| halolysin r4, a serine proteinase from the halophilic archaeon haloferax mediterranei; gene cloning, expression and structural studies. | a gene encoding a halophilic serine proteinase, halolysin r4, from a halophilic archaeon haloferax mediterranei strain r4 was cloned, its nucleotide sequence determined, and expressed in haloferax volcanii wfd11. the deduced amino-acid sequence (403 aa in length) showed the highest similarity to halolysin 172p1, produced by another halophilic archaeon, strain 172p1 (now designated as natrialba asiatica). both halolysins belong to the thermitase branch of class i subtilases, but show long c-termi ... | 1996 | 8645734 |
| diversity of alkaliphilic halobacteria: proposals for transfer of natronobacterium vacuolatum, natronobacterium magadii, and natronobacterium pharaonis to halorubrum, natrialba, and natronomonas gen. nov., respectively, as halorubrum vacuolatum comb. nov., natrialba magadii comb. nov., and natronomonas pharaonis comb. nov., respectively. | the 16s rrna genes of three species of the genus natronobacterium (natronobacterium gregoryi, natronobacterium pharaonis, and natronobacterium vacuolatum) were sequenced and compared to that of the previously sequenced species natronobacterium magadii. the sequences revealed that natronobacterium pharaonis was phylogenetically distinct from the other members of the genus and also from other recognized genera of the family halobacteriaceae. however, natronobacterium vacuolatum and natronobacteriu ... | 1997 | 9226918 |
| diversity of extremely halophilic bacteria. | in this review, the history of the classification of the family halobacteriaceae, the extremely halophilic aerobic archaea, is reviewed with some emphasis on the recently described new genera halobaculum, halorubrum, natrialba, natronomonas, and "haloterrigena." speculation is made about the evolutionary relationship between members of the halobacteriaceae and the extremely halophilic, anaerobic methanogens of the genera methanohalobium and methanohalophilus. efforts to find missing links betwee ... | 1998 | 9783176 |
| characterization of two novel haloalkaliphilic archaea natronorubrum bangense gen. nov., sp. nov. and natronorubrum tibetense gen. nov., sp. nov. | two haloalkaliphilic archaea were isolated from a soda lake in tibet. the two strains, designated a33t and ga33t, were gram-negative, pleomorphic, flat, non-motile and strictly aerobic. growth required at least 12% nacl. growth was between ph 8.0 and ph 11 with an optimum at ph 9.0-9.5. cells were chemo-organotrophic. polar lipids were c20-c25 derivatives of phosphatidylglycerol and phosphatidylglycerol phosphate. the nucleotide sequences of the 16s rrna genes from the two strains were obtained ... | 1999 | 10028271 |
| the archaeal halophilic virus-encoded dam-like methyltransferase m. phich1-i methylates adenine residues and complements dam mutants in the low salt environment of escherichia coli. | the genome of the archaeal virus phich1, infecting natrialba magadii (formerly natronobacterium magadii), is composed of 58.5 kbp linear ds dna. virus particles contain several rna species in sizes of 100-800 nucleotides. a fraction of phich1 genomes is modified within 5'-gatc-3' and related sequences, as determined by various restriction enzyme digestion analyses. high performance liquid chromatography revealed a fifth base, in addition to the four nucleosides, which was identified as n6-methyl ... | 2000 | 10712697 |
| extracellular protease of natrialba magadii: purification and biochemical characterization. | a serine protease secreted by the haloalkaliphilic archaeon natrialba magadii at the end of the exponential growth phase was isolated. this enzyme was purified 83 fold with a total yield of 25% by ethanol precipitation, affinity chromatography, and gel filtration. the native molecular mass of the enzyme determined by gel filtration was 45 kda. na. magadii extracellular protease was dependent on high salt concentrations for activity and stability, and it had an optimum temperature of 60 degrees c ... | 2000 | 10879563 |
