of helix F occurs upon receptor activation. The data obtained from the NpSRII/NpHtrII157 complex reconstituted in purple membrane lipids are compared with those obtained from the X-ray structure of the late M-state of the complex which shows some discrepancies. The results are discussed in the context also of other biophysical and EPR experimental evidences.

Assignment of the hydrogen-out-of-plane and -in-plane vibrations of the retinal chromophore in the K intermediate of pharaonis phoborhodopsin

pharaonis phoborhodopsin (ppR; also called pharaonis sensory rhodopsin II, psR-II) is a photoreceptor protein for negative phototaxis in Natronomonas pharaonis. Photoisomerization of the retinal chromophore from all-trans to 13-cis initiates conformational changes of the protein leading to activation of the cognate transducer protein (pHtrII). Elucidation of the initial photoreaction, formation of the K intermediate of ppR, is important for understanding the mechanism of storage of photon energy. We have reported the K minus ppR Fourier transform infrared (FTIR) spectra, including several vibrational bands of the retinal, the protein, and internal water molecules. It is interesting that more vibrational bands were observed in the hydrogen-out-of-plane (HOOP) region than for the light-driven proton pump, bacteriorhodopsin. This result implied that the steric constraints on the retinal chromophore in the binding pocket of ppR are distributed more widely upon formation of the initial intermediate. In this study, we assigned the HOOP and hydrogen-in-plane vibrations by means of low-temperature FTIR spectroscopy applied to ppR reconstituted with retinal deuterated at C7, C8, C10-C12, C14, and C15. As a result, the 966 (+)/971 (-) and 958 (+)/961 (-) cm(-1) bands were assigned to the C7=C8 and C11=C12 Au HOOP modes, respectively, suggesting that the structural changes spread to the middle part of the retinal. The positive bands at 1001, 994, 987, and 979 cm(-1) were assigned to the C15-HOOP vibrations of the K intermediate, whose frequencies are similar to those of the K(L) intermediate of bacteriorhodopsin trapped at 135 K. Another positive band at 864 cm(-1) was assigned to the C14-HOOP vibration. Relatively many positive bands of hydrogen-in-plane vibrations supported the wide distribution of structural changes of the retinal as well. These results imply that the light energy was stored mainly in the distortions around the Schiff base region while some part of the energy was transferred to the distal part of the retinal.

[Characterization of extremely halophilic archaea isolated from saline environment in different parts of Turkey]

Ninety-five extremely halophilic strains were isolated from six distinct saline regions of Turkey by using complex medium containing 25% NaCl. The selected regions are Tuz Golu (salt lake), Ankara; Aci Lake, Denizli; Salda Lake, Denizli; Seyfe Lake, Kirsehir; Tuzla Lake, Kayseri; and Bolluk Lake, Konya. The isolated strains were tested for motility, Gram reaction, cell and colony morphologies, pigmentation, biochemical characteristics, and antibiotic sensitivities. According to membrane glycerol diether moieties and antibiotic susceptibilities, all isolated strains were found to belong to the domain Archaea. All isolates were examined for the presence of plasmids by agarose gel electrophoresis and it was established that most isolates contained plasmids that varied in number and whose molecular sizes ranged from 1 to 36.9 kbp. Whole-cell protein profiles from isolates were analyzed by SDS-PAGE and a similarity dendogram was constructed using the UPGMA method. Significant similarities and differences were observed among the isolates. The strains were clustered in eight groups and ten of our isolates were placed in the same group with the standard strains. The current study represents the first isolation and characterization of such a large collection of archeal strains from Turkey.

