| transcriptional analysis of biofilm formation processes in the anaerobic, hyperthermophilic bacterium thermotoga maritima. | thermotoga maritima, a fermentative, anaerobic, hyperthermophilic bacterium, was found to attach to bioreactor glass walls, nylon mesh, and polycarbonate filters during chemostat cultivation on maltose-based media at 80 degrees c. a whole-genome cdna microarray was used to examine differential expression patterns between biofilm and planktonic populations. mixed-model statistical analysis revealed differential expression (twofold or more) of 114 open reading frames in sessile cells (6% of the ge ... | 2004 | 15466556 |
| comparative genomics of the ftsk-hera superfamily of pumping atpases: implications for the origins of chromosome segregation, cell division and viral capsid packaging. | recently, it has been shown that a predicted p-loop atpase (the hera or mlaa protein), which is highly conserved in archaea and also present in many bacteria but absent in eukaryotes, has a bidirectional helicase activity and forms hexameric rings similar to those described for the trwb atpase. in this study, the ftsk-hera superfamily of p-loop atpases, in which the hera clade comprises one of the major branches, is analyzed in detail. we show that, in addition to the ftsk and hera clades, this ... | 2004 | 15466593 |
| interaction of mitochondrial initiation factor 2 with mitochondrial fmet-trna. | the mammalian mitochondrial genome contains a single trna(met) gene that gives rise to the initiator and elongator trna(met). it is generally believed that mitochondrial protein synthesis begins with formylmethionyl-trna, which indicates that the formylation of mitochondrial met-trna specifies its participation in initiation through its interaction with initiation factor 2 (if-2). however, recent studies in yeast mitochondria, suggest that formylation is not required for protein synthesis. in ad ... | 2004 | 15477394 |
| the a2453-c2499 wobble base pair in escherichia coli 23s ribosomal rna is responsible for ph sensitivity of the peptidyltransferase active site conformation. | peptide bond formation, catalyzed by the ribosomal peptidyltransferase, has long been known to be sensitive to monovalent cation concentrations and ph. more recently, we and others have shown that residue a2451 in the peptidyltransferase center of the escherichia coli 50s ribosomal subunit changes conformation in response to alterations in ph, depending on ionic conditions and temperature. two wobble pairs, a2453-c2499 and a2450-c2063, have been proposed as potential candidates to convey ph-depe ... | 2004 | 15479786 |
| human mitochondrial peptide deformylase, a new anticancer target of actinonin-based antibiotics. | peptide deformylase activity was thought to be limited to ribosomal protein synthesis in prokaryotes, where new peptides are initiated with an n-formylated methionine. we describe here a new human peptide deformylase (homo sapiens pdf, or hspdf) that is localized to the mitochondria. hspdf is capable of removing formyl groups from n-terminal methionines of newly synthesized mitochondrial proteins, an activity previously not thought to be necessary in mammalian cells. we show that actinonin, a pe ... | 2004 | 15489958 |
| the prc-barrel domain of the ribosome maturation protein rimm mediates binding to ribosomal protein s19 in the 30s ribosomal subunits. | the rimm protein in escherichia coli is associated with free 30s ribosomal subunits but not with 70s ribosomes. a deltarimm mutant is defective in 30s maturation and accumulates 17s rrna. to study the interaction of rimm with the 30s and its involvement in 30s maturation, rimm amino acid substitution mutants were constructed. a mutant rimm (rimm-yy-->aa), containing alanine substitutions for two adjacent tyrosines within the prc beta-barrel domain, showed a reduced binding to 30s and an accumula ... | 2004 | 15496525 |
| maturation of the unusual single-cysteine (xxxch) mitochondrial c-type cytochromes found in trypanosomatids must occur through a novel biogenesis pathway. | the c-type cytochromes are characterized by the covalent attachment of haem to the polypeptide via thioether bonds formed from haem vinyl groups and, normally, the thiols of two cysteines in a cxxch motif. intriguingly, the mitochondrial cytochromes c and c1 from two euglenids and the trypanosomatidae contain only a single cysteine within the haem-binding motif (xxxch). there are three known distinct pathways by which c-type cytochromes are matured post-translationally in different organisms. th ... | 2004 | 15500440 |
| fluoroquinolone resistance in penicillin-resistant streptococcus pneumoniae clones, spain. | among 2,882 streptococcus pneumoniae sent to the spanish reference laboratory during 2002, 75 (2.6%) were ciprofloxacin-resistant. resistance was associated with older patients (3.9% in adults and 7.2% in patients > or =65 years of age), with isolation from noninvasive sites (4.3% vs. 1.0%), and with penicillin and macrolide resistance. among 14 low-level resistant (mic 4-8 microg/ml) strains, 1 had a fluoroquinolone efflux phenotype, and 13 showed single parc changes. the 61 high-level ciproflo ... | 2004 | 15504260 |
| nosocomial acquisition of dengue. | recent transmission of dengue viruses has increased in tropical and subtropical areas and in industrialized countries because of international travel. we describe a case of nosocomial transmission of dengue virus in germany by a needlestick injury. diagnosis was made by taqman reverse transcription-polymerase chain reaction when serologic studies were negative. | 2004 | 15504282 |
| analysis of mupirocin resistance and fitness in staphylococcus aureus by molecular genetic and structural modeling techniques. | chromosomal resistance to mupirocin in clinical isolates of staphylococcus aureus arises from v(588)f or v(631)f mutations in isoleucyl-trna synthetase (irs). whether these are the only irs mutations that confer mupirocin resistance or simply those that survive in the clinic is unknown. mupirocin-resistant mutants of s. aureus 8325-4 were therefore generated to examine their iles genotypes and the in vitro and in vivo fitness costs associated with them before and after compensatory evolution. mo ... | 2004 | 15504866 |
| guanosine tetra- and pentaphosphate synthase activity in chloroplasts of a higher plant: association with 70s ribosomes and inhibition by tetracycline. | chloroplasts possess bacterial-type systems for transcription and translation. on the basis of the identification of a chlamydomonas reinhardtii gene encoding a rela-spot homolog (rsh) that catalyzes the synthesis of guanosine tetra- or pentaphosphate [(p)ppgpp], we have previously suggested the operation of stringent control in the chloroplast genetic system. although rsh genes have also been identified in several higher plants, the activities of the encoded enzymes and their mode of action in ... | 2004 | 15507686 |
| multiple defects in translation associated with altered ribosomal protein l4. | the ribosomal proteins l4 and l22 form part of the peptide exit tunnel in the large ribosomal subunit. in escherichia coli, alterations in either of these proteins can confer resistance to the macrolide antibiotic, erythromycin. the structures of the 30s as well as the 50s subunits from each antibiotic resistant mutant differ from wild type in distinct ways and l4 mutant ribosomes have decreased peptide bond-forming activity. our analyses of the decoding properties of both mutants show that ribo ... | 2004 | 15509870 |