| polymer production by two newly isolated extremely halophilic archaea: application of a novel corrosion-resistant bioreactor. | a novel corrosion-resistant bioreactor composed of polyetherether ketone (peek), tech glass and silicium nitrite ceramics was constructed and applied for the cultivation of two newly isolated, extremely halophilic archaea producing poly(gamma-glutamic acid) (pga), or poly(beta-hydroxy butyric acid) (phb), respectively. these bacteria were isolated from hypersaline soil close to aswan (egypt). the isolate strain 40, which is related to the genus natrialba, produced large amounts of pga when culti ... | 2000 | 11030566 |
| the structural protein e of the archaeal virus phich1: evidence for processing in natrialba magadii during virus maturation. | phich1 is a lysogenic virus for the haloalkalophilic archaeon natrialba magadii. the virus morphology resembles other members of myoviridae infecting halobacterium species. the gene of the major capsid protein e of virus phich1 was cloned and the dna sequence was determined. gene e was mapped to a 3.2-kbp clai fragment, localized to the 5'-end of the phich1 genome. the complete nucleotide sequence of this region was determined and the identity of gene e was confirmed by comparing the experimenta ... | 2000 | 11040128 |
| transfer of natrialba asiatica b1t to natrialba taiwanensis sp. nov. and description of natrialba aegyptiaca sp. nov., a novel extremely halophilic, aerobic, non-pigmented member of the archaea from egypt that produces extracellular poly(glutamic acid). | a novel extremely halophilic member of the archaea, strain 40t, was isolated from egypt (aswan). this isolate requires at least 1.6 m sodium chloride for growth and exhibits optimal growth between 37 and 42 degrees c. determination of the entire 16s rrna gene sequence revealed the highest similarity to the type strain of natrialba asiatica (> 99%). polar lipid analysis indicated that strain 40t and natrialba asiatica have essentially identical compositions, indicating that the former is a member ... | 2001 | 11411682 |
| natrialba hulunbeirensis sp. nov. and natrialba chahannaoensis sp. nov., novel haloalkaliphilic archaea from soda lakes in inner mongolia autonomous region, china. | two haloalkaliphilic archaeal strains, x21t and c112t, were isolated from soda lakes in inner mongolia autonomous region, china. their morphology, physiology, biochemical features, polar lipid composition and 16s rrna genes were characterized in order to elucidate their taxonomy. according to these data, strains x21t and c112t belong to the genus natrialba, although there are clear differences with respect to their physiology and polar lipid composition between the two strains and the type speci ... | 2001 | 11594597 |
| sequencing of flagellin genes from natrialba magadii provides new insight into evolutionary aspects of archaeal flagellins. | we have determined the nucleotide sequence of a flagellin gene locus from the haloalkaliphilic archaeon natrialba magadii, identified the gene products among proteins forming flagella, and demonstrated cotranscription of the genes. based on the sequence analysis we suggest that different regions of the genes might have distinct evolutionary histories including possible genetic exchange with bacterial flagellin genes. | 2002 | 11741874 |
| stability of natrialba magadii ndp kinase: comparisons with other halophilic proteins. | nucleoside diphosphate kinase from the haloalkaliphilic archaeon natrialba magadii (nm ndpk) is a homooligomeric hexamer with a monomer molecular weight of 23 kda. its main function is to exchange gamma-phosphates between nucleoside triphosphates and diphosphates. previously it was shown that nm ndpk is active over a wide range of nacl concentrations, which is not typical of extremely halophilic proteins. in this paper more detailed investigations of kinase function and stability were carried ou ... | 2002 | 12013434 |
| two immunologically distinct types of protofilaments can be identified in natrialba magadii flagella. | we examine distribution of flagellins along multicomponent flagellar filaments (ff) and protofilaments (pf) of the haloalkaliphilic archaeon natrialba magadii using immunogold electron microscopy. a high specific polyclonal antibody raised to one of the flagellin types bound homogeneously to the undissociated ff along the full length. at the same time both uniformly labelled and completely unlabelled pf, outwardly indistinguishable one from another, were observed. | 2002 | 12076782 |