Halorubrum ezzemoulense sp. nov., a halophilic archaeon isolated from Ezzemoul sabkha, Algeria

A novel extremely halophilic archaeon was isolated from Ezzemoul sabkha, Algeria. The strain, designated 5.1(T), was neutrophilic, motile and Gram-negative. At least 15 % (w/v) NaCl was required for growth. The isolate grew at pH 6.5-9.0, with optimum growth at pH 7.0-7.5. Mg(2+) was required for growth. Polar lipids were C(20)C(20) derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate methyl ester, and phosphatidylglycerol sulfate and sulfated diglycosyl diether. The genomic DNA G+C content of strain 5.1(T) was 61.9 mol% (T(m)). Phylogenetic analysis based on comparison of 16S rRNA gene sequences revealed that strain 5.1(T) clustered with Halorubrum species. The results of DNA-DNA hybridization and biochemical tests allowed genotypic and phenotypic differentiation of strain 5.1(T) from other Halorubrum species. The name Halorubrum ezzemoulense sp. nov. (type strain 5.1(T)=CECT 7099(T)=DSM 17463(T)) is proposed.

Development of the signal in sensory rhodopsin and its transfer to the cognate transducer

The microbial phototaxis receptor sensory rhodopsin II (NpSRII, also named phoborhodopsin) mediates the photophobic response of the haloarchaeon Natronomonas pharaonis by modulating the swimming behaviour of the bacterium. After excitation by blue-green light NpSRII triggers, by means of a tightly bound transducer protein (NpHtrII), a signal transduction chain homologous with the two-component system of eubacterial chemotaxis. Two molecules of NpSRII and two molecules of NpHtrII form a 2:2 complex in membranes as shown by electron paramagnetic resonance and X-ray structure analysis. Here we present X-ray structures of the photocycle intermediates K and late M (M2) explaining the evolution of the signal in the receptor after retinal isomerization and the transfer of the signal to the transducer in the complex. The formation of late M has been correlated with the formation of the signalling state. The observed structural rearrangements allow us to propose the following mechanism for the light-induced activation of the signalling complex. On excitation by light, retinal isomerization leads in the K state to a rearrangement of a water cluster that partly disconnects two helices of the receptor. In the transition to late M the changes in the hydrogen bond network proceed further. Thus, in late M state an altered tertiary structure establishes the signalling state of the receptor. The transducer responds to the activation of the receptor by a clockwise rotation of about 15 degrees of helix TM2 and a displacement of this helix by 0.9 A at the cytoplasmic surface.

Unsaturated diether lipids in the psychrotrophic archaeon Halorubrum lacusprofundi

The major phospholipids of Halorubrum lacusprofundi grown at 25 degrees C were archaeol phosphatidylglycerol, archaeol phosphatidylglycerylsulphate and archaeol phosphatidylglycerylphosphate methyl ester. Glycolipids included a monoglycosyl archaeol and the sulphate ester of a diglycosyl archaeol. Cultures grown at 12 degrees C contained the same suite of phospho- and glycolipids, with the addition of a series of unsaturated analogues with up to six double bonds. The patterns of unsaturation were similar for all the phospholipid series, but a different pattern occurred in the glycolipids. The analytical techniques used in this study allow facile detection of unsaturated archaeal cell membrane lipids that are degraded by commonly used chemical derivatization procedures.

Intracellular ion and organic solute concentrations of the extremely halophilic bacterium Salinibacter ruber

Salinibacter ruber is a red obligatory aerobic chemoorganotrophic extremely halophilic Bacterium, related to the order Cytophagales. It was isolated from saltern crystallizer ponds, and requires at least 150 g l(-1) salt for growth. The cells have an extremely high potassium content, the ratio K(+)/protein being in the same range as in halophilic Archaea of the order Halobacteriales. X-ray microanalysis in the electron microscope of cells grown in medium of 250 g l(-1) salt confirmed the high intracellular K(+)concentrations, and showed intracellular chloride to be about as high as the cation concentrations within the cells. A search for intracellular organic osmotic solutes, using (13)C-NMR and HPLC techniques, showed glutamate, glycine betaine, and N-alpha-acetyllysine to be present in low concentrations only, contributing very little to the overall osmotic balance. The results presented suggest that the extremely halophilic Bacterium Salinibacteruses a similar mode of haloadaptation to that of the Archaea of the order Halobacteriales, and does not accumulate organic osmotic solutes such as are used by all other known halophilic and halotolerant aerobic Bacteria.

