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Archaeal Proteins (4):
Recent article
Archaeal Proteins
Abstract
We provide an updated analysis of the evolutionary relationships between CRISPR-Cas systems and Cas proteins. Three major types of CRISPR-Cas system are delineated, with a further division into several subtypes and a few chimeric variants. Given the complexity of the genomic architectures and the ex...
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PMID: 21552286
PDF is available here.
PDF is available here.
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Abstract
Abstract
We studied how nucleotides bind to PAN. Although PAN has six identical subunits, it binds ATPs in pairs, and its subunits exhibit three conformational states with high, low, or no affinity for ATP. When PAN binds two ATPγS molecules or two ATPγS plus two ADP molecules, it is maximally active in bi...
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PMID: 21335235
PDF is available here.
PDF is available here.
Metallomics (3)1 2011
Abstract
We treat the changes in copper proteins in historically the same increasingly oxidising environmental conditions. The study is a bioinformatic analysis of the types and the numbers of copper domains of proteins from 435 DNA sequences of a wide range of organisms available in NCBI, using the method d...
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PMID: 21085721
PDF is available here.
PDF is available here.
Abstract
Journal of Biological Chemistry (285)45 2010
Abstract
We characterized the Lsm protein from the haloarchaeon Haloferax volcanii using in vitro and in vivo approaches. H. volcanii encodes a single Lsm protein, which belongs to the Lsm1 subfamily. The lsm gene is co-transcribed and overlaps with the gene for the ribosomal protein L37e. Northern blot anal...
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PMID: 20826804
PDF is available here.
PDF is available here.
Microbial Ecology (60)3 2010
Abstract
We found that non-bleached and cyclically bleached tissues of X. muta harbored a unique Crenarchaeota community closely related to those reported for other sponges. In contrast, bleached tissue from the most degraded sponge contained a Crenarchaeota community that was more similar to those found in...
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PMID: 20390264
PDF is available here.
PDF is available here.
Abstract
We measured low-frequency spectra of bacteriorhodopsin (BR) by terahertz (THz; 1 THz approximately = 33 cm(-1)) time-domain spectroscopy. Both the absorption coefficient and the refractive index were obtained simultaneously in the THz frequency region. The dependence of the THz spectra on hydration...
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PMID: 20607183
PDF is available here.
PDF is available here.
Molecular Cell (39)3 2010
Abstract
We determined the crystal structures of the archaeal tRNA(Sec).PSTK complex. PSTK consists of two independent linker-connected domains, the N-terminal catalytic domain (NTD) and the C-terminal domain (CTD). The D-arm.CTD binding occurs independently of and much more strongly than the acceptor-arm.NT...
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PMID: 20705242
PDF is available here.
PDF is available here.
Abstract
We systematically screened 71 fully sequenced archaeal genomes, and identified some proteins containing homologous regions to the functional domains of eukaryotic RNA silencing pathway key proteins. The phylogenetic relationships of these proteins were analyzed. The conserved functional amino acids...
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PMID: 20816382
PDF is available here.
PDF is available here.
Abstract
Our data revealed PabRNase HII as a dual-function enzyme likely required for the completion of DNA replication and DNA repair....
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PMID: 20472790
PDF is available here.
PDF is available here.
Abstract
We studied the cellular localization of the archaeal exosome, an RNA-processing protein complex containing orthologs of the eukaryotic proteins Rrp41, Rrp42, Rrp4 and Csl4, and an archaea-specific subunit annotated as DnaG. Fractionation of cell-free extracts of Sulfolobus solfataricus in sucrose de...
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PMID: 20488181
PDF is available here.
PDF is available here.
Abstract
We studied the substrate specificity of the exosome of Sulfolobus solfataricus using the catalytically active Rrp41-Rrp42-hexamer and complexes containing the RNA-binding subunits Rrp4 or Csl4. The conservation of both Rrp4 and Csl4 in archaeal and eukaryotic exosomes suggests specific functions for...
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PMID: 20488184
PDF is available here.
PDF is available here.
Archives of Microbiology (192)7 2010
Abstract
Both the lipid and the protein components of biological membranes can be modified by the covalent addition of polysaccharides. Whereas eukaryal and bacterial pathways of lipid and protein glycosylation are relatively well defined, considerably less is known of the parallel processes in Archaea. Rece...