| natrialba magadii virus phich1: first complete nucleotide sequence and functional organization of a virus infecting a haloalkaliphilic archaeon. | the double-stranded (ds)dna virus phich1 infects the haloalkaliphilic archaeon natrialba magadii. the complete dna sequence of 58 498 bp of the temperate virus was established, and the probable functions of 21 of 98 phich1-encoded open reading frames (orfs) have been assigned. this knowledge has been used to propose functional modules each required for specific functions during virus development. the phich1 dna is terminally redundant and circularly permuted and therefore appears to be packaged ... | 2002 | 12139629 |
| detection of an intracellular protease inhibitor in archaea. | proteolytic activity and a subtilisin inhibitor (nsi) were detected in natrialba magadii cells. the proteolytic activity was due to two different proteases: a approximately 90-kda metallo protease (nmp) produced during exponential growth and a 246-kda serine protease (nsp) detected in the stationary phase. both proteases were detected in the cytosolic fraction. nsi activity was maximal during early stages of growth and decreased in the stationary phase. nsi is a 35-kda thermosensitive protein; i ... | 2003 | 12732960 |
| low-pass sequencing for microbial comparative genomics. | we studied four extremely halophilic archaea by low-pass shotgun sequencing: (1) the metabolically versatile haloarcula marismortui; (2) the non-pigmented natrialba asiatica; (3) the psychrophile halorubrum lacusprofundi and (4) the dead sea isolate halobaculum gomorrense. approximately one thousand single pass genomic sequences per genome were obtained. the data were analyzed by comparative genomic analyses using the completed halobacterium sp. nrc-1 genome as a reference. low-pass shotgun sequ ... | 2004 | 14718067 |
| inversion within the haloalkaliphilic virus phi ch1 dna results in differential expression of structural proteins. | the sequence of phi ch1 contains an open reading frame (int1) in the central part of its genome that belongs to the lambda integrase family of site-specific recombinases. sequence similarities to known integrases include the highly conserved tetrad r-h-r-y. the flanking sequences of int1 contain several direct repeats of 30 bp in length (ir-l and ir-r), which are orientated in an inverted direction. here, we show that a recombination active region exists in the genome of phi ch1: the number of t ... | 2004 | 15066030 |
| siderophores of halophilic archaea and their chemical characterization. | nine halophilic archaea viz., halobacterium salinarum, halobacterium sp.1, halobacterium sp.2, halobaculum sp., halococcus saccharolyticus, halorubrum saccharovorum, haloterrigena turkmenica, halogeometricum sp. and natrialba sp. isolated from marine salterns around bhavnagar coast were screened for siderophore production. five isolates viz., halococcus saccharolyticus, halorubrum saccharovorum, haloterrigena turkmenica, halogeometricum sp. and natrialba sp. produced siderophores as evidenced by ... | 2006 | 16629380 |
| phylogenetic relationships within the order halobacteriales inferred from 16s rrna gene sequences. | phylogenetic relationships within the halophilic archaea were inferred from comparisons of the 16s rrna gene sequences from 61 strains, representing 18 genera with validly published names within the order halobacteriales. trees produced using distance-matrix (least-squares and neighbour-joining) methods affirm with strong bootstrap support that the members of the order halobacteriales are a monophyletic group. ten genera were supported as monophyletic groups [haloarcula, halobiforma, halococcus, ... | 2006 | 16738095 |
| halostagnicola larsenii gen. nov., sp. nov., an extremely halophilic archaeon from a saline lake in inner mongolia, china. | strain xh-48(t) was isolated from the sediment of lake xilinhot, a saline lake in inner mongolia (china). the organism is pleomorphic, neutrophilic and requires at least 2.5 m (15 %) nacl, but not mgcl(2), for growth; it exhibits optimal growth at 3.4 m (20 %) nacl. the g+c content of its dna is 61 mol%. 16s rrna gene sequence analysis revealed that strain xh-48(t) is a member of the family halobacteriaceae, but there were low levels of similarity with other members of this family. the highest s ... | 2006 | 16825623 |