Comparisons of the polar lipid and pigment profiles of two solar salterns located in Newark, California, USA, and Eilat, Israel

The whole community pigments and lipids have been examined during a 5-year period in two commercial solar salterns located in the United States and in Israel. There were significant differences in the complexity of the lipid and pigment patterns within the California saltern system, and these differences were not consistent over the sampling period despite examination of ponds with the same salinity. The solar saltern system in Eilat, Israel, showed greater consistency during this sampling period and compared directly with previous studies. The complexity of the saltern in Newark, California, could be explained on the basis of the prevailing weather conditions (cooler and more rainfall) and the nutrient-enriched source water. The Eilat saltern, however, has an oligotrophic water source and has a considerably warmer and drier climate. This difference resulted in more diverse and more complex pigment and lipid patterns and presumably microbial populations in the Newark, California, plant than in the saltern in Eilat, Israel.

Structural diversity of membrane lipids in members of Halobacteriaceae

This minireview gives an updated and consolidated summary of taxonomic classification correlated with membrane phospholipid, glycolipid, and core lipid structural diversity within the family Halobacteriaceae. We also point out that the recently reported diversity in the membrane core lipid structure of a putative strain of Halobacterium (Halobacterium halobium strain IAM 13167) (Morita et al., Biosci. Biotechnol. Biochem., 62, 596-598, 1998) is not correct since the strain used by the authors has for some time been recognized not to be a member of the genus Halobacterium but a member of halobacteria group 2 (Grant and Larsen, Bergey's Manual of Systematic Bacteriology, Vol.3, pp. 2216-2233, 1989), which has recently been designated as a new genus, Natrinema (McGenity et al., Int. J. Syst. Bacteriol. 48, 1187-1196, 1998).

The effect of carboxyl group modification on the chromophore regeneration of archaeopsin-1 and bacterioopsin

Carboxyl group modification with DCCD and NCD-4 was employed to investigate the chemical environment of the side chains of archaeopsin-1 (aO-1) and bacterioopsin (bO). Some differences were observed between aO-1 and bO. Although DCCD or NCD-4 did not modify aO-1 in bleached membrane, they modified bO in bleached membrane and in mixed DMPC/CHAPS/SDS micelles at neutral pH, thereby affecting the opsin shift and the photocycle of the regenerated chromophore. On the contrary, after solubilization with SDS, aO-1 and bO were modified by DCCD and NCD-4, which decreased the chromophore regeneration. In particular, the reaction of aO-1 in SDS with NCD-4 proceeded in a 1:1 ratio at neutral pH. The fluorescence and CD spectra indicated that the modified site was located in the hydrophobic, asymmetrical region. Lysyl-endopeptidase digestion of NCD-4 modified aO-1 produced a fluorescent fragment and amino acid sequence analysis showed that Asp85 or Asp96 in helix C is a probable candidate for the modified residue at present. Kinetic CD measurements revealed that the introduction of N-acylurea at an Asp residue in helix C did not affect the formation of the transient intermediate but inhibited the side chain packing during refolding.

Halobacterial rhodopsins

Following the discovery of the bacteriorhodopsin proton pump in Halobacterium halobium (salinarum), not only the halorhodopsin halide pump and two photosensor rhodopsins (sensory rhodopsin and phoborhodopsin) in the same species, but also homologs of these four rhodopsins in strains of other genera of Halobacteriaceae have been reported. Twenty-eight full (and partial) sequences of the genomic DNA of these rhodopsins have been analyzed. The deduced amino acid sequences have led to new strategies and tactics for understanding bacterial rhodopsins on a comparative basis, as summarized briefly in this article. The data discussed include (i) alignment of the sequences to qualify/characterize the conserved residues; (ii) assignment of residues that cause differences in function(s)/properties; and (iii) phylogeny of the halobacterial rhodopsins to suggest their evolutionary paths. The four kinds of rhodopsin in each strain are assumed, on the basis of their genera-specific distributions, to have arisen by at least two gene-duplication processes during evolution prior to generic speciation. The first duplication of the rhodopsin ancestor gene yielded two genes, each of which was duplicated again to give four genes in the ancestor halobacterium. The bacterium carrying four rhodopsin genes, after accumulating mutations, became ready for generic speciation and the delivery of four rhodopsins to each species. The original rhodopsin ancestor is speculated to be closest to the proton pump (bacteriorhodopsin).

