Publications

salt-induced detour through compact regions of the protein folding landscape.	in several cases, inorganic salts have been used to induce partly structured states in protein folding. but what is the nature of these states: do they represent key stepping stones in the folding process, or are they circumstantial pitfalls in the energy landscape? here we report that, in the case of the two-state protein s6, the salt-induced collapsed state is off the usual folding routes in the sense that it is prematurely collapsed and slows down folding by several orders of magnitude. altho ...	1999	10518521
crystal structure of the dna nucleotide excision repair enzyme uvrb from thermus thermophilus.	nucleotide excision repair (ner) is the most important dna-repair mechanism in living organisms. in prokaryotes, three enzymes forming the uvrabc system initiate ner of a variety of structurally different dna lesions. uvrb, the central component of this system, is responsible for the ultimate dna damage recognition and participates in the incision of the damaged dna strand. the crystal structure of thermus thermophilus uvrb reveals a core that is structurally similar to core regions found in hel ...	1999	10518516
p1 parb domain structure includes two independent multimerization domains.	parb is one of two p1-encoded proteins that are required for active partition of the p1 prophage in escherichia coli. to probe the native domain structure of parb, we performed limited proteolytic digestions of full-length parb, as well as of several n-terminal and c-terminal deletion fragments of parb. the c-terminal 140 amino acids of parb form a very trypsin-resistant domain. in contrast, the n terminus is more susceptible to proteolysis, suggesting that it forms a less stably folded domain o ...	1999	10498700
bioenergetics of the archaea.	in the late 1970s, on the basis of rrna phylogeny, archaea (archaebacteria) was identified as a distinct domain of life besides bacteria (eubacteria) and eucarya. though forming a separate domain, archaea display an enormous diversity of lifestyles and metabolic capabilities. many archaeal species are adapted to extreme environments with respect to salinity, temperatures around the boiling point of water, and/or extremely alkaline or acidic ph. this has posed the challenge of studying the molecu ...	1999	10477309
cloning of the gene encoding a novel thermostable alpha-galactosidase from thermus brockianus iti360.	an alpha-galactosidase gene from thermus brockianus iti360 was cloned, sequenced, and expressed in escherichia coli, and the recombinant protein was purified. the gene, designated agat, codes for a 476-residue polypeptide with a calculated molecular mass of 53, 810 da. the native structure of the recombinant enzyme (agat) was estimated to be a tetramer. agat displays amino acid sequence similarity to the alpha-galactosidases of thermotoga neapolitana and thermotoga maritima and a low-level seque ...	1999	10473401
marine bacterial isolates display diverse responses to uv-b radiation.	the molecular and biological consequences of uv-b radiation were investigated by studying five species of marine bacteria and one enteric bacterium. laboratory cultures were exposed to an artificial uv-b source and subjected to various post-uv irradiation treatments. significant differences in survival subsequent to uv-b radiation were observed among the isolates, as measured by culturable counts. uv-b-induced dna photodamage was investigated by using a highly specific radioimmunoassay to measur ...	1999	10473381
comparison of the d-glutamate-adding enzymes from selected gram-positive and gram-negative bacteria.	the biochemical properties of the d-glutamate-adding enzymes (murd) from escherichia coli, haemophilus influenzae, enterococcus faecalis, and staphylococcus aureus were investigated to detect any differences in the activity of this enzyme between gram-positive and gram-negative bacteria. the genes (murd) that encode these enzymes were cloned into pmal-c2 fusion vector and overexpressed as maltose-binding protein-murd fusion proteins. each fusion protein was purified to homogeneity by affinity to ...	1999	10464212