| a novel archaeal alanine dehydrogenase homologous to ornithine cyclodeaminase and mu-crystallin. | a novel alanine dehydrogenase (aladh) showing no significant amino acid sequence homology with previously known bacterial aladhs was purified to homogeneity from the soluble fraction of the hyperthermophilic archaeon archaeoglobus fulgidus. aladh catalyzed the reversible, nad+-dependent deamination of l-alanine to pyruvate and nh4+. nadp(h) did not serve as a coenzyme. the enzyme is a homodimer of 35 kda per subunit. the km values for l-alanine, nad+, pyruvate, nadh, and nh4+ were estimated at 0 ... | 2004 | 15516582 |
| identification and functional verification of archaeal-type phosphoenolpyruvate carboxylase, a missing link in archaeal central carbohydrate metabolism. | despite the fact that phosphoenolpyruvate carboxylase (pepc) activity has been measured and in some cases even purified from some archaea, the gene responsible for this activity has not been elucidated. using sensitive sequence comparison methods, we detected a highly conserved, uncharacterized archaeal gene family that is distantly related to the catalytic core of the canonical pepc. to verify the predicted function of this archaeal gene family, we cloned a representative from the hyperthermoph ... | 2004 | 15516590 |
| use of an antisense rna strategy to investigate the functional significance of mn-catalase in the extreme thermophile thermus thermophilus. | the expression of an antisense rna revealed that an mn-catalase was required in thermus thermophilus for aerobic but not for anaerobic growth. the antisense system is based on the constitutive expression of a "bicistronic" transcript consisting of the kanamycin resistance gene mrna followed by the antisense rna against the selected target. | 2004 | 15516595 |
| cold sensitivity of thermophilic and mesophilic rna polymerases. | rna polymerase from mesophilic deinococcus radiodurans displays the same cold sensitivity of promoter opening as rna polymerase from the closely related thermophilic thermus aquaticus. this suggests that, contrary to the accepted view, cold sensitivity of promoter opening by thermophilic rna polymerases may not be a consequence of their thermostability. | 2004 | 15516599 |
| staphylococcus aureus isdg and isdi, heme-degrading enzymes with structural similarity to monooxygenases. | heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. all mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. here we describe the crystal structures of isdg and isdi, two heme-degrading enzymes from staphylococcus aureus. the structures of both enzymes resemble ... | 2005 | 15520015 |
| staphylococcus aureus isdg and isdi, heme-degrading enzymes with structural similarity to monooxygenases. | heme-degrading enzymes are involved in human diseases ranging from stroke, cancer, and multiple sclerosis to infectious diseases such as malaria, diphtheria, and meningitis. all mammalian and microbial enzymes identified to date are members of the heme oxygenase superfamily and assume similar monomeric structures with an all alpha-helical fold. here we describe the crystal structures of isdg and isdi, two heme-degrading enzymes from staphylococcus aureus. the structures of both enzymes resemble ... | 2005 | 15520015 |
| cleavage of double-stranded rna by rnase hi from a thermoacidophilic archaeon, sulfolobus tokodaii 7. | st0753, the orthologous gene of type 1 rnase h found in a thermoacidophilic archaeon, sulfolobus tokodaii, was analyzed. the recombinant st0753 protein exhibited rnase h activity in both in vivo and in vitro assays. the protein expressed in an rnase h-deficient mutant escherichia coli strain functioned to suppress the temperature-sensitive phenotype associated with the lack of rnase h. the in vitro characteristics of the gene's rnase h activity were similar to those of halobacterium rnase hi, th ... | 2004 | 15520465 |
| assembly of the 30s ribosomal subunit: positioning ribosomal protein s13 in the s7 assembly branch. | studies of escherichia coli 30s ribosomal subunit assembly have revealed a hierarchical and cooperative association of ribosomal proteins with 16s ribosomal rna; these results have been used to compile an in vitro 30s subunit assembly map. in single protein addition and omission studies, ribosomal protein s13 was shown to be dependent on the prior association of ribosomal protein s20 for binding to the ribonucleoprotein particle. while the overwhelming majority of interactions revealed in the as ... | 2004 | 15525707 |
| post-transfer editing in vitro and in vivo by the beta subunit of phenylalanyl-trna synthetase. | translation of the genetic code requires attachment of trnas to their cognate amino acids. errors during amino-acid activation and trna esterification are corrected by aminoacyl-trna synthetase-catalyzed editing reactions, as extensively described for aliphatic amino acids. the contribution of editing to aromatic amino-acid discrimination is less well understood. we show that phenylalanyl-trna synthetase misactivates tyrosine and that it subsequently corrects such errors through hydrolysis of ty ... | 2004 | 15526031 |
| testing the conservation of the translational machinery over evolution in diverse environments: assaying thermus thermophilus ribosomes and initiation factors in a coupled transcription-translation system from escherichia coli. | ribosomes from the extreme thermophile thermus thermophilus are capable of translation in a coupled transcription-translation system derived from escherichia coli. at 45 degrees c, t.thermophilus ribosomes translate at approximately 25-30% of the maximal rate of e.coli ribosomes, and synthesize full-length protein. t.thermophilus and e.coli subunits can be combined to effect translation, with the spectrum of proteins produced depending upon the source of the 30s subunit. in this system, t.thermo ... | 2004 | 15534366 |
| the bag or the spindle: the cell factory at the time of systems' biology. | genome programs changed our view of bacteria as cell factories, by making them amenable to systematic rational improvement. as a first step, isolated genes (including those of the metagenome), or small gene clusters are improved and expressed in a variety of hosts. new techniques derived from functional genomics (transcriptome, proteome and metabolome studies) now allow users to shift from this single-gene approach to a more integrated view of the cell, where it is more and more considered as a ... | 2004 | 15537427 |
| interaction of the n-terminal domain of escherichia coli heat-shock protein clpb and protein aggregates during chaperone activity. | the escherichia coli heat-shock protein clpb reactivates protein aggregates in cooperation with the dnak chaperone system. the clpb n-terminal domain plays an important role in the chaperone activity, but its mechanism remains unknown. in this study, we investigated the effect of the clpb n-terminal domain on malate dehydrogenase (mdh) refolding. clpb reduced the yield of mdh refolding by a strong interaction with the intermediate. however, the refolding kinetics was not affected by deletion of ... | 2004 | 15537752 |
| crystal structure of yeast v-atpase subunit c reveals its stator function. | vacuolar h(+)-atpase (v-atpase) has a crucial role in the vacuolar system of eukaryotic cells. it provides most of the energy required for transport systems that utilize the proton-motive force that is generated by atp hydrolysis. some, but not all, of the v-atpase subunits are homologous to those of f-atpase and the nonhomologous subunits determine the unique features of v-atpase. we determined the crystal structure of v-atpase subunit c (vma5p), which does not show any homology with f-atpase s ... | 2004 | 15540116 |