Typing of halophilic Archaea and characterization of their cell surface carbohydrates by use of lectins

Lectins are important tools for cell typing and for the study of cell surface components. They have been widely used for the analysis of carbohydrates on the surface of many eukaryotic and prokaryotic cells, but they have not yet been exploited in the study of the halophilic Archaea (family Halobacteriaceae), because of the high salinity required for the structural integrity of these microorganisms. We have defined the salt concentration threshold high enough for survival of the Archaea, but sufficiently low for lectins to bind to them. Under these conditions we studied the interactions of a series of lectins, exhibiting different sugar specificities, with diverse halophilic Archaea. Concanavalin A was the most reactive by virtue of its glucose (and mannose) binding. The other lectins varied in their interactions. The results indicate that lectins might be useful probes for both archaeal typing and analysis of their cell surface carbohydrates.

2-Sulfotrehalose, a novel osmolyte in haloalkaliphilic archaea

A novel 1-->1 alpha-linked glucose disaccharide with sulfate at C-2 of one of the glucose moieties, 1-(2-O-sulfo-alpha-D-glucopyranosyl)-alpha-D-glycopyranose, was found to be the major organic solute accumulated by a Natronococcus sp. and several Natronobacterium species. The concentration of this novel disaccharide, termed sulfotrehalose, increased with increasing concentrations of external NaCl, behavior consistent with its identity as an osmolyte. A variety of noncharged disaccharides (trehalose, sucrose, cellobiose, and maltose) were added to the growth medium to see if they could suppress synthesis and accumulation of sulfotrehalose. Sucrose was the most effective in suppressing biosynthesis and accumulation of sulfotrehalose, with levels as low as 0.1 mM being able to significantly replace the novel charged osmolyte. Other common osmolytes (glycine betaine, glutamate, and proline) were not accumulated or used for osmotic balance in place of the sulfotrehalose by the halophilic archaeons.

Electron transfer proteins from the haloalkaliphilic archaeon Natronobacterium pharaonis: possible components of the respiratory chain include cytochrome bc and a terminal oxidase cytochrome ba3

Natronobacterium pharaonis, an aerobic haloalkaliphilic archaebacterium, expresses high concentrations of redox proteins as do alkaliphilic eubacteria. The first redox protein characterized from N. pharaonis was halocyanin [Scharf, B., & Engelhard, M. (1993) Biochemistry 32, 12894-12900], a small blue copper protein. It is a peripheral membrane protein and is conjectured to function in a manner similar to plastocyanin. In the present work, the respiratory chain is further elucidated and the purification and characterization of the most abundant components cytochrome bc and cytochrome ba3 from the membrane fraction are described. The cytochrome bc complex consists of a 14 and an 18 kDa subunit in a 1:1 ratio, with heme c bound to the larger polypeptide. An Fe-S subunit similar to that found in eukaryotic bc complexes has not yet been identified. The second membrane complex carries two different heme groups of the ba3-type as well as copper. It contains two subunits of 36 and 40 kDa. This cytochrome ba3 binds carbon monoxide, a feature common to terminal oxidases. There is no spectroscopic evidence for a second terminal oxidase; hence, under the growth conditions chosen the respiratory chain of N. pharaonis appears to be unbranched. In addition to these cytochromes, a succinate dehydrogenase which is solubilized from the membrane by detergents was isolated. A cytochrome c which was isolated from the cytosol has an unusually high molecular weight and a redox potential of -142 mV. A second cytosolic protein, ferredoxin, was purified to homogeneity. A comparison of the redox potentials of the isolated proteins with those obtained from the native membrane allows the construction of a possible electron transfer chain.