active-site mutations in the xrn1p exoribonuclease of saccharomyces cerevisiae reveal a specific role in meiosis.	xrn1p of saccharomyces cerevisiae is a major cytoplasmic rna turnover exonuclease which is evolutionarily conserved from yeasts to mammals. deletion of the xrn1 gene causes pleiotropic phenotypes, which have been interpreted as indirect consequences of the rna turnover defect. by sequence comparisons, we have identified three loosely defined, common 5'-3' exonuclease motifs. the significance of motif ii has been confirmed by mutant analysis with xrn1p. the amino acid changes d206a and d208a abol ...	1999	10454540
the accessory subunit of mtdna polymerase shares structural homology with aminoacyl-trna synthetases: implications for a dual role as a primer recognition factor and processivity clamp.	the accessory subunit of the heterodimeric mtdna polymerase (polgamma) from drosophila embryos is required to maintain the structural integrity or catalytic efficiency of the holoenzyme. cdnas for the accessory subunit from drosophila, man, mouse, and rat have been identified, and comparative sequence alignment reveals that the c-terminal region of about 120 aa is the most conserved. furthermore, we demonstrate that the accessory subunit of animal polgamma has both sequence and structural simila ...	1999	10449726
an inducible human immunodeficiency virus type 1 (hiv-1) vector which effectively suppresses hiv-1 replication.	recently, gene therapy vectors based upon the human immunodeficiency virus type 1 (hiv-1) genome have been developed. here, we create an hiv-1 vector which is defective for all hiv-1 genes, but which maintains cis-acting elements required for efficient packaging, infection, and expression. in t cells transduced by this vector, vector expression is low but efficiently induced following hiv-1 infection. remarkably, although the hiv-1 vector does not contain specific anti-hiv-1 therapeutic genes, t ...	1999	10438857
in thermoanaerobacterium thermosulfurigenes em1 s-layer homology domains do not attach to peptidoglycan.	three exocellular enzymes of thermoanaerobacterium thermosulfurigenes em1 possess a c-terminal triplicated sequence related to a domain of bacterial cell surface proteins (s-layer proteins). at least one copy of this sequence, named the slh (for s-layer homology) domain, is also present at the n terminus of the s-layer protein of this bacterium. the hypothesis that slh domains serve to anchor proteins to the cell surface was investigated by using the slh domain-containing xylanase. this enzyme w ...	1999	10438774
characterization of an atypical superoxide dismutase from sinorhizobium meliloti.	sinorhizobium meliloti rm5000 is an aerobic bacterium that can live free in the soil or in symbiosis with the roots of leguminous plants. a single detectable superoxide dismutase (sod) was found in free-living growth conditions. the corresponding gene was isolated from a genomic library by using a sod fragment amplified by pcr from degenerate primers as a probe. the soda gene was located in the chromosome. it is transcribed monocistronically and encodes a 200-amino-acid protein with a theoretica ...	1999	10419947
the kinetoplast structure-specific endonuclease i is related to the 5' exo/endonuclease domain of bacterial dna polymerase i and colocalizes with the kinetoplast topoisomerase ii and dna polymerase beta during replication.	the mitochondrial dna (kinetoplast dna) of the trypanosomatid crithidia fasciculata has an unusual structure composed of minicircles and maxicircles topologically interlocked into a single network and organized in a disc-shaped structure at the base of the flagellum. we previously purified a structure-specific endonuclease (sse1), based on its rnase h activity, that is enriched in isolated kinetoplasts. the endonuclease gene has now been cloned, sequenced, and found to be closely related to the ...	1999	10411896
improved dna sequencing accuracy and detection of heterozygous alleles using manganese citrate and different fluorescent dye terminators.	the use of dideoxynucleotide triphosphates labeled with different fluorescent dyes (dye terminators) is the most versatile method for automated dna sequencing. however, variation in peak heights reduces base-calling accuracy and limits heterozygous allele detection, favoring use of dye-labeled primers for this purpose. we have discovered that the addition of a manganese salt to the pe applied biosystems dye-terminator sequencing kits overcomes these limitations for the older rhodamine dyes as we ...	1999	10400927