| artificial tertiary motifs stabilize trans-cleaving hammerhead ribozymes under conditions of submillimolar divalent ions and high temperatures. | tertiary stabilizing motifs (tsms) between terminal loops or internal bulges facilitate folding of natural hammerhead ribozymes (hrz) under physiological conditions. however, both substrate and enzyme strands contribute nucleotides to the tsms of trans-cleaving hrz, complicating the design of hrz that exploit tsms to target specific mrna. to overcome this limitation, we used selex to identify new, artificial tsms that are less sensitive to sequence context. nucleotides in loop ii or in a bulge w ... | 2004 | 15547137 |
| two outer membrane proteins are required for maximal type i secretion of the caulobacter crescentus s-layer protein. | transport of rsaa, the crystalline s-layer subunit protein of caulobacter crescentus, is mediated by a type i secretion mechanism. two proteins have been identified that play the role of the outer membrane protein (omp) component in the rsaa secretion machinery. the genes rsaf(a) and rsaf(b) were identified by similarity to the escherichia coli hemolysin secretion omp tolc by using the c. crescentus genome sequence. the rsaf(a) gene is located several kilobases downstream of the other transporte ... | 2004 | 15547272 |
| divergent anticodon recognition in contrasting glutamyl-trna synthetases. | the pathogenic bacterium helicobacter pylori utilizes two essential glutamyl-trna synthetases (glurs1 and glurs2). these two enzymes are closely related in evolution and yet they aminoacylate contrasting trnas. glurs1 is a canonical discriminating glurs (d-glurs) that biosynthesizes glu-trna(glu) and cannot make glu-trna(gln). in contrast, glurs2 is non-canonical as it is only essential for the production of misacylated glu-trna(gln). the co-existence and evident divergence of these two enzymes ... | 2004 | 15561136 |
| cloning of cvipii nicking and modification system from chlorella virus nys-1 and application of nt.cvipii in random dna amplification. | the cloning and expression of the cvipii dna nicking and modification system encoded by chlorella virus nys-1 is described. the system consists of a co-linear mtase encoding gene (cvipiim) and a nicking endonuclease encoding gene (cvipiint) separated by 12 nt. m.cvipii possesses eight conserved amino acid motifs (i to viii) typical of c5 mtases, but, like another chlorella virus mtase m.cviji, lacks conserved motifs ix and x. in addition to modification of the first cytosine in ccd (d = a, g or ... | 2004 | 15570069 |
| mechanistic approach to the problem of hybridization efficiency in fluorescent in situ hybridization. | in fluorescent in situ hybridization (fish), the efficiency of hybridization between the dna probe and the rrna has been related to the accessibility of the rrna when ribosome content and cell permeability are not limiting. published rrna accessibility maps show that probe brightness is sensitive to the organism being hybridized and the exact location of the target site and, hence, it is highly unpredictable based on accessibility only. in this study, a model of fish based on the thermodynamics ... | 2004 | 15574909 |
| characterization of a novel amylolytic enzyme encoded by a gene from a soil-derived metagenomic library. | it has been estimated that less than 1% of the microorganisms in nature can be cultivated by conventional techniques. thus, the classical approach of isolating enzymes from pure cultures allows the analysis of only a subset of the total naturally occurring microbiota in environmental samples enriched in microorganisms. to isolate useful microbial enzymes from uncultured soil microorganisms, a metagenome was isolated from soil samples, and a metagenomic library was constructed by using the puc19 ... | 2004 | 15574921 |
| in vivo 31p nuclear magnetic resonance investigation of tellurite toxicity in escherichia coli. | here we compare the physiological state of escherichia coli exposed to tellurite or selenite by using the noninvasive technique of phosphorus-31 nuclear magnetic resonance (nmr) spectroscopy. we studied glucose-fed escherichia coli hb101 cells containing either a normal puc8 plasmid with no tellurite resistance determinants present or the ptwt100 plasmid which contains the resistance determinants tehab. no differences could be observed in intracellular atp levels, the presence or absence of a tr ... | 2004 | 15574934 |
| thermoadaptation trait revealed by the genome sequence of thermophilic geobacillus kaustophilus. | we present herein the first complete genome sequence of a thermophilic bacillus-related species, geobacillus kaustophilus hta426, which is composed of a 3.54 mb chromosome and a 47.9 kb plasmid, along with a comparative analysis with five other mesophilic bacillar genomes. upon orthologous grouping of the six bacillar sequenced genomes, it was found that 1257 common orthologous groups composed of 1308 genes (37%) are shared by all the bacilli, whereas 839 genes (24%) in the g.kaustophilus genome ... | 2004 | 15576355 |
| paradoxical homozygous expression from heterozygotes and heterozygous expression from homozygotes as a consequence of transcriptional infidelity through a polyadenine tract in the ap3b1 gene responsible for canine cyclic neutropenia. | canine cyclic neutropenia is an autosomal recessive disease in which the number of neutrophils, the primary blood phagocyte, oscillates between almost zero and normal values with two week frequency. we previously found that the causative mutation is an insertion of an extra adenine residue within a tract of nine a's in exon 21 of the 27 exon canine ap3b1 gene. in the course of identifying the mutation, however, we observed an unusual phenomenon: heterozygous carrier dogs, who have one normal all ... | 2004 | 15576359 |
| control of rrna synthesis in escherichia coli: a systems biology approach. | the first part of this review contains an overview of the various contributions and models relating to the control of rrna synthesis reported over the last 45 years. the second part describes a systems biology approach to identify the factors and effectors that control the interactions between rna polymerase and rrna (rrn) promoters of escherichia coli bacteria during exponential growth in different media. this analysis is based on measurements of absolute rrn promoter activities as transcripts ... | 2004 | 15590778 |
| pa-agog, the founding member of a new family of archaeal 8-oxoguanine dna-glycosylases. | oxidative damage represents a major threat to genomic stability, as the major product of dna oxidation, 8-oxoguanine (go), frequently mispairs with adenine during replication. in order to prevent these mutagenic events, organisms have evolved go-dna glycosylases that remove this oxidized base from dna. we were interested to find out how go is processed in the hyperthermophilic archaeon pyrobaculum aerophilum, which lives at temperatures around 100 degrees c. to this end, we searched its genome f ... | 2004 | 15604455 |
| enzyme adaptation to alkaline ph: atomic resolution (1.08 a) structure of phosphoserine aminotransferase from bacillus alcalophilus. | the crystal structure of the vitamin b(6)-dependent enzyme phosphoserine aminotransferase from the obligatory alkaliphile bacillus alcalophilus has been determined at 1.08 a resolution. the model was refined to an r-factor of 11.7% (r(free) = 13.9%). the enzyme displays a narrow ph optimum of enzymatic activity at ph 9.0. the final structure was compared to the previously reported structure of the mesophilic phosphoserine aminotransferase from escherichia coli and to that of phosphoserine aminot ... | 2005 | 15608117 |
| genetic determinant of intrinsic quinolone resistance in fusobacterium canifelinum. | fourteen fluoroquinolone-resistant fusobacterial strains, originating from cats or dogs, were characterized by sequencing of the 16s-23s and 16s rrna genes and dna-dna hybridization and were described as a new species, fusobacterium canifelinum. all of the strains are intrinsically resistant (mic, >4 g/ml) to levofloxacin and other fluoroquinolones. compared to the quinolone resistance-determining region (gyra) of the susceptible relative f. nucleatum, we found that ser79 was replaced with leuci ... | 2005 | 15616329 |