A family of halobacterial transducer proteins

A DNA probe to the signaling domain of a halobacterial transducer for phototaxis (HtrI) was used to clone and sequence four members of a new family of transducer proteins (Htps) in Halobacterium salinarium potentially involved in chemo- or phototactic signal transduction. The signaling domains in these proteins have 31-43% identity when compared with each other or with their bacterial analogs, the methyl-accepting chemotaxis proteins. An additional region of homology found in three of the Htps has 31-43% identity with HtrI. The Htps contain from 0 to 3 transmembrane helices and Western blotting showed that HtpIII is soluble. The arrangement of the domains in these Htps suggests a modular architecture in their construction.

Insights into protein adaptation to a saturated salt environment from the crystal structure of a halophilic 2Fe-2S ferredoxin

Haloarcula marismortui is an archaebacterium that flourishes in the world's saltiest body of water, the Dead Sea. The cytosol of this organism is a supersaturated salt solution in which proteins are soluble and active. The crystal structure of a 2Fe-2S ferredoxin from H. marismortui determined at 1.9 A is similar to those of plant-type 2Fe-2S ferredoxins of known structure, with two important distinctions. The entire surface of the protein is coated with acidic residues except for the vicinity of the iron-sulphur cluster, and there is an insertion of two amphipathic helices near the N-terminus. These form a separate hyperacidic domain whose postulated function to provide extra surface carboxylates for solvation. These data and the fact that bound surface water molecules have on the average 40% more hydrogen bonds than in a typical non-halophilic protein crystal structure support the notion that haloadaptation involves better water binding capacity.

An Archaea 5S rRNA analog is stably expressed in Escherichia coli

Mini-genes for 5S-like rRNA were constructed. These genes had a sequence which largely resembles that of the naturally occurring 5S rRNA of a bacterium, Halococcus morrhuae, which phylogenetically belongs to the Archaea. Plasmids carrying the mini-genes were transformed into Escherichia coli (Ec). Ribosomal incorporation was not a prerequisite for stable accumulation of the RNA product. However, only those constructs with a well-base-paired helix I accumulated RNA product. This result strongly implies that this aspect of the structure is likely to be an important condition for stabilizing 5S rRNA-like products. The results are consistent with our current understanding of 5S rRNA processing in Ec. When used in conjunction with rRNA probe technology, the resulting chimeric RNA may be useful as a monitoring tool for genetically engineered microorganisms or naturally occurring organisms that are released into the environment.

Isolation of individual amino acids from various microbiological sources using reversed-phase high-performance liquid chromatography

A new method for the preparative isolation of individual amino acids on a milligram scale based on reversed-phase high-performance liquid chromatography (RP-HPLC) after pre-column derivatization with carbobenzoxychloride (Z-Cl) has been developed. The chromatographic procedure was tested by the investigation of jack bean urease hydrolysate. The method has been applied to the preparative separation of Z-amino acids (from 10 up to 16) obtained from protein hydrolysates of various sources (green microalgae, blue-green algae, halophilic and methylotrophic microorganisms) and was proved to be reliable by the separation of deuterated amino acids (enrichment 97-99%) from Methylobacillus flagellatum (due to the bioconversion of CD3OD and D2O). Independent of the biological source of the protein, the amino acids were isolated with high recovery (from 68% up to 89%) and chromatographic purity (from 96% up to 99%). The method was also applied for the isolation of phenylalanine and leucine excreted by amino-acid overproducing microorganisms.

Raman spectroscopic study of the blue copper protein halocyanin from Natronobacterium pharaonis

Halocyanin, a blue copper protein from Natronobacterium pharaonis was studied by Raman spectroscopic techniques. Near-infrared Fourier transform Raman spectra, which for the first time have been employed to study copper proteins in both oxidation states, display the Raman bands of the protein and, in the oxidized state, also the preresonance-enhanced bands of the copper center. The frequency of the amide I band at 1676 cm-1 indicates a predominant beta-sheet protein structure, which is typical for small blue copper proteins. The Raman spectra provide no evidence for major redox-linked changes of the secondary structure. Resonance Raman spectra of the oxidized protein obtained upon excitation close to the 600-nm absorption band were measured in the pH range between 7.7 and 4.5. The vibrational band pattern in the Cu-cysteine stretching region is closely related to that of azurin, indicating far-reaching similarities of the coordination geometry of the copper center in both proteins. Significantly lower frequencies, however, are noted for the Cu-histidine stretches, which appear as a closely spaced doublet at ca. 260 cm-1. Lowering the pH to 4.5 leads to an increase of this band splitting with one component shifting down to 247 cm-1. This downshift is attributed to the rupture of a hydrogen bond between one of the histidine ligands and a nearby carboxyl group, which becomes protonated at such a low pH. On the other hand, no major changes in the Cu-cysteine stretching region are noted at pH 4.5, implying that the coordination geometry remains largely unchanged.(ABSTRACT TRUNCATED AT 250 WORDS)