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PMID: 20458469
PDF is available here.
PDF is available here.
Biochemistry (New York) (75)7 2010
Abstract
We have characterized the ST0519 RNase HII from S. tokodaii as a new form. The enzyme utilized hybrid RNA/DNA as a substrate and had an optimal temperature between 37 to 50 degrees C. The activity of wild-type protein was stimulated by Mn2+, whereas this cation significantly inhibited the activity o...
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PMID: 20673218
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Abstract
We report the results of a bioinformatic screen of the genomes of two bacteria and one archeon. We find that all three of these prokaryotes contain TA proteins in proportions approaching those found in eukaryotic cells, indicating that this protein group is present in all three domains of life. Alth...
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PMID: 20406421
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)13 2010
Abstract
A 401-residue-long protein, ST0452, has been identified from a thermophilic archaeon, Sulfolobus tokodaii strain 7, as a glucose-1-phosphate thymidylyltransferase (Glc-1-P TTase) homolog with a 170-residue-long extra C-terminus portion. Functional analyses of the ST0452 protein have confirmed that t...
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PMID: 20400541
PDF is available here.
PDF is available here.
Journal of Molecular Biology (399)4 2010
Abstract
We have characterized the enzyme by means of X-ray crystallography. Structures of Mth212 wild-type or mutant proteins either alone or in complex with DNA substrates and products have been determined to a resolution of up to 1.2 A, suggesting key residues for the uridine endonuclease activity. The in...
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PMID: 20434457
PDF is available here.
PDF is available here.
Journal of Molecular Biology (399)4 2010
Abstract
We have studied the interaction between PFD and CPN using those from a hyperthermophilic archaeon, Thermococcus strain KS-1 (T. KS-1). In this study, we determined the crystal structure of the T. KS-1 PFDbeta2 subunit and characterized the interactions between T. KS-1 CPNs (CPNalpha and CPNbeta) and...
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PMID: 20434454
PDF is available here.
PDF is available here.
Abstract
We present evidence that these two steps in methanogenesis are physically linked. We identify a protein complex from the hydrogenotrophic methanogen, Methanococcus maripaludis, that contains heterodisulfide reductase, formylmethanofuran dehydrogenase, F(420)-nonreducing hydrogenase, and formate dehy...
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PMID: 20534465
PDF is available here.
PDF is available here.
Abstract
Our data describe variability in the rate of mutation and likelihoods for phylogenetic trees based on protein sequence data and endorse the extension of substitution models by incorporating data on conservation and distance to C/ACs rather than only using cumulative levels. The data support the view...
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PMID: 20069373
PDF is available here.
PDF is available here.
Molecular Microbiology (76)5 2010
Abstract
Bacteria, Archaea and Eukaryotes have evolved a plethora of mechanisms to translocate proteins across their various membranes. The bacterial Sec pathway is ubiquitous and essential for cell viability and is used by most proteins destined for the inner membrane, the periplasm or beyond. In bacteria,...
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PMID: 20444093
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)12 2010
Abstract
SSO1273 of Sulfolobus solfataricus was identified as a cell surface-bound protein by a proteomics approach. Sequence inspection of the genome revealed that the open reading frame of sso1273 is associated in an operon-like structure with genes encoding all the remaining components of a canonical prot...
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PMID: 20382765
PDF is available here.
PDF is available here.
Abstract
We investigated a potential for glucose production from cellulose material using two kinds of hyperthermophilic enzymes, endo-cellulase (EG) and beta-glucosidase (BGL). Two BGLs from hyperthermophile Pyrococcus furiosus and mesophile Aspergillus aculeatus were compared for complete hydrolysis of cel...
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PMID: 20519912
PDF is available here.
PDF is available here.
Journal of Physical Chemistry B (114)16 2010
Abstract
We focused our attention on the consequences of ATP hydrolysis in the NBDs, especially on the structural changes that occur during this process. For that, we use molecular dynamics simulation techniques taking as a starting point the X-ray structure of the MJ0796 dimer from Methanococcus jannaschii....
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PMID: 20369870
PDF is available here.
PDF is available here.