the unique chaperone operon of thermotoga maritima: cloning and initial characterization of a functional hsp70 and small heat shock protein.	the hyperthermophilic eubacterium thermotoga maritima possesses an operon encoding an hsp70 molecular chaperone protein and a protein with meaningful homology to the small heat shock protein family of chaperones. this represents the first demonstrated co-operon organization for these two important classes of molecular chaperones. we have cloned and initially characterized these proteins as functional chaperones in vitro: the hsp70 is capable of atp hydrolysis and substrate binding, and the small ...	1999	10400580
sulfolobus acidocaldarius inorganic pyrophosphatase: structure, thermostability, and effect of metal ion in an archael pyrophosphatase.	the first crystal structure of an inorganic pyrophosphatase (s-ppase) from an archaebacterium, the thermophile sulfolobus acidocaldarius, has been solved by molecular replacement and refined to an r-factor of 19.7% at 2.7 a. s-ppase is a d3 homohexameric protein with one mg2+ per active site in a position similar to, but not identical with, the first activating metal in mesophilic pyrophosphatases (ppase). in mesophilic ppases, asp65, asp70, and asp102 coordinate the mg2+, while only asp65 and a ...	1999	10386872
analysis of peptidoglycan structure from vegetative cells of bacillus subtilis 168 and role of pbp 5 in peptidoglycan maturation.	the composition and fine structure of the vegetative cell wall peptidoglycan from bacillus subtilis were determined by analysis of its constituent muropeptides. the structures of 39 muropeptides, representing 97% of the total peptidoglycan, were elucidated. about 99% analyzed muropeptides in b. subtilis vegetative cell peptidoglycan have the free carboxylic group of diaminopimelic acid amidated. anhydromuropeptides and products missing a glucosamine at the nonreducing terminus account for 0.4 an ...	1999	10383963
heat-inactivated proteins are rescued by the dnak.j-grpe set and clpb chaperones.	functional chaperone cooperation between hsp70 (dnak) and hsp104 (clpb) was demonstrated in vitro. in a eubacterium thermus thermophilus, dnak and dnaj exist as a stable trigonal ring complex (tdnak.j complex) and the dnak gene cluster contains a clpb gene. when substrate proteins were heated at high temperature, none of the chaperones protected them from heat inactivation, but the tdnak.j complex could suppress the aggregation of proteins in an atp- and tgrpe-dependent manner. subsequent incuba ...	1999	10377389
the morphological transition of helicobacter pylori cells from spiral to coccoid is preceded by a substantial modification of the cell wall.	the peptidoglycan (murein) of helicobacter pylori has been investigated by high-performance liquid chromatography and mass spectrometric techniques. murein from h. pylori corresponded to the a1gamma chemotype, but the muropeptide elution patterns were substantially different from the one for escherichia coli in that the former produced high proportions of muropeptides with a pentapeptide side chain (about 60 mol%), with gly residues as the c-terminal amino acid (5 to 10 mol%), and with (1-->6)an ...	1999	10368145
nitrate and nitrite control of respiratory nitrate reduction in denitrifying pseudomonas stutzeri by a two-component regulatory system homologous to narxl of escherichia coli.	bacterial denitrification is expressed in response to the concurrent exogenous signals of low-oxygen tension and nitrate or one of its reduction products. the mechanism by which nitrate-dependent gene activation is effected was investigated in the denitrifying bacterium pseudomonas stutzeri atcc 14405. we have identified and isolated from this organism the chromosomal region encoding the two-component sensor-regulator pair narxl and found that it is linked with the narg operon for respiratory ni ...	1999	10368138
translation elongation factor 1-alpha interacts specifically with the human immunodeficiency virus type 1 gag polyprotein.	human immunodeficiency virus type 1 (hiv-1) gag-encoded proteins play key functions at almost all stages of the viral life cycle. since these functions may require association with cellular factors, the hiv-1 matrix protein (ma) was used as bait in a yeast two-hybrid screen to identify ma-interacting proteins. ma was found to interact with elongation factor 1-alpha (ef1alpha), an essential component of the translation machinery that delivers aminoacyl-trna to ribosomes. ef1alpha was then shown t ...	1999	10364286