| x-ray crystallography study on ribosome recycling: the mechanism of binding and action of rrf on the 50s ribosomal subunit. | this study presents the crystal structure of domain i of the escherichia coli ribosome recycling factor (rrf) bound to the deinococcus radiodurans 50s subunit. the orientation of rrf is consistent with the position determined on a 70s-rrf complex by cryoelectron microscopy (cryo-em). alignment, however, requires a rotation of 7 degrees and a shift of the cryo-em rrf by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. at 3.3 a resolution, rrf is se ... | 2004 | 15616575 |
| x-ray crystallography study on ribosome recycling: the mechanism of binding and action of rrf on the 50s ribosomal subunit. | this study presents the crystal structure of domain i of the escherichia coli ribosome recycling factor (rrf) bound to the deinococcus radiodurans 50s subunit. the orientation of rrf is consistent with the position determined on a 70s-rrf complex by cryoelectron microscopy (cryo-em). alignment, however, requires a rotation of 7 degrees and a shift of the cryo-em rrf by a complete turn of an alpha-helix, redefining the contacts established with ribosomal components. at 3.3 a resolution, rrf is se ... | 2004 | 15616575 |
| selenocysteine trna-specific elongation factor selb is a structural chimaera of elongation and initiation factors. | in all three kingdoms of life, selb is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a uga stop codon in the presence of a downstream mrna hairpin loop. here, we present the x-ray structures of selb from the archaeon methanococcus maripaludis in the apo-, gdp- and gppnhp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. all three s ... | 2004 | 15616587 |
| selenocysteine trna-specific elongation factor selb is a structural chimaera of elongation and initiation factors. | in all three kingdoms of life, selb is a specialized translation elongation factor responsible for the cotranslational incorporation of selenocysteine into proteins by recoding of a uga stop codon in the presence of a downstream mrna hairpin loop. here, we present the x-ray structures of selb from the archaeon methanococcus maripaludis in the apo-, gdp- and gppnhp-bound form and use mutational analysis to investigate the role of individual amino acids in its aminoacyl-binding pocket. all three s ... | 2004 | 15616587 |
| the structure of a rigorously conserved rna element within the sars virus genome. | we have solved the three-dimensional crystal structure of the stem-loop ii motif (s2m) rna element of the sars virus genome to 2.7-a resolution. sars and related coronaviruses and astroviruses all possess a motif at the 3' end of their rna genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable rna genome. we find that this extreme conservation is clearly explained by the requirement to form a highly structured rna ... | 2004 | 15630477 |
| the structure of a rigorously conserved rna element within the sars virus genome. | we have solved the three-dimensional crystal structure of the stem-loop ii motif (s2m) rna element of the sars virus genome to 2.7-a resolution. sars and related coronaviruses and astroviruses all possess a motif at the 3' end of their rna genomes, called the s2m, whose pathogenic importance is inferred from its rigorous sequence conservation in an otherwise rapidly mutable rna genome. we find that this extreme conservation is clearly explained by the requirement to form a highly structured rna ... | 2004 | 15630477 |
| bacterial chromosome segregation: structure and dna binding of the soj dimer--a conserved biological switch. | soj and spo0j of the gram-negative hyperthermophile thermus thermophilus belong to the conserved parab family of bacterial proteins implicated in plasmid and chromosome partitioning. spo0j binds to dna near the replication origin and localises at the poles following initiation of replication. soj oscillates in the nucleoid region in an atp- and spo0j-dependent fashion. here, we show that soj undergoes atp-dependent dimerisation in solution and forms nucleoprotein filaments with dna. crystal stru ... | 2005 | 15635448 |
| high-level overproduction of his-tagged tth dna polymerase in thermus thermophilus. | a new plasmid for the overexpression of his-tagged thermozymes in thermus thermophilus was developed. with this plasmid, soluble and active histidine-tagged dna polymerase from t. thermophilus was overproduced in larger amounts in the thermophile than in escherichia coli. the protein purified from the thermophile was active in pcr. | 2005 | 15640243 |
| isolation and characterization of a thermostable rna ligase 1 from a thermus scotoductus bacteriophage ts2126 with good single-stranded dna ligation properties. | we have recently sequenced the genome of a novel thermophilic bacteriophage designated as ts2126 that infects the thermophilic eubacterium thermus scotoductus. one of the annotated open reading frames (orfs) shows homology to t4 rna ligase 1, an enzyme of great importance in molecular biology, owing to its ability to ligate single-stranded nucleic acids. the orf was cloned, and recombinant protein was expressed, purified and characterized. the recombinant enzyme ligates single-stranded nucleic a ... | 2005 | 15642699 |
| crystal structure of mil (mth680): internal duplication and similarity between the imp4/brix domain and the anticodon-binding domain of class iia aminoacyl-trna synthetases. | proteins of the imp4/brix superfamily are involved in ribosomal rna processing, an essential function in all cells. we report the first structure of an imp4/brix superfamily protein, the mil (for methanothermobacter thermautotrophicus imp4-like) protein (gene product mth680), from the archaeon m. thermautotrophicus. the amino- and carboxy-terminal halves of mil show significant structural similarity to one another, suggesting an origin by means of an ancestral duplication. both halves show the s ... | 2005 | 15654320 |
| breaking sieve for steric exclusion of a noncognate amino acid from active site of a trna synthetase. | the genetic code is fixed in aminoacylation reactions catalyzed by aminoacyl-trna synthetases. amino acid discrimination occurs at two sites: one for amino acid activation and aminoacylation and one for editing misactivated amino acids. although the active site sieves out bulkier amino acids, misactivation occurs with substrates whose side chains are smaller than the cognate one. paradoxically, although alanyl-trna synthetase activates glycine as well as alanine, the sterically larger (than alan ... | 2005 | 15657145 |
| the snrnp 15.5k protein folds its cognate k-turn rna: a combined theoretical and biochemical study. | the human 15.5k protein binds to the 5' stem-loop of u4 snrna, promotes the assembly of the spliceosomal u4/u6 snrnp, and is required for the recruitment of the 61k protein and the 20/60/90k protein complex to the u4 snrna. in the crystallographic structure of the 15.5k-u4 snrna complex, the conformation of the rna corresponds to the family of kink-turn (k-turn) structural motifs. we simulated the complex and the free rna, showing how the protein binding and the intrinsic flexibility contribute ... | 2005 | 15659359 |