Blue halorhodopsin from Natronobacterium pharaonis: wavelength regulation by anions

Halorhodopsin, the chloride pump from Natronobacterium pharaonis (pharaonis hR), was isolated under conditions of low ionic strength. The quotient between the optical densities of pharaonis hR in 4 M NaCl at 280 and 577 nm amounts to 1.1, indicating a high purity of the protein and integrity of the chromophore. Gel filtration chromatography of the purified pharaonos hR at neutral pH and in the absence of inorganic salts leads to a shift to the absorption maximum to 600 nm (pharaonis hRblue). The purple color can be regained by the addition of anions such as chloride, iodide, azide, nitrate, and also fluoride. The absorption maxima are dependent on the nature of the anion and the pH. At pH 7, sulfate does not influence the 600-nm absorption, while at pH 4.5 the absorption maximum is shifted to 581 nm. The blue form of halorhodopsin (pharaonis hRblue) was titrated with different sodium salts, such as chloride, azide, and nitrate. The half-maximal binding is in the millimolar range, with Br < Cl < NO3 < N3 < BrO3. Deprotonation of the Schiff base can be accomplished by treatment of pharaonis hR or pharaonis hRblue with base. The apparent pK of the Schiff base in pharaonis hRblue was determined to be 8.5. The pK shifted to 8.0 in the presence of 150 mM Na2SO4, whereas the pK of pharaonis hR in 150 mM NaCl is 9.6. In the photocycle of the chloride- and nitrate-containing pharaonis hR, a species similar to hR520 could be detected. Pharaonis hR reconstituted with azide shows photochemical reactions similar to the photocycle of bacteriorhodopsin.(ABSTRACT TRUNCATED AT 250 WORDS)

The primary structure of halocyanin, an archaeal blue copper protein, predicts a lipid anchor for membrane fixation

Halocyanin, a small blue copper protein, was isolated from the haloalkaliphilic archaeon Natronobacterium pharaonis. The NH2 terminus was not accessible to Edman degradation. About 70% of the amino acid sequence was determined by protein sequence analysis. The sequence information of two peptides was used for cloning and sequencing the halocyanin gene (hcy). The open reading frame codes for 489 base pairs, which account for a protein with 163 amino acids and a molecular mass of 17,223 Da. The discrepancy between this value and the molecular mass of 15,456 +/- 1.5 Da for the copper-free protein determined by electrospray mass spectrometry can be explained by a post-translational processing of the gene product. The NH2-terminal sequence of the open reading frame contains a motif that is characteristic for prokaryotic lipoproteins. Assuming a similar processing for halocyanin, Cys at position 25 of the primary transcript would be modified by a diphytanyl (glycerol)diether. Subsequently, the precursor is cleaved by a signal peptidase II-like protease and then acetylated at its NH2-terminal alpha-amino group. These modifications would yield a protein with a calculated molecular mass of 15,456 Da. A comparison of the primary structure of halocyanin with a number of other blue copper proteins places it into the plastocyanin-related group.