cloning of the glutamyl-trna synthetase (gltx) gene from pseudomonas aeruginosa.	the glutamyl-trna synthetase (gltx) gene from pseudomonas aeruginosa was identified. a plasmid containing a 2.3-kb insert complemented the temperature-sensitive gltx mutation of escherichia coli jp1449, and gltx activity was demonstrated. the inferred amino acid sequence of this gene showed 50.6% identity with gltx from rhizobium meliloti.	1999	10348873
cd(ii)-responsive and constitutive mutants implicate a novel domain in merr.	expression of the tn21 mercury resistance (mer) operon is controlled by a metal-sensing repressor-activator, merr. when present, merr always binds to the same position on the dna (the operator mero), repressing transcription of the structural genes mertpcad in the absence of hg(ii) and inducing their transcription in the presence of hg(ii). although it has two potential binding sites, the purified merr homodimer binds only one hg(ii) ion, employing cys82 from one monomer and cys117 and cys126 fr ...	1999	10348859
maltose metabolism in the hyperthermophilic archaeon thermococcus litoralis: purification and characterization of key enzymes.	maltose metabolism was investigated in the hyperthermophilic archaeon thermococcus litoralis. maltose was degraded by the concerted action of 4-alpha-glucanotransferase and maltodextrin phosphorylase (malp). the first enzyme produced glucose and a series of maltodextrins that could be acted upon by malp when the chain length of glucose residues was equal or higher than four, to produce glucose-1-phosphate. phosphoglucomutase activity was also detected in t. litoralis cell extracts. glucose deriv ...	1999	10348846
mannan-degrading enzymes from cellulomonas fimi.	the genes man26a and man2a from cellulomonas fimi encode mannanase 26a (man26a) and beta-mannosidase 2a (man2a), respectively. mature man26a is a secreted, modular protein of 951 amino acids, comprising a catalytic module in family 26 of glycosyl hydrolases, an s-layer homology module, and two modules of unknown function. exposure of man26a produced by escherichia coli to c. fimi protease generates active fragments of the enzyme that correspond to polypeptides with mannanase activity produced by ...	1999	10347049
the accessory subunit of xenopus laevis mitochondrial dna polymerase gamma increases processivity of the catalytic subunit of human dna polymerase gamma and is related to class ii aminoacyl-trna synthetases.	peptide sequences obtained from the accessory subunit of xenopus laevis mitochondrial dna (mtdna) polymerase gamma (pol gamma) were used to clone the cdna encoding this protein. amino-terminal sequencing of the mitochondrial protein indicated the presence of a 44-amino-acid mitochondrial targeting sequence, leaving a predicted mature protein with 419 amino acids and a molecular mass of 47.3 kda. this protein is associated with the larger, catalytic subunit in preparations of active mtdna polymer ...	1999	10330144
the type ii pullulanase of thermococcus hydrothermalis: molecular characterization of the gene and expression of the catalytic domain.	the gene encoding a hyperthermostable type ii pullulanase produced by thermococcus hydrothermalis (th-apu) has been isolated. analysis of a total of 5.2 kb of genomic dna has revealed the presence of three open reading frames, one of which (apua) encodes the pullulanase. this enzyme is composed of 1,339 amino acid residues and exhibits a multidomain structure. in addition to a typical n-terminal signal peptide, th-apu possesses a catalytic domain, a domain bearing s-layer homology-like motifs, a ...	1999	10322035
three surface layer homology domains at the n terminus of the clostridium cellulovorans major cellulosomal subunit enge.	the gene enge, coding for endoglucanase e, one of the three major subunits of the clostridium cellulovorans cellulosome, has been isolated and sequenced. enge is comprised of an open reading frame (orf) of 3,090 bp and encodes a protein of 1,030 amino acids with a molecular weight of 111,796. the amino acid sequence derived from enge revealed a structure consisting of catalytic and noncatalytic domains. the n-terminal-half region of enge consisted of a signal peptide of 31 amino acid residues an ...	1999	10322032
sodium-dependent glutamate uptake by an alkaliphilic, thermophilic bacillus strain, ta2.a1.	a strain of bacillus designated ta2.a1, isolated from a thermal spring in te aroha, new zealand, grew optimally at ph 9.2 and 70 degrees c. bacillus strain ta2.a1 utilized glutamate as a sole carbon and energy source for growth, and sodium chloride (>5 mm) was an obligate requirement for growth. growth on glutamate was inhibited by monensin and amiloride, both inhibitors that collapse the sodium gradient (deltapna) across the cell membrane. n, n-dicyclohexylcarbodiimide inhibited the growth of b ...	1999	10322019