| genetic analysis reveals domain interactions of arabidopsis hsp100/clpb and cooperation with the small heat shock protein chaperone system. | we have defined amino acids important for function of the arabidopsis thaliana hsp100/clpb chaperone (athsp101) in acquired thermotolerance by isolating recessive, loss-of-function mutations and a novel semidominant, gain-of-function allele [hot1-4 (a499t)]. the hot1-4 allele is unusual in that it not only fails to develop thermotolerance to 45 degrees c after acclimation at 38 degrees c, but also is sensitive to 38 degrees c, which is a permissive temperature for wild-type and loss-of-function ... | 2005 | 15659638 |
| biogenesis of a putative channel protein, comec, required for dna uptake: membrane topology, oligomerization and formation of disulphide bonds. | comec is a putative channel protein for dna uptake in bacillus subtilis and other genetically transformable bacteria. membrane topology studies suggest a model of comec as a multispanning membrane protein with seven transmembrane segments (tmss), and possibly with one laterally inserted amphipathic helix. we show that comec contains an intramolecular disulphide bond in its n-terminal extracellular loop (between the residues c131 and c172), which is required for the stability of the protein, and ... | 2005 | 15661011 |
| interaction of rrf and ef-g from e. coli and t. thermophilus with ribosomes from both origins--insight into the mechanism of the ribosome recycling step. | ribosome recycling factor (rrf), elongation factor-g (ef-g), and ribosomes from thermus thermophilus (tt-) and escherichia coli (ec-) were used to study the disassembly mechanism of post-termination ribosomal complexes by these factors. with tt-rrf, ec-ef-g can release bound-trna from ec-model post-termination complexes. however, tt-rrf is not released by ec-ef-g from ec-ribosomes. this complex with tt-rrf and ec-ribosomes after the trna release by ec-ef-g is regarded as an intermediate of the d ... | 2005 | 15661844 |
| the diversity of dolichol-linked precursors to asn-linked glycans likely results from secondary loss of sets of glycosyltransferases. | the vast majority of eukaryotes (fungi, plants, animals, slime mold, and euglena) synthesize asn-linked glycans (alg) by means of a lipid-linked precursor dolichol-pp-glcnac2man9glc3. knowledge of this pathway is important because defects in the glycosyltransferases (alg1-alg12 and others not yet identified), which make dolichol-pp-glycans, lead to numerous congenital disorders of glycosylation. here we used bioinformatic and experimental methods to characterize alg glycosyltransferases and doli ... | 2005 | 15665075 |
| stabilization of nucleic acids by unusual polyamines produced by an extreme thermophile, thermus thermophilus. | extreme thermophiles produce two types of unusual polyamine: long linear polyamines such as caldopentamine and caldohexamine, and branched polyamines such as quaternary ammonium compounds [e.g. tetrakis(3-aminopropyl)ammonium]. to clarify the physiological roles of long linear and branched polyamines in thermophiles, we synthesized them chemically and tested their effects on the stability of ds (double-stranded) and ss (single-stranded) dnas and trna in response to thermal denaturation, as measu ... | 2005 | 15673283 |
| the high-affinity maltose/trehalose abc transporter in the extremely thermophilic bacterium thermus thermophilus hb27 also recognizes sucrose and palatinose. | we have studied the transport of trehalose and maltose in the thernophilic bacterium thermus thermophilus hb27, which grows optimally in the range of 70 to 75 degrees c. the k(m) values at 70 degrees c were 109 nm for trehalose and 114 nm for maltose; also, a high k(m) (424 nm) was found for the uptake of sucrose. competition studies showed that a single transporter recognizes trehalose, maltose, and sucrose, while d-galactose, d-fucose, l-rhamnose, l-arabinose, and d-mannose were not competitiv ... | 2005 | 15687184 |
| dna binding: a novel function of pseudomonas aeruginosa type iv pili. | the opportunistic pathogen pseudomonas aeruginosa produces multifunctional, polar, filamentous appendages termed type iv pili. type iv pili are involved in colonization during infection, twitching motility, biofilm formation, bacteriophage infection, and natural transformation. electrostatic surface analysis of modeled pilus fibers generated from p. aeruginosa strain pak, k122-4, and kb-7 pilin monomers suggested that a solvent-exposed band of positive charge may be a common feature of all type ... | 2005 | 15687210 |
| contribution of the atp binding site of pare to susceptibility to novobiocin and quinolones in streptococcus pneumoniae. | in streptococcus pneumoniae, an h103y substitution in the atp binding site of the pare subunit of topoisomerase iv was shown to confer quinolone resistance and hypersensitivity to novobiocin when associated with an s84f change in the a subunit of dna gyrase. we reconstituted in vitro the wild-type topoisomerase iv and its pare mutant. the pare mutant enzyme showed a decreased activity for decatenation at subsaturating atp levels and was more sensitive to inhibition by novobiocin but was as sensi ... | 2005 | 15687222 |
| crystal structure of a predicted phosphoribosyltransferase (tt1426) from thermus thermophilus hb8 at 2.01 a resolution. | tt1426, from thermus thermophilus hb8, is a conserved hypothetical protein with a predicted phosphoribosyltransferase (prtase) domain, as revealed by a pfam database search. the 2.01 a crystal structure of tt1426 has been determined by the multiwavelength anomalous dispersion (mad) method. tt1426 comprises a core domain consisting of a central five-stranded beta sheet surrounded by four alpha-helices, and a subdomain in the c terminus. the core domain structure resembles those of the type i prta ... | 2005 | 15689504 |
| analysis of subsecond protein dynamics by amide hydrogen exchange and mass spectrometry using a quenched-flow setup. | amide hydrogen exchange (hx) in combination with mass spectrometry (ms) is a powerful tool to analyze the folding and dynamics of proteins. in the traditional methodology the exchange time is controlled by manual pipetting, thereby limiting the time resolution to several seconds. some conformational changes in proteins, however, occur in the subsecond time scale, making it desirable to perform hx at shorter time intervals down to the limit set by the intrinsic chemical exchange rate. we now repo ... | 2005 | 15689511 |
| processivity clamp gp45 and ssdna-binding-protein gp32 modulate the fidelity of bacteriophage rb69 dna polymerase in a sequence-specific manner, sometimes enhancing and sometimes compromising accuracy. | numerous studies of the impact of accessory proteins upon the fidelity of dna synthesis have provided a complex and sometimes discordant picture. we previously described such an analysis conducted in vitro using various bacteriophage rb69 gp43 mutator dna polymerases with or without the accessory proteins gp32 (which binds single-stranded dna) plus gp45/44/62 (processivity clamp and its loaders). mutations were scored at many sites in the laczalpha mutation reporter sequence. unexpectedly, the a ... | 2005 | 15695359 |
| a previously uncharacterized role for small protein b (smpb) in transfer messenger rna-mediated trans-translation. | ssra is a versatile rna molecule found in all bacteria that functions as both a trna and an mrna. ssra rescues ribosomes stalled on damaged mrnas and directs the tagging and degradation of their aberrant protein products. small protein b (smpb) is required for all known activities of ssra. the two known functions of smpb are binding ssra rna and promoting stable association of the smpb.ssra complex with 70s ribosomes. using mutational analysis and biochemical experiments, we have discovered a pr ... | 2005 | 15699355 |