Comparative analysis of the protein components from 5S rRNA.protein complexes of halophilic archaebacteria

The 5S RNA.protein complexes have been isolated from the 50S subunit of the halophilic archaebacteria Halobacterium cutirubrum, Halobacterium halobium, Halobacterium salinarium, Haloferax mediterranei, Haloferax volcanii and Haloarcula marismortui. The 50S subunits from most of the halophiles released a multiprotein ribonucleoprotein particle similar to that previously observed with the H. cutirubrum 5S RNA.protein complex, which contained proteins from the L5 and L18 ribosomal protein families. Ribosomes from H. marismortui, however, released an RNA.protein complex containing a single protein (L18) that is homologous to the single protein found in the eukaryotic 5S ribonucleoprotein complexes. N-terminal sequence analyses of the halophilic 5S RNA-binding proteins suggest that the L18 protein primary structure is highly conserved, with only the H. marismortui protein having a sequence difference in at least the first twenty amino acids. Although the L5 group of ribosomal proteins also shows a high conservation, it appears that the proteins may have had more freedom to diverge throughout evolution.

Halocyanin, an archaebacterial blue copper protein (type I) from Natronobacterium pharaonis

A small blue copper protein with a molecular mass of about 15.5 kDa has been isolated from the haloalkaliphilic Natronobacterium pharaonis. This protein, which was named halocyanin, contains one Cu2+. The circular dichroism spectrum in the region of the absorption of the peptide bond reveals mainly beta-structural elements. The absorption spectrum in the visible range has three maxima with the main band at 600 nm. The circular dichroism spectrum in this region is characterized by four extrema with maxima at 413 and 590 nm and minima at 477 nm as well as 721 nm. The electron paramagnetic resonance spectrum displays a hyperfine structure which shows a close resemblance to those of plastocyanin. The cumulative spectral data agree well with those of other small blue copper proteins with axial symmetry of the Cu ligands. In analogy, one can deduce that halocyanin may adopt a type I copper binding site with two His, one Met, and one Cys as probable ligands. This conclusion is confirmed by the C-terminal sequence which contains, homologous to other known sequences of type I copper proteins, three of the four copper ligands. Halocyanin can only be removed from the membrane by mild treatment with detergents. This observation indicates that halocyanin is a peripheral membrane protein which serves as a mobile electron carrier. The presence of type I blue copper proteins is archaebacteria might lead to further insights into their phylogenetic origin.

HL35e and HLA: primary structure of two very basic and cysteine-rich ribosomal proteins from Haloarcula marismortui

Two small and very basic ribosomal proteins have been purified from the 50S ribosomal subunit of the archaebacterium Haloarcula marismortui by RP-HPLC. The complete primary structures of these two proteins, which we refer to as HL35e and HLA, have been determined by protein chemical methods. Both proteins are characterized by a high content of basic amino acids and the presence of two pairs of cysteines in each polypeptide chain, one of which resembles the C4-zinc-finger motif. Comparison of the protein sequences with those of other ribosomal proteins revealed that HL35e shows significant sequence homology exclusively to eukaryotic ribosomal proteins, namely to yeast L35 and to L37 from rat. For HLA no homologous ribosomal protein so far known could be found. Obviously, HL35e and HLA have no counterparts in eubacterial ribosomes.

Chromophore configuration of pharaonis phoborhodopsin and its isomerization on photon absorption

The configuration of the retinylidene chromophore in pharaonis phoborhodopsin (ppR) and its changes during the photoreaction cycle were investigated by means of a chromophore extraction method followed by HPLC analysis. The ppR has an all-trans chromophore, and unlike bacteriorhodopsin, it exhibits no dark isomerization of the chromophore. Irradiation of a ppR sample in the presence of 10 mM hydroxylamine, at which concentration a negligible amount of ppR was bleached, caused the formation of 90% 13-cis- and 10% all-trans-retinal oximes. Because the ppR sample under the continuous irradiation was a mixture containing original ppR, ppRM, and a small amount of ppRO, the above results showed that the chromophores of ppRM and ppRO are in a 13-cis form and an all-trans form, respectively. Therefore, the all-trans chromophore of ppR is isomerized to the 13-cis form on photon absorption, and it is thermally reisomerized to the all-trans form on the conversion process from ppRM to ppRO. The extracted retinal oximes from ppR and ppRO were mainly the 15-syn form, while that from ppRM was mainly the 15-anti form. This fact indicated that the attack of hydroxylamine on the chromophore is stereoselective owing to the unique structure of the chromophore binding site near the Schiff base region of the chromophore.