Isolation, characterization and phylogenetic analysis of halophilic archaea from a salt mine in central Anatolia (Turkey).
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The haloarchaeal diversity of a salt mine, a natural cave in central Anatolia, was investigated using convential microbiological and molecular biology methods. Eight halophilic archaeal isolates selected based on their colony morphology and whole cell protein profiles were taxonomically classified on the basis of their morphological, physiological, biochemical properties, polar lipid and protein profiles and 16S rDNA sequences. From the 16S rDNA sequences comparisons it was established that the isolates CH2, CH3 and CHC resembled Halorubrum saccharovorum by 98.8%, 98.9% and 99.5%, respectively. There was a 99.7% similarity between the isolate CH11 and Halobacterium noricense and 99.2% between the isolate CHA1 and Haloarcula argentinensis. The isolate CH8K and CH8B revealed a similarity rate of 99.8% and 99.3% to Halococcus dombrowskii, respectively. It was concluded that the isolates named CH2, CH3 and CHC were clustered in the genus Halorubrum and that CHA1 and CH7 in the genus Haloarcula, CH8K and CH8B in the genus Halococcus and CH11 in the genus Halobacterium. (+info)
Structural studies on archaeal phytanyl-ether lipids isolated from membranes of extreme halophiles by linear ion-trap multiple-stage tandem mass spectrometry with electrospray ionization.
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The primary structure of sensory rhodopsin II: a member of an additional retinal protein subgroup is coexpressed with its transducer, the halobacterial transducer of rhodopsin II.
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The blue-light receptor genes (sopII) of sensory rhodopsin (SR) II were cloned from two species, the halophilic bacteria Haloarcula vallismortis (vSR-II) and Natronobacterium pharaonis (pSR-II). Upstream of both sopII gene loci, sequences corresponding to the halobacterial transducer of rhodopsin (Htr) II were recognized. In N. pharaonis, psopII and phtrII are transcribed as a single transcript. Comparison of the amino acid sequences of vHtr-II and pHtr-II with Htr-I and the chemotactic methyl-accepting proteins from Escherichia coli revealed considerable identities in the signal domain and methyl-accepting sites. Similarities with Htr-I in Halobacterium salinarium suggest a common principle in the phototaxis of extreme halophiles. Alignment of all known retinal protein sequences from Archaea identifies both SR-IIs as an additional subgroup of the family. Positions defining the retinal binding site are usually identical with the exception of Met-118 (numbering is according to the bacteriorhodopsin sequence), which might explain the typical blue color shift of SR-II to approximately 490 nm. In archaeal retinal proteins, the function can be deduced from amino acids in positions 85 and 96. Proton pumps are characterized by Asp-85 and Asp-96; chloride pumps by Thr-85 and Ala-96; and sensors by Asp-85 and Tyr-96 or Phe-96. (+info)
Reason for the lack of light-dark adaptation in pharaonis phoborhodopsin: reconstitution with 13-cis-retinal.
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The reconstitution of pharaonis phoborhodopsin was performed by incubation of its opsin with 13-cis-retinal. Spectrum change was very slow, and two phases of the change were observed: the first and second phases are due to the transient formation of 13-cis pigment and spontaneous isomerization to all-trans-retinal, respectively. Slow binding supports an idea that the retinal binding pocket of ppR is highly restricted. Being bent in the configuration, 13-cis-retinal cannot be accommodated in the pocket due to the steric hindrance. This is a possible reason for the lack of light-dark adaptation. (+info)
Genomic stability in the archaeae Haloferax volcanii and Haloferax mediterranei.
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Through hybridization of available probes, we have added nine genes to the macrorestriction map of the Haloferax mediterranei chromosome and five genes to the contig map of Haloferax volcanii. Additionally, we hybridized 17 of the mapped cosmid clones from H. volcanii to the H. mediterranei genome. The resulting 35-point chromosomal comparison revealed only two inversions and a few translocations. Forces known to promote rearrangement, common in the haloarchaea, have been ineffective in changing global gene order throughout the nearly 10(7) years of these species' divergent evolution. (+info)
Lipids of extremely halophilic archaeobacteria from saline environments in India: a novel glycolipid in Natronobacterium strains.
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Several strains of extremely halophilic archaeobacteria, both non-alkaliphilic and alkaliphilic, including Halobacterium, Haloferax and Natronobacterium species, were isolated from salt locales in India. The major phospholipids in these strains were the C20-C20-glycerol diether analogues of phosphatidylglycerolmethylphosphate (PGP-Me), phosphatidylglycerol (PG) and phosphatidic acid (PA). In addition, the Halobacterium strains possessed the characteristic glycolipids, sulfated triglycosyl and tetraglycosyl diethers (S-TGD-1 and S-TeGD, respectively) and the unsulfated triglycosyl diether (TGD-1); and the Haloferax strains had the characteristic sulfated and unsulfated diglycosyl glycerol diethers (S-DGD-1 and DGD-1, respectively). The PGP-Me, and PG components of the haloalkaliphiles each occurred as two molecular species with C20-C20- and C20-C25-(isopranoid) glycerol diether lipid cores. In contrast to previous reports of the absence of glycolipids in natronobacteria, the Natronobacterium strains from India were found to contain small amounts of a novel glycolipid identified as glucopyranosyl-1-->6-glucopyranosyl-1-->1-glycerol diether (DGD-4). The lipid cores of DGD-4 also contained mainly unhydroxylated or hydroxylated C20-C20, C20-C25 and C25-C25 molecular species with unsaturated (isoprenoid) chains. Hydroxylated lipid cores have previously been identified only in some methanogenic archaeobacteria. (+info)
A transcriptional reporter for in vivo promoter analysis in the archaeon Haloferax volcanii.
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We have used a modified intron-containing tRNA(Pro(UGG) gene (tRNA(ProM), derived from the Saccharomyces cerevisiae tRNA(Pro(UGG) gene, as a reporter to measure in vivo transcription from a halophilic archaeon promoter. Coupling of the yeast tRNA(ProM) gene to the Haloferax volcanii tRNA(Lys) promoter on the H. volcanii plasmid pWL201 led to the production of a single stable transcript that was readily quantitated by Northern (RNA) blot analysis. Comparison of tRNA(ProM) RNA production from constructs containing the wild-type tRNA(Lys) promoter and those containing mutant tRNA(Lys) promoters demonstrated that this assay system can be used to measure expression from strong and weak promoters. (+info)
Halobacterial S9 operon contains two genes encoding proteins homologous to subunits shared by eukaryotic RNA polymerases I, II, and III.
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One key component of the eukaryotic transcriptional apparatus is the multisubunit enzyme RNA polymerase II. We have discovered that two of the subunits shared by the three nuclear RNA polymerases in the yeast Saccharomyces cerevisiae, RPB6 and RPB10, have counterparts among the Archaea. (+info)