| effect of organic solvents on the activity and stability of an extracellular protease secreted by the haloalkaliphilic archaeon natrialba magadii. | the effect of various organic solvents on the activity and stability of an extracellular protease produced by the haloalkaliphilic archaeon natrialba magadii was tested. this protease was active and stable in aqueous-organic solvent mixtures containing 1.5 m nacl and glycerol, dimethylsulfoxide (dmso), n,n-dimethyl formamide, propylenglycol, and dioxane. among the solvents tested, dmso, propylenglycol, and glycerol were effective in preserving enzyme stability in suboptimal nacl concentrations. ... | 2007 | 17024426 |
| the lysogenic region of virus phich1: identification of a repressor-operator system and determination of its activity in halophilic archaea. | phich1 is a temperate virus infecting the haloalkaliphilic archaeon natrialba magadii. as for all temperate viruses, a control of the lysogenic state versus the lytic life cycle is essential. two open reading frames (orfs) have been identified as putative repressor encoding genes: orf48 and orf49. the protein of orf48 showed sequence similarities to putative repressor molecules. orf49 was identified by the analysis of a mutant of phich1: the lysogenic strain carrying mutant phich1-1 showed a dif ... | 2007 | 17123129 |
| a traditional japanese-style salt field is a niche for haloarchaeal strains that can survive in 0.5% salt solution. | most of the haloarchaeal strains have been isolated from hypersaline environments such as solar evaporation ponds, salt lakes, or salt deposits, and they, with some exceptions, lyse or lose viability in very low-salt concentrations. there are no salty environments suitable for the growth of haloarchaea in japan. although natrialba asiatica and haloarcula japonica were isolated many years ago, the question, "are haloarchaea really thriving in natural environments of japan?" has remained unanswere ... | 2007 | 17346353 |
| effect of nutritional conditions on extracellular protease production by the haloalkaliphilic archaeon natrialba magadii. | the effect of various nitrogen sources and nutritional starvation was examined on the production of an extracellular protease secreted by the haloalkaliphilic archaeon natrialba magadii. | 2007 | 17576226 |
| phylogenetic relationships within the family halobacteriaceae inferred from rpob' gene and protein sequences. | in order to clarify the current phylogeny of the haloarchaea, particularly the closely related genera that have been difficult to sort out using 16s rrna gene sequences, the dna-dependent rna polymerase subunit b' gene (rpob') was used as a complementary molecular marker. partial sequences of the gene were determined from 16 strains of the family halobacteriaceae. comparisons of phylogenetic trees inferred from the gene and protein sequences as well as from corresponding 16s rrna gene sequences ... | 2007 | 17911299 |
| diversity of halophilic archaea from six hypersaline environments in turkey. | the diversity of archaeal strains from six hypersaline environments in turkey was analyzed by comparing their phenotypic characteristics and 16s rdna sequences. thirty-three isolates were characterized in terms of their phenotypic properties including morphological and biochemical characteristics, susceptibility to different antibiotics, and total lipid and plasmid contents, and finally compared by 16s rdna gene sequences. the results showed that all isolates belong to the family halobacteriacea ... | 2007 | 18050917 |
| gene cloning and heterologous synthesis of a haloalkaliphilic extracellular protease of natrialba magadii (nep). | the gene encoding the protease nep secreted by the haloalkaliphilic archaeon natrialba magadii was cloned and sequenced. upstream of the nep gene, a region related to haloarchaeal tata-box and bre-like consensus sequences was identified. the nep-encoded polypeptide had a molecular mass of 56.4 kda, a pi of 3.77 and included a 121-amino acid propeptide not present in the mature nep. a tat motif (grrsvl) was also identified at residues 10-15 suggesting it is a substrate of the tat pathway. the pri ... | 2008 | 18553052 |