Microbiology (156)Pt 5 2010
Abstract
We have identified an archaeal order that possesses multiple MCM homologues. blast searches of available Methanococcales genomes reveal that members of this order possess between two and eight MCM homologues. Phylogenetic analysis suggests that an ancient duplication in the Methanococcales gave rise...
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PMID: 20133362
PDF is available here.
PDF is available here.
Abstract
We were able to choose the detergent composition in which the membrane-like structure of the VSD is preserved....
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PMID: 20356311
PDF is available here.
PDF is available here.
Abstract
The structure and dynamics of the isolated voltage-sensing domain (VSD) of the archaeal potassium channel KvAP was studied by high-resolution NMR. The almost complete backbone resonance assignment and partial side-chain assignment of the (2)H,(13)C,(15)N-labeled VSD were obtained for the protein dom...
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PMID: 20356312
PDF is available here.
PDF is available here.
Abstract
We used methyl-transverse relaxation optimized nuclear magnetic resonance spectroscopy to show that the amino-terminal residues that compose the gates of the alpha subunits of the Thermoplasma acidophilum proteasome are highly dynamic over a broad spectrum of time scales and that gating termini are...
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PMID: 20360109
PDF is available here.
PDF is available here.
Abstract
The (1)H, (13)C and (15)N resonance assignment of a type-B zinc-binding methionine sulfoxide reductase lacking a 'recycling' cysteine from the thermophilic archeabacterium Methanothermobacter thermoautotrophicus is reported.
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PMID: 20229362
PDF is available here.
PDF is available here.
Abstract
We expressed a putative beta-galactosidase from Sulfolobus acidocaldarius in Escherichia coli and purified the recombinant enzyme using heat treatment and Hi-Trap ion-exchange chromatography. The resultant protein gave a single 57-kDa band by SDS-PAGE and had a specific activity of 58 U/mg. The nati...
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PMID: 19626290
PDF is available here.
PDF is available here.
Abstract
During signal transduction by two-component regulatory systems, sensor kinases detect and encode input information while response regulators (RRs) control output. Most receiver domains function as phosphorylation-mediated switches within RRs, but some transfer phosphoryl groups in multistep phosphor...
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PMID: 20211578
PDF is available here.
PDF is available here.
Abstract
Response regulators (RRs) within two-component signal transduction systems control a variety of cellular processes. Most RRs contain DNA-binding output domains and serve as transcriptional regulators. Other RR types contain RNA-binding, ligand-binding, protein-binding or transporter output domains a...
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PMID: 20226724
PDF is available here.
PDF is available here.
Abstract
Protein histidine kinases (PHKs) function in Two Component Signaling pathways utilized extensively by bacteria and archaea. Many PHKs participate in three distinct, but interrelated signaling reactions: autophoshorylation, phosphotransfer (to a partner Response Regulator (RR) protein), and dephospho...
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PMID: 20117042
PDF is available here.
PDF is available here.
Biochemical Journal (426)3 2010
Abstract
We found that wild-type Pf-RNase HII (P. furiosus, RNase HII) digests RNA-RNA duplexes in the presence of Mn2+ ions. To characterize the substrate specificity of Pf-RNase HII, we aligned the amino acid sequences of Pf-RNase HII and Pf-Ago, based on their protein secondary structures. We found that o...
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PMID: 20047562
PDF is available here.
PDF is available here.
Methods in Molecular Biology (607)607 2010
Abstract
We have shown that the wheat-germ-based cell-free protein synthesis is useful for X-ray crystallography of one of the 4-bp cutter restriction enzymes, which are expected to be very toxic to all forms of cells retaining the genome. Our report on its structure represents the first report of structure...
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PMID: 20204855
PDF is available here.
PDF is available here.
Abstract
We characterized the regioselectivity of lauric acid by CYP119 using the auxiliary redox partner proteins putidaredoxin (Pd) and putidaredoxin reductase (PdR). Purified CYP119 protein showed a tight binding affinity to lauric acid (K(d)=1.1+/-0.1 microM) and dominantly hydroxylated (omega-1) positio...
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PMID: 20372030
PDF is available here.
PDF is available here.