detection of viable listeria monocytogenes with a 5' nuclease pcr assay.	a 5' nuclease assay has been developed to detect viable listeria monocytogenes. the assay targets the hemolysin a (hlya) transcript, which is found only in l. monocytogenes. the single-tube, reverse transcriptase (rt), fluorogenic probe-based assay was formatted by using tth dna polymerase whose activity was modulated by using the manganese-chelating morpholinepropanesulfonic acid (mops) buffer. this assay was quantitative over a 3-log-unit range of template concentrations when tested with an in ...	1999	10224010
purification and characterization of thermotoga maritima endonuclease iv, a thermostable apurinic/apyrimidinic endonuclease and 3'-repair diesterase.	an endonuclease iv homolog was identified as the product of a conceptual open reading frame in the genome of the hyperthermophilic bacterium thermotoga maritima. the t. maritima endonuclease iv gene encodes a 287-amino-acid protein with 32% sequence identity to escherichia coli endonuclease iv. the gene was cloned, and the expressed protein was purified and shown to have enzymatic activities that are characteristic of the endonuclease iv family of dna repair enzymes, including apurinic/apyrimidi ...	1999	10217775
location of translational initiation factor if3 on the small ribosomal subunit.	the location of translational initiation factor if3 bound to the 30s subunit of the thermus thermophilus ribosome has been determined by cryoelectron microscopy. both the 30s.if3 complex and control 30s subunit structures were determined to 27-a resolution. the difference map calculated from the two reconstructions reveals three prominent lobes of positive density. the previously solved crystal structure of if3 fits very well into two of these lobes, whereas the third lobe probably arises from c ...	1999	10200257
cis-acting elements responsible for low-temperature-inducible expression of the gene coding for the thermolabile isocitrate dehydrogenase isozyme of a psychrophilic bacterium, vibrio sp. strain abe-1.	transcriptional control of the low-temperature-inducible icdii gene, encoding the thermolabile isocitrate dehydrogenase of a psychrophilic bacterium, vibrio sp. strain abe-1, was found to be mediated in part by a transcriptional silencer locating at nucleotide positions -560 to -526 upstream from the transcription start site of icdii. deletion of the silencer resulted in a 20-fold-increased level of expression of the gene at low temperature (15 degrees c) but not at high temperature (37 degrees ...	1999	10198027
distinct affinity of binding sites for s-layer homologous domains in clostridium thermocellum and bacillus anthracis cell envelopes.	binding parameters were determined for the slh (s-layer homologous) domains from the clostridium thermocellum outer layer protein olpb, from the c. thermocellum s-layer protein slpa, and from the bacillus anthracis s-layer proteins ea1 and sap, using cell walls from c. thermocellum and b. anthracis. each slh domain bound to c. thermocellum and b. anthracis cell walls with a different kd, ranging between 7.1 x 10(-7) and 1.8 x 10(-8) m. cell wall binding sites for slh domains displayed different ...	1999	10198008
nadh-quinone oxidoreductase: psst subunit couples electron transfer from iron-sulfur cluster n2 to quinone.	the proton-translocating nadh-quinone oxidoreductase (ec 1.6.99.3) is the largest and least understood enzyme complex of the respiratory chain. the mammalian mitochondrial enzyme (also called complex i) contains more than 40 subunits, whereas its structurally simpler bacterial counterpart (ndh-1) in paracoccus denitrificans and thermus thermophilus hb-8 consists of 14 subunits. a major unsolved question is the location and mechanism of the terminal electron transfer step from iron-sulfur cluster ...	1999	10097178
isolation of rnase h genes that are essential for growth of bacillus subtilis 168.	two genes encoding functional rnase h (ec 3.1.26.4) were isolated from a gram-positive bacterium, bacillus subtilis 168. two dna clones exhibiting rnase h activities both in vivo and in vitro were obtained from a b. subtilis dna library. one (28.2 kda) revealed high similarity to escherichia coli rnase hii, encoded by the rnhb gene. the other (33.9 kda) was designated rnhc and encodes b. subtilis rnase hiii. the b. subtilis genome has an rnha homologue, the product of which has not yet shown rna ...	1999	10094689