| analysis of yeast and archaeal population dynamics in kimchi using denaturing gradient gel electrophoresis. | kimchi is a traditional korean food that is fermented from vegetables such as chinese cabbage and radish. many bacteria are involved in kimchi fermentation and lactic acid bacteria are known to perform significant roles. although kimchi fermentation presents a range of environmental conditions that could support many different archaea and yeasts, their molecular diversity within this process has not been studied. here, we use pcr-denaturing gradient gel electrophoresis (dgge) targeting the 16s a ... | 2008 | 18562030 |
| emended descriptions of genera of the family halobacteriaceae. | the family halobacteriaceae currently contains 96 species whose names have been validly published, classified in 27 genera (as of september 2008). in recent years, many novel species have been added to the established genera but, in many cases, one or more properties of the novel species do not agree with the published descriptions of the genera. authors have often failed to provide emended genus descriptions when necessary. following discussions of the international committee on systematics of ... | 2009 | 19244452 |
| presence of structural homologs of ubiquitin in haloalkaliphilic archaea. | ubiquitin, a protein widely conserved in eukaryotes, is involved in many cellular processes, including proteolysis. while sequences encoding ubiquitin-like proteins have not been identified in prokaryotic genomes sequenced so far, they have revealed the presence of structural and functional homologs of ubiquitin in bacteria and archaea. this work describes the amplification and proteomic analysis of a 400-bp dna fragment from the haloalkaliphilic archaeon natrialba magadii. the encoded polypepti ... | 2009 | 19784923 |
| an alkaline serine-proteinase from a bacterium isolated from bat feces: purification and characterization. | an alkaline serine-proteinase from bacillus sp. pn51 isolated from bat feces collected in phang nga, thailand, was purified and characterized. the molecular mass was estimated to be 35.0 kda. the n-terminal 25 amino acid sequence was about 70% identical with that of natrialba magadii halolysin-like extracellular serine protease. the enzyme showed the highest proteinase activity at 60 degrees c at ph 10.0. the activity was strongly inhibited by pmsf and chymostatin. the proteinase activity was no ... | 2009 | 19897920 |
| further refinement of the phylogeny of the halobacteriaceae based on the full-length rna polymerase subunit b' (rpob') gene. | a considerable number of species of the halobacteriaceae possess multiple copies of the 16s rrna gene that exhibit more than 5 % divergence, complicating phylogenetic interpretations. two additional problems have been pointed out: (i) the genera haloterrigena and natrinema show a very close relationship, with some species being shown to overlap in phylogenetic trees reconstructed by the neighbour-joining method, and (ii) alkaliphilic and neutrophilic species of the genus natrialba form definitel ... | 2010 | 19946058 |
| natronoarchaeum mannanilyticum gen. nov., sp. nov., an aerobic, extremely halophilic archaeon isolated from commercial salt. | strain ysm-123(t) was isolated from commercial salt made from japanese seawater in niigata prefecture. optimal nacl and mg(2+) concentrations for growth were 4.0-4.5 m and 5 mm, respectively. the isolate was a mesophilic and slightly alkaliphilic haloarchaeon, whose optimal growth temperature and ph were 37 °c and ph 8.0-9.0. phylogenetic analysis based on 16s rrna gene sequence analysis suggested that strain ysm-123(t) is a member of the phylogenetic group defined by the family halobacteriaceae ... | 2010 | 19965994 |