| quantitative pcr-enhanced immunoassay for measurement of enteroviral immunoglobulin m antibody and diagnosis of aseptic meningitis. | a pcr-enhanced immunoassay (pia) to detect enterovirus (ev) immunoglobulin m (igm) for diagnosis of recent ev infection was recently developed. this test was compared with another ev igm capture technique, the solid-phase reverse immunosorbent test (sprist). fourteen of 43 serum samples from aseptic meningitis patients were positive by pia, whereas 10 were positive by sprist. one of 39 control serum samples was weakly positive by pia. a single-serum-dilution real-time pcr-based pia for ev igm (q ... | 2005 | 15699416 |
| complete genome sequence of the hyperthermophilic archaeon thermococcus kodakaraensis kod1 and comparison with pyrococcus genomes. | the genus thermococcus, comprised of sulfur-reducing hyperthermophilic archaea, belongs to the order thermococcales in euryarchaeota along with the closely related genus pyrococcus. the members of thermococcus are ubiquitously present in natural high-temperature environments, and are therefore considered to play a major role in the ecology and metabolic activity of microbial consortia within hot-water ecosystems. to obtain insight into this important genus, we have determined and annotated the c ... | 2005 | 15710748 |
| increasing stability of water-soluble pqq glucose dehydrogenase by increasing hydrophobic interaction at dimeric interface. | water-soluble quinoprotein glucose dehydrogenase (pqqgdh-b) from acinetobacter calcoaceticus has a great potential for application as a glucose sensor constituent. because this enzyme shows no activity in its monomeric form, correct quaternary structure is essential for the formation of active enzyme. we have previously reported on the increasing of the stability of pqqgdh-b by preventing the subunit dissociation. previous studies were based on decreasing the entropy of quaternary structure diss ... | 2005 | 15715904 |
| genomic analysis of anaerobic respiration in the archaeon halobacterium sp. strain nrc-1: dimethyl sulfoxide and trimethylamine n-oxide as terminal electron acceptors. | we have investigated anaerobic respiration of the archaeal model organism halobacterium sp. strain nrc-1 by using phenotypic and genetic analysis, bioinformatics, and transcriptome analysis. nrc-1 was found to grow on either dimethyl sulfoxide (dmso) or trimethylamine n-oxide (tmao) as the sole terminal electron acceptor, with a doubling time of 1 day. an operon, dmsreabcd, encoding a putative regulatory protein, dmsr, a molybdopterin oxidoreductase of the dmso reductase family (dmseabc), and a ... | 2005 | 15716436 |
| structure of the nucleotide complex of pyrr, the pyr attenuation protein from bacillus caldolyticus, suggests dual regulation by pyrimidine and purine nucleotides. | pyrr is a protein that regulates the expression of genes and operons of pyrimidine nucleotide biosynthesis (pyr genes) in many bacteria. pyrr acts by binding to specific sequences on pyr mrna and causing transcriptional attenuation when intracellular levels of uridine nucleotides are elevated. pyrr from bacillus subtilis has been purified and extensively studied. in this work, we describe the purification to homogeneity and characterization of recombinant pyrr from the thermophile bacillus caldo ... | 2005 | 15716449 |
| characterization of the atpase and unwinding activities of the yeast dead-box protein has1p and the analysis of the roles of the conserved motifs. | the yeast dead-box protein has1p is required for the maturation of 18s rrna, the biogenesis of 40s r-subunits and for the processing of 27s pre-rrnas during 60s r-subunit biogenesis. we purified recombinant has1p and characterized its biochemical activities. we show that has1p is an rna-dependent atpase in vitro and that it is able to unwind rna/dna duplexes in an atp-dependent manner. we also report a mutational analysis of the conserved residues in motif i (86aktgsgkt93), motif iii (228sat230) ... | 2005 | 15718299 |
| crystal structure and dna-binding analysis of reco from deinococcus radiodurans. | the recfor pathway has been shown to be essential for dna repair through the process of homologous recombination in bacteria and, recently, to be important in the recovery of stalled replication forks following uv irradiation. reco, along with recr, recf, recq and recj, is a principal actor in this fundamental dna repair pathway. here we present the three-dimensional structure of a member of the reco family. the crystal structure of deinococcus radiodurans reco (drreco) reveals possible binding ... | 2005 | 15719017 |
| identification of a new family of putative pd-(d/e)xk nucleases with unusual phylogenomic distribution and a new type of the active site. | prediction of structure and function for uncharacterized protein families by identification of evolutionary links to characterized families and known structures is one of the cornerstones of genomics. theoretical assignment of three-dimensional folds and prediction of protein function even at a very general level can facilitate the experimental determination of the molecular mechanism of action and the role that members of a given protein family fulfill in the cell. here, we predict the three-di ... | 2005 | 15720711 |
| hinge-like motions in rna kink-turns: the role of the second a-minor motif and nominally unpaired bases. | kink-turn (k-turn) motifs are asymmetric internal loops found at conserved positions in diverse rnas, with sharp bends in phosphodiester backbones producing v-shaped structures. explicit-solvent molecular dynamics simulations were carried out for three k-turns from 23s rrna, i.e., kt-38 located at the base of the a-site finger, kt-42 located at the base of the l7/l12 stalk, and kt-58 located in domain iii, and for the k-turn of human u4 snrna. the simulations reveal hinge-like k-turn motions on ... | 2005 | 15722438 |
| separation of mutation avoidance and antirecombination functions in an escherichia coli muts mutant. | dna mismatch repair in escherichia coli has been shown to be involved in two distinct processes: mutation avoidance, which removes potential mutations arising as replication errors, and antirecombination which prevents recombination between related, but not identical (homeologous), dna sequences. we show that cells with the mutsdelta800 mutation (which removes the c-terminal 53 amino acids of muts) on a multicopy plasmid are proficient for mutation avoidance. in interspecies genetic crosses, how ... | 2005 | 15731339 |
| tolerance of the rieske-type [2fe-2s] cluster in recombinant ferredoxin bpha3 from pseudomonas sp. kks102 to histidine ligand mutations. | bpha3 from pseudomonas sp. kks102 is a rieske-type [2fe-2s] ferredoxin that transfers electrons from an nadh-dependent oxidoreductase, bpha4, to a biphenyl dioxygenase complex. a high-level expression and purification system for the recombinant bpha3 in escherichia coli was constructed. two histidine ligands of the rieske-type cluster in bpha3, were each replaced with serine, cysteine, asparagine and tyrosine. the single mutants, in which either his44 or his65 was replaced with a cysteine residu ... | 2005 | 15733056 |
| crystal structure of a novel polyisoprenoid-binding protein from thermus thermophilus hb8. | the isoprenoid quinones exist widely among prokaryotes and eukaryotes. they play essential roles in respiratory electron transport and in controlling oxidative stress and gene regulation. in the isoprenoid quinone biosynthetic pathway, polyprenyl pyrophosphates are used as isoprenoid side-chain precursors. here we report the crystal structure of a novel polyprenyl pyrophosphate binding protein, tt1927b, from thermus thermophilus hb8, complexed with its ligand. this protein belongs to the ycei-li ... | 2005 | 15741337 |