an engineered class i transfer rna with a class ii tertiary fold.	structure-based engineering of the tertiary fold of escherichia coli trna(gln)2 has enabled conversion of this transfer rna to a class ii structure while retaining recognition properties of a class i glutamine trna. the new trna possesses the 20-nt variable stem-loop of thermus thermophilus trna(ser). enlargement of the d-loop appears essential to maintaining a stable tertiary structure in this species, while rearrangement of a base triple in the augmented d-stem is critical for efficient glutam ...	1999	10094311
detection and induction of equine infectious anemia virus-specific cytotoxic t-lymphocyte responses by use of recombinant retroviral vectors.	cytotoxic t lymphocytes (ctl) appear to be critical in resolving or reducing the severity of lentivirus infections. retroviral vectors expressing the gag/pr or su protein of the lentivirus equine infectious anemia virus (eiav) were constructed and used to evaluate eiav-specific ctl responses in horses. three promoters, cytomegalovirus, simian virus sv40, and moloney murine sarcoma virus (momsv) long terminal repeat (ltr), were used, and there was considerable variation in their ability to direct ...	1999	10074123
aspartate 205 in the catalytic domain of naphthalene dioxygenase is essential for activity.	the naphthalene dioxygenase enzyme system carries out the first step in the aerobic degradation of naphthalene by pseudomonas sp. strain ncib 9816-4. the crystal structure of naphthalene dioxygenase (b. kauppi, k. lee, e. carredano, r. e. parales, d. t. gibson, h. eklund, and s. ramaswamy, structure 6:571-586, 1998) indicates that aspartate 205 may provide the most direct route of electron transfer between the rieske [2fe-2s] center of one alpha subunit and mononuclear iron in the adjacent alpha ...	1999	10074076
aspartate kinase-independent lysine synthesis in an extremely thermophilic bacterium, thermus thermophilus: lysine is synthesized via alpha-aminoadipic acid not via diaminopimelic acid.	an aspartate kinase-deficient mutant of thermus thermophilus, ak001, was constructed. the mutant strain did not grow in a minimal medium, suggesting that t. thermophilus contains a single aspartate kinase. growth of the mutant strain was restored by addition of both threonine and methionine, while addition of lysine had no detectable effect on growth. to further elucidate the lysine biosynthetic pathway in t. thermophilus, lysine auxotrophic mutants of t. thermophilus were obtained by chemical m ...	1999	10074061
surface proteins of gram-positive bacteria and mechanisms of their targeting to the cell wall envelope.	the cell wall envelope of gram-positive bacteria is a macromolecular, exoskeletal organelle that is assembled and turned over at designated sites. the cell wall also functions as a surface organelle that allows gram-positive pathogens to interact with their environment, in particular the tissues of the infected host. all of these functions require that surface proteins and enzymes be properly targeted to the cell wall envelope. two basic mechanisms, cell wall sorting and targeting, have been ide ...	1999	10066836
dissimilatory reduction of fe(iii) and other electron acceptors by a thermus isolate.	a thermophilic bacterium that can use o2, no3-, fe(iii), and s0 as terminal electron acceptors for growth was isolated from groundwater sampled at a 3.2-km depth in a south african gold mine. this organism, designated sa-01, clustered most closely with members of the genus thermus, as determined by 16s rrna gene (rdna) sequence analysis. the 16s rdna sequence of sa-01 was >98% similar to that of thermus strain nmx2 a.1, which was previously isolated by other investigators from a thermal spring i ...	1999	10049886
molecular characterization of the nitrite-reducing system of staphylococcus carnosus.	characterization of a nitrite reductase-negative staphylococcus carnosus tn917 mutant led to the identification of the nir operon, which encodes nirbd, the dissimilatory nadh-dependent nitrite reductase; sira, the putative oxidase and chelatase, and sirb, the uroporphyrinogen iii methylase, both of which are necessary for biosynthesis of the siroheme prosthetic group; and nirr, which revealed no convincing similarity to proteins with known functions. we suggest that nirr is essential for nir pro ...	1999	10049379