Physical Biology (7)1 2010
Abstract
We computationally investigate the relationship between thermostability and rigidity using rubredoxin as a case study. The mechanical rigidity is calculated using atomic models of homologous rubredoxin structures from the hyperthermophile Pyrococcus furiosus and mesophile Clostridium pasteurianum us...
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PMID: 20009190
PDF is available here.
PDF is available here.
Abstract
We examined the functional equivalency between Escherichia coli RNase P protein (C5) and Pyrococcus horikoshii RNase P proteins (PhoPop5, PhoRpp21, PhoRpp29, PhoRpp30, and PhoRpp38) for RNase P activity. The C5 protein and P. horikoshii RNase P proteins were unable to activate non-congnate RNase P R...
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PMID: 20139629
PDF is available here.
PDF is available here.
Abstract
Proteomic studies have proven useful for studying the Antarctic archaeon Methanococcoides burtonii; however, little has been learned about the hydrophobic and membrane proteins, despite knowledge of their biological importance. In this study, new methods were developed to analyze and...
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PMID: 19968327
PDF is available here.
PDF is available here.
Abstract
Comparative transcriptomic analysis of autotrophic, heterotrophic, and mixotrophic growth of the archaeon Metallosphaera sedula (70 degrees C, pH 2.0) revealed candidates for yet-to-be-confirmed components of the 3-hydroxypropionate/4-hydroxybutyrate pathway and implicated a membrane-bound hydrogena...
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PMID: 20008169
PDF is available here.
PDF is available here.
Abstract
Abstract
These results revealed that TfMA is a novel maltogenic amylase....
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PMID: 19707756
PDF is available here.
PDF is available here.
Abstract
Biodegradable materials with plastic or elastomeric properties are in great demand for a variety of applications. Polyhydroxyalkanoates (PHAs), polyesters synthesized by microorganisms, possess such desired features. Industrial production of PHAs is currently achieved using recombina...
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PMID: 20024541
PDF is available here.
PDF is available here.
Abstract
Keratinases are exciting proteolytic enzymes that display the capability to degrade the insoluble protein keratin. These enzymes are produced by diverse microorganisms belonging to the Eucarya, Bacteria, and Archea domains. Keratinases display a great diversity in their biochemical a...
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PMID: 20039036
PDF is available here.
PDF is available here.
Biochemical Society transactions (38)Pt 1 2010
Abstract
These results do not exclude a parallel CP-independent pathway of assembly. Ongoing work should soon clarify the roles of both the CP and the four chaperones in RP assembly....
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PMID: 20074027
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)4 2010
Abstract
We conclude that P. torridus degrades glucose via a strictly nonphosphorylative ED pathway with a novel KDG-specific aldolase, thus excluding the operation of the branched ED pathway involving a bifunctional KD(P)GA as a key enzyme....
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PMID: 20023024
PDF is available here.
PDF is available here.
Journal of Bacteriology (192)3 2010
Abstract
We present a detailed analysis of a Methanosarcina mazei Delta ech mutant which shows decreased ferredoxin-dependent membrane-bound electron transport activity, a lower growth rate, and faster substrate consumption. Evidence is presented that a second protein whose identity is unknown oxidizes reduc...
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PMID: 19948802
PDF is available here.
PDF is available here.
Abstract
We show that archaeal homologs of Thg1 catalyze G(-1) addition, in vitro and in vivo in yeast, but only in a templated reaction, i.e. with tRNA(His) substrates that contain a C(73) discriminator nucleotide. Because tRNA(His) from archaea contains C(73), these findings are consistent with a physiolog...
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PMID: 20080734
PDF is available here.
PDF is available here.
Abstract
We report two small archaeal modifier proteins, SAMP1 and SAMP2, with a beta-grasp fold and carboxy-terminal diglycine motif similar to ubiquitin, that form protein conjugates in the archaeon Haloferax volcanii. The levels of SAMP-conjugates were altered by nitrogen-limitation and proteasomal gene k...
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PMID: 20054389
PDF is available here.
PDF is available here.
Abstract
We can check to see if the known mass distribution of peptides for a given protein is present in the recorded mass distribution of the mixture being analyzed. Unfortunately, this general approach suffers from high false-positive rates, since in a complex mixture, the likelihood that we will observe...
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PMID: 20865518
PDF is available here.
PDF is available here.