| a mutation in the decoding center of thermus thermophilus 16s rrna suggests a novel mechanism of streptomycin resistance. | a spontaneous kanamycin resistance and capreomycin resistance mutation, a1408g, in the decoding center of 16s rrna, was identified in the extreme thermophile thermus thermophilus. unexpectedly, this mutation also confers resistance to streptomycin. we propose a novel mechanism of streptomycin resistance by which a1408g influences conformational changes in 16s rrna during trna selection. | 2005 | 15743969 |
| modular rna architecture revealed by computational analysis of existing pseudoknots and ribosomal rnas. | modular architecture is a hallmark of rna structures, implying structural, and possibly functional, similarity among existing rnas. to systematically delineate the existence of smaller topologies within larger structures, we develop and apply an efficient rna secondary structure comparison algorithm using a newly developed two-dimensional rna graphical representation. our survey of similarity among 14 pseudoknots and subtopologies within ribosomal rnas (rrnas) uncovers eight pairs of structurall ... | 2005 | 15745998 |
| the interaction between sigma70 and the beta-flap of escherichia coli rna polymerase inhibits extension of nascent rna during early elongation. | the sigma-subunit of bacterial rna polymerase (rnap) is required for promoter-specific transcription initiation. this function depends on specific intersubunit interactions that occur when sigma associates with the rnap core enzyme to form rnap holoenzyme. among these interactions, that between conserved region 4 of sigma and the flap domain of the rnap beta-subunit (beta-flap) is critical for recognition of the major class of bacterial promoters. here, we describe the isolation of amino acid su ... | 2005 | 15761057 |
| molecular analysis of a synthetic tetracycline-binding riboswitch. | riboswitches are newly discovered regulatory elements that consist solely of rna, sense their ligand in a preformed binding pocket, and perform a conformational switch in response to ligand binding, resulting in altered gene expression. regulation by a tetracycline (tc)-binding aptamer when inserted into the 5' untranslated region (utr) of a reporter gene exhibits all characteristics of a riboswitch. chemical and enzymatic probing reveals that the aptamer consists of two stems, p1 and p2, which ... | 2005 | 15769877 |
| leucyl-trna synthetase from the ancestral bacterium aquifex aeolicus contains relics of synthetase evolution. | the editing reactions catalyzed by aminoacyl-trna synthetases are critical for the faithful protein synthesis by correcting misactivated amino acids and misaminoacylated trnas. we report that the isolated editing domain of leucyl-trna synthetase from the deep-rooted bacterium aquifex aeolicus (alphabeta-leurs) catalyzes the hydrolytic editing of both mischarged trna(leu) and minihelix(leu). within the domain, we have identified a crucial 20-amino-acid peptide that confers editing capacity when t ... | 2005 | 15775966 |
| ldpa: a component of the circadian clock senses redox state of the cell. | the endogenous 24-h (circadian) rhythms exhibited by the cyanobacterium synechococcus elongatus pcc 7942 and other organisms are entrained by a variety of environmental factors. in cyanobacteria, the mechanism that transduces environmental input signals to the central oscillator of the clock is not known. an earlier study identified ldpa as a gene involved in light-dependent modulation of the circadian period, and a candidate member of a clock-entraining input pathway. here, we report that the l ... | 2005 | 15775978 |
| modification at position 9 with 1-methyladenosine is crucial for structure and function of nematode mitochondrial trnas lacking the entire t-arm. | the mitochondria of the nematode ascaris suum have trnas with unusual secondary structures that lack either the t-arm or d-arm found in most other organisms. of the twenty-two trna species present in the mitochondria of a.suum, twenty lack the entire t-arm and two serine trnas lack the d-arm. to understand how such unusual trnas work in the nematode mitochondrial translation system, we analyzed post-transcriptional modifications of 11 mitochondrial trna species purified from a.suum, 10 of which ... | 2005 | 15781491 |
| single-stranded dna-binding protein of deinococcus radiodurans: a biophysical characterization. | the highly conserved bacterial single-stranded dna-binding (ssb) proteins play an important role in dna replication, repair and recombination and are essential for the survival of the cell. they are functional as tetramers, in which four ob(oligonucleotide/oligosaccharide binding)-folds act as dna-binding domains. the protomer of the ssb protein from the extremely radiation-resistant organism deinococcus radiodurans (drassb) has twice the size of the other bacterial ssb proteins and contains two ... | 2005 | 15781492 |
| the thermophilic, homohexameric aminopeptidase of borrelia burgdorferi is a member of the m29 family of metallopeptidases. | proteases are implicated in several aspects of the physiology of microorganisms, as well as in host-pathogen interactions. aminopeptidases are also emerging as novel drug targets in infectious agents. in this study, we have characterized an aminopeptidase from the spirochete borrelia burgdorferi, the causative agent of lyme disease. the aminopeptidolytic activity was identified in cell extracts from b. burgdorferi by using the substrate leucine-7-amido-4-methylcoumarin. a protein displaying this ... | 2005 | 15784569 |
| structure of p-protein of the glycine cleavage system: implications for nonketotic hyperglycinemia. | the crystal structure of the p-protein of the glycine cleavage system from thermus thermophilus hb8 has been determined. this is the first reported crystal structure of a p-protein, and it reveals that p-proteins do not involve the alpha(2)-type active dimer universally observed in the evolutionarily related pyridoxal 5'-phosphate (plp)-dependent enzymes. instead, novel alphabeta-type dimers associate to form an alpha(2)beta(2) tetramer, where the alpha- and beta-subunits are structurally simila ... | 2005 | 15791207 |
| crystal structure of yeast yhr049w/fsh1, a member of the serine hydrolase family. | yhr049w/fsh1 was recently identified in a combined computational and experimental proteomics analysis for the detection of active serine hydrolases in yeast. this analysis suggested that fsh1 might be a serine-type hydrolase belonging to the broad functional alphabeta-hydrolase superfamily. in order to get insight into the molecular function of this gene, it was targeted in our yeast structural genomics project. the crystal structure of the protein confirms that it contains a ser/his/asp catalyt ... | 2005 | 15802654 |
| molecular analysis of the role of two aromatic aminotransferases and a broad-specificity aspartate aminotransferase in the aromatic amino acid metabolism of pyrococcus furiosus. | the genes encoding aromatic aminotransferase ii (aroat ii) and aspartate aminotransferase (aspat) from pyrococcus furiosus have been identified, expressed in escherichia coli and the recombinant proteins characterized. the aroat ii enzyme was specific for the transamination reaction of the aromatic amino acids, and uses a-ketoglutarate as the amino acceptor. like the previously characterized aroat i, aroat ii has highest efficiency for phenylalanine (k(cat)/km = 923 s(-1) mm(-1)). northern blot ... | 2002 | 15803651 |
| proteolysis in hyperthermophilic microorganisms. | proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. in this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genus pyrococcus, the crenarchaeote sulfolobus ... | 2002 | 15803660 |