characterization of is1547, a new member of the is900 family in the mycobacterium tuberculosis complex, and its association with is6110.	unlike classically defined insertion sequence (is) elements, which are delimited by their inverted terminal repeats, some is elements do not have inverted terminal repeats. among this group of atypical is elements, is116, is900, is901, and is1110 have been proposed as members of the is900 family of elements, not only because they do not have inverted terminal repeats but also because they share other features such as homologous transposases and particular insertion sites. in this study, we repor ...	1999	9922269
biochemical properties of a high fidelity dna ligase from thermus species ak16d.	nad+-dependent dna ligases from thermophilic bacteria thermus species are highly homologous with amino acid sequence identities ranging from 85 to 98%. thermus species ak16d ligase, the most divergent of the seven thermus isolates collected worldwide, was cloned, expressed in escherichia coli and purified to homogeneity. this thermus ligase is similar to thermus thermophilus hb8 ligase with respect to ph, salt, nad+, divalent cation profiles and steady-state kinetics.however, the former is more ...	1999	9889274
discontinuous occurrence of the hsp70 (dnak) gene among archaea and sequence features of hsp70 suggest a novel outlook on phylogenies inferred from this protein.	occurrence of the hsp70 (dnak) gene was investigated in various members of the domain archaea comprising both euryarchaeotes and crenarchaeotes and in the hyperthermophilic bacteria aquifex pyrophilus and thermotoga maritima representing the deepest offshoots in phylogenetic trees of bacterial 16s rrna sequences. the gene was not detected in 8 of 10 archaea examined but was found in a. pyrophilus and t. maritima, from which it was cloned and sequenced. comparative analyses of the hsp70 amino aci ...	1999	9882656
characterization of functionally active subribosomal particles from thermus aquaticus.	peptidyl transferase activity of thermus aquaticus ribosomes is resistant to the removal of a significant number of ribosomal proteins by protease digestion, sds, and phenol extraction. to define the upper limit for the number of macromolecular components required for peptidyl transferase, particles obtained by extraction of t. aquaticus large ribosomal subunits were isolated and their rna and protein composition was characterized. active subribosomal particles contained both 23s and 5s rrna ass ...	1999	9874776
the alpha subunit of toluene dioxygenase from pseudomonas putida f1 can accept electrons from reduced ferredoxintol but is catalytically inactive in the absence of the beta subunit.	the oxygenase component of toluene dioxygenase from pseudomonas putida f1 is an iron-sulfur protein (isptol) consisting of alpha (todc1) and beta (todc2) subunits. purified todc1 gave absorbance and electron paramagnetic resonance spectra identical to those given by purified isptol. todc1 was reduced by nadh and catalytic amounts of reductasetol and ferredoxintol. reduced todc1 did not oxidize toluene, and catalysis was strictly dependent on the presence of purified todc2.	1999	9872799
peptidoglycan fine structure of the radiotolerant bacterium deinococcus radiodurans sark.	peptidoglycan from deinococcus radiodurans was analyzed by high-performance liquid chromatography and mass spectrometry. the monomeric subunit was: n-acetylglucosamine-n-acetylmuramic acid-l-ala-d-glu-(gamma)-l-orn-[(delta)gly-gly]-d-ala-d-ala. cross-linkage was mediated by (gly)2 bridges, and glycan strands were terminated in (1-->6)anhydro-muramic acid residues. structural relations with the phylogenetically close thermus thermophilus are discussed.	1999	9864347
identification of two binding domains, one for peptidoglycan and another for a secondary cell wall polymer, on the n-terminal part of the s-layer protein sbsb from bacillus stearothermophilus pv72/p2.	first studies on the structure-function relationship of the s-layer protein from b. stearothermophilus pv72/p2 revealed the coexistence of two binding domains on its n-terminal part, one for peptidoglycan and another for a secondary cell wall polymer (scwp). the peptidoglycan binding domain is located between amino acids 1 to 138 of the mature s-layer protein comprising a typical s-layer homologous domain. the scwp binding domain lies between amino acids 240 to 331 and possesses a high serine pl ...	1998	9852032
campylobacter fetus surface layer proteins are transported by a type i secretion system.	the virulence of campylobacter fetus, a bacterial pathogen of ungulates and humans, is mediated in part by the presence of a paracrystalline surface layer (s-layer) that confers serum resistance. the subunits of the s-layer are s-layer proteins (slps) that are secreted in the absence of an n-terminal signal sequence and attach to either type a or b c. fetus lipopolysaccharide in a serospecific manner. antigenic variation of multiple slps (encoded by sapa homologs) of type a strain 23d occurs by ...	1998	9851986
a novel, rapid in cell rna amplification technique for the detection of low copy mrna transcripts.	growing interest now focuses on improvements of in situ polymerase chain reaction (pcr) technology for the detection of dna and rna cellular sequences. in this study, reverse transcription pcr in situ hybridisation (rt pcr-ish) was developed and used to determine gene expression of pyruvate dehydrogenase in a cell model system, using human peripheral blood lymphocytes (pbls). the success of in cell rna amplification depends on the type of cell/tissue fixation, cell permeabilisation, and the effi ...	1998	9850340
the genome of melanoplus sanguinipes entomopoxvirus.	the family poxviridae contains two subfamilies: the entomopoxvirinae (poxviruses of insects) and the chordopoxvirinae (poxviruses of vertebrates). here we present the first characterization of the genome of an entomopoxvirus (epv) which infects the north american migratory grasshopper melanoplus sanguinipes and other important orthopteran pests. the 236-kbp m. sanguinipes epv (msepv) genome consists of a central coding region bounded by 7-kbp inverted terminal repeats and contains 267 open readi ...	1999	9847359
tracking molecular evolution of photosynthesis by characterization of a major photosynthesis gene cluster from heliobacillus mobilis.	a dna sequence has been obtained for a 35.6-kb genomic segment from heliobacillus mobilis that contains a major cluster of photosynthesis genes. a total of 30 orfs were identified, 20 of which encode enzymes for bacteriochlorophyll and carotenoid biosynthesis, reaction-center (rc) apoprotein, and cytochromes for cyclic electron transport. donor side electron-transfer components to the rc include a putative rc-associated cytochrome c553 and a unique four-large-subunit cytochrome bc complex consis ...	1998	9843979
posttranscriptional control of gene expression in yeast.	studies of the budding yeast saccharomyces cerevisiae have greatly advanced our understanding of the posttranscriptional steps of eukaryotic gene expression. given the wide range of experimental tools applicable to s. cerevisiae and the recent determination of its complete genomic sequence, many of the key challenges of the posttranscriptional control field can be tackled particularly effectively by using this organism. this article reviews the current knowledge of the cellular components and me ...	1998	9841679
inorganic cation transport and energy transduction in enterococcus hirae and other streptococci.	energy metabolism by bacteria is well understood from the chemiosmotic viewpoint. we know that bacteria extrude protons across the plasma membrane, establishing an electrochemical potential that provides the driving force for various kinds of physiological work. among these are the uptake of sugars, amino acids, and other nutrients with the aid of secondary porters and the regulation of the cytoplasmic ph and of the cytoplasmic concentration of potassium and other ions. bacteria live in diverse ...	1998	9841664
nadp-isocitrate dehydrogenase from pseudomonas nautica: kinetic constant determination and carbon limitation effects on the pool of intracellular substrates.	variations of intracellular concentrations of isocitrate and nadp+ were measured throughout all growth phases of the marine bacterium pseudomonas nautica. the intracellular isocitrate concentration tracked the intracellular protein concentration throughout all phases of growth. it rapidly increased in early exponential phase to a maximum and fell to nearly zero in parallel with pyruvate exhaustion in the culture medium. the intracellular nadp+ and protein concentrations increased in parallel dur ...	1998	9835589
the bacillus subtilis nucleotidyltransferase is a trna cca-adding enzyme.	there has been increased interest in bacterial polyadenylation with the recent demonstration that 3' poly(a) tails are involved in rna degradation. poly(