| growth phase-dependent biosynthesis of nep, a halolysin-like protease secreted by the alkaliphilic haloarchaeon natrialba magadii. | the alkaliphilic haloarchaeon natrialba magadii secretes a halolysin-like protease (nep) that is active and stable in high salt and in organic solvents, which represents a potential resource for biocatalysis in low water activity conditions. in this study, the effect of the growth stage on nep biosynthesis was examined. | 2010 | 20477957 |
| 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)) co ... | 2010 | 20718295 |
| 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 84kda polypeptide with a pi of 4.42 ... | 2010 | 20869220 |
| peptide synthesis catalysed by a haloalkaliphilic serine protease from the archaeon natrialba magadii (nep). | haloarchaeal proteases function optimally in high salt (low water activity); thus, they offer an advantage over the nonhalophilic counterparts as biocatalysts for protease-catalysed peptide synthesis. the haloalkaliphilic archaeon natrialba magadii secretes a solvent-tolerant protease, nep (natrialba magadii extracellular protease). in this work, the ability of nep to catalyse peptide synthesis was examined. | 2010 | 21039670 |
| secondary structure determination by ftir of an archaeal ubiquitin-like polypeptide from natrialba magadii. | the ubiquitin protein belongs to the +¦-grasp fold family, characterized by four or five +¦-sheets with a single +¦-helical middle region. ubiquitin-like proteins (ubls) are structural homologues with low sequence identity to ubiquitin and are widespread among both eukaryotes and prokaryotes. we previously demonstrated by bioinformatics that p400, a polypeptide from the haloalkaliphilic archaeon natrialba magadii, has structural homology with both ubiquitin and ubls. this work examines the secon ... | 2011 | 21701865 |
| Correlation between catalysis and tertiary structure arrangement in an archaeal halophilic subtilase. | Nep (Natrialba magadii extracellular protease) is a halolysin-like peptidase secreted by the haloalkaliphilic archaeon N.magadii that exhibits optimal activity and stability in salt-saturated solutions. In this work, the effect of salt on the function and structure of Nep was investigated. In absence of salt, Nep became unfolded and aggregated, leading to the loss of activity. The enzyme did not recover its structural and functional properties even after restoring the ideal conditions for cataly ... | 2011 | 22177966 |
| comparative survival analysis of deinococcus radiodurans and the haloarchaea natrialba magadii and haloferax volcanii exposed to vacuum ultraviolet irradiation. | abstract the haloarchaea natrialba magadii and haloferax volcanii, as well as the radiation-resistant bacterium deinococcus radiodurans, were exposed to vacuum uv (vuv) radiation at the brazilian synchrotron light laboratory. cell monolayers (containing 10(5) to 10(6) cells per sample) were prepared over polycarbonate filters and irradiated under high vacuum (10(-5) pa) with polychromatic synchrotron radiation. n. magadii was remarkably resistant to high vacuum with a survival fraction of (3.7 ... | 2011 | 22165956 |
| Haloarchaeal myovirus fCh1 harbours a phase variation system for the production of protein variants with distinct cell surface adhesion specificities. | The fCh1 myovirus, which infects the haloalkaliphilic archaeon Natrialba magadii, contains an invertible region that comprises the convergent open reading frames (ORFs) 34 and 36, which code for the putative tail fibre proteins gp34 and gp36 respectively. The inversion leads to an exchange of the C-termini of these proteins, thereby creating different types of tail fibres. Gene expression experiments revealed that only ORF34 is transcribed, indicating that fCh1 produces tail fibre proteins exclu ... | 2012 | 22111759 |
| archaea-based microbial fuel cell operating at high ionic strength conditions. | in this work, two archaea microorganisms (haloferax volcanii and natrialba magadii) used as biocatalyst at a microbial fuel cell (mfc) anode were evaluated. both archaea are able to grow at high salt concentrations. by increasing the media conductivity, the internal resistance was diminished, improving the mfc's performance. without any added redox mediator, maximum power (p (max)) and current at p (max) were 11.87/4.57/0.12 μw cm(-2) and 49.67/22. ... | 2011 | 21894491 |