| trna m7g methyltransferase trm8p/trm82p: evidence linking activity to a growth phenotype and implicating trm82p in maintaining levels of active trm8p. | we show that saccharomyces cerevisiae strains lacking trm8p/trm82p trna m7g methyltransferase are temperature-sensitive in synthetic media containing glycerol. bacterial trm8 orthologs complement the growth defect of trm8-delta, trm82-delta, and trm8-delta trm82-delta double mutants, suggesting that bacteria employ a single subunit for trm8p/trm82p function. the growth phenotype of trm8 mutants correlates with lack of trna m7g methyltransferase activity in vitro and in vivo, based on analysis of ... | 2005 | 15811913 |
| the affinity of the dynein microtubule-binding domain is modulated by the conformation of its coiled-coil stalk. | the microtubule-binding domain (mtbd) of dynein is separated from the aaa (atpase with any other activity) core of the motor by an approximately 15-nm stalk that is predicted to consist of an antiparallel coiled coil. however, the structure of this coiled coil and the mechanism it uses to mediate communication between the mtbd and atp-binding core are unknown. here, we sought to identify the optimal alignment between the hydrophobic heptad repeats in the two strands of the stalk coiled coil. to ... | 2005 | 15826937 |
| functional characterization of a novel arga from mycobacterium tuberculosis. | the mycobacterium tuberculosis gene rv2747 encodes a novel 19-kda arga that catalyzes the initial step in l-arginine biosynthesis, namely the conversion of l-glutamate to alpha-n-acetyl-l-glutamate. initial velocity studies reveal that rv2747 proceeds through a sequential kinetic mechanism, with k(m) values of 280 mm for l-glutamine and 150 microm for acetyl-coenzyme a and with a k(cat) value of 200 min(-1). initial velocity studies with l-glutamate showed that even at concentrations of 600 mm, ... | 2005 | 15838030 |
| human mitochondrial tyrrs disobeys the tyrosine identity rules. | human tyrosyl-trna synthetase from mitochondria (mt-tyrrs) presents dual sequence features characteristic of eubacterial and archaeal tyrrss, especially in the region containing amino acids recognizing the n1-n72 tyrosine identity pair. this would imply that human mt-tyrrs has lost the capacity to discriminate between the g1-c72 pair typical of eubacterial and mitochondrial trnatyr and the reverse pair c1-g72 present in archaeal and eukaryal trnatyr. this expectation was verified by a functional ... | 2005 | 15840810 |
| crystal structures of apo wild-type m. jannaschii tyrosyl-trna synthetase (tyrrs) and an engineered tyrrs specific for o-methyl-l-tyrosine. | the methanococcus jannaschii trna(tyr)/tyrrs pair has been engineered to incorporate unnatural amino acids into proteins in e. coli. to reveal the structural basis for the altered specificity of mutant tyrrs for o-methyl-l-tyrosine (ometyr), the crystal structures for the apo wild-type and mutant m. jannaschii tyrrs were determined at 2.66 and 3.0 a, respectively, for comparison with the published structure of tyrrs complexed with trna(tyr) and substrate tyrosine. a large conformational change w ... | 2005 | 15840835 |
| inhibition of archaeal growth and dna topoisomerase vi activities by the hsp90 inhibitor radicicol. | type ii dna topoisomerases have been classified into two families, topo iia and topo iib, based on structural and mechanistic dissimilarities. topo iia is the target of many important antibiotics and antitumoural drugs, most of them being inactive on topo iib. the effects and mode of action of topo iia inhibitors in vitro and in vivo have been extensively studied for the last twenty-five years. in contrast, studies of topo iib inhibitors were lacking. to document this field, we have studied two ... | 2005 | 15849317 |
| structural and functional divergence of muts2 from bacterial muts1 and eukaryotic msh4-msh5 homologs. | muts homologs, identified in nearly all bacteria and eukaryotes, include the bacterial proteins muts1 and muts2 and the eukaryotic muts homologs 1 to 7, and they often are involved in recognition and repair of mismatched bases and small insertion/deletions, thereby limiting illegitimate recombination and spontaneous mutation. to explore the relationship of muts2 to other muts homologs, we examined conserved protein domains. fundamental differences in structure between muts2 and other muts homolo ... | 2005 | 15866941 |
| severity of the streptomycin resistance and streptomycin dependence phenotypes of ribosomal protein s12 of thermus thermophilus depends on the identity of highly conserved amino acid residues. | the structural basis for the streptomycin dependence phenotype of ribosomal protein s12 mutants is poorly understood. here we describe the application of site-directed mutagenesis and gene replacement of thermus thermophilus rpsl to assess the importance of side chain identity and tertiary interactions as phenotypic determinants of drug-dependent mutants. | 2005 | 15866943 |
| developmental-stage-specific assembly of parb complexes in streptomyces coelicolor hyphae. | in streptomyces coelicolor parb is required for accurate chromosome partitioning during sporulation. using a functional parb-enhanced green fluorescent protein fusion, we observed bright tip-associated foci and other weaker, irregular foci in s. coelicolor vegetative hyphae. in contrast, in aerial hyphae regularly spaced bright foci accompanied sporulation-associated chromosome condensation and septation. | 2005 | 15866947 |
| nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. | since operons are unstable across prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. thus, genes belonging to a given operon in one genome might re-associate in other genomes revealing functional relationships among gene products. we developed a system to build networks of functional relationships of gene products based on their organization into operons in any available genome. the operon predictions are based on inter-genic distances. our system can use d ... | 2005 | 15867197 |
| distribution of genes for synthesis of trehalose and mannosylglycerate in thermus spp. and direct correlation of these genes with halotolerance. | in this study we correlate the presence of genes leading to the synthesis of trehalose and mannosylglycerate (mg) in 17 strains of the genus thermus with the ability of the strains to grow and accumulate these compatible solutes in a defined medium containing nacl. the two sets of genes, namely, otsa/otsb for the synthesis of trehalose and mpgs/mpgp for the synthesis of mg, were necessary for the growth of thermus thermophilus in a defined medium containing up to 6% nacl. strains lacking a compl ... | 2005 | 15870334 |
| a functional relationship between helix 1 and the 900 tetraloop of 16s ribosomal rna within the bacterial ribosome. | the conserved 900 tetraloop that caps helix 27 of 16s ribosomal rna (rrna) interacts with helix 24 of 16s rrna and also with helix 67 of 23s rrna, forming the intersubunit bridge b2c, proximal to the decoding center. in previous studies, we investigated how the interaction between the 900 tetraloop and helix 24 participates in subunit association and translational fidelity. in the present study, we investigated whether the 900 tetraloop is involved in other undetected interactions with different ... | 2005 | 15872184 |
| strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. | the x-ray susceptibility of the lysine-pyridoxal-5'-phosphate schiff base in bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 k to 1.3 a resolution, complemented by on-line spectroscopic studies. x-rays induce deprotonation of the internal aldimine, changes in the schiff base conformation, displacement of the cofactor molecule, and disruption of the schiff base linkage between pyridoxal-5'-phosphate and the lys residue. analy ... | 2005 | 15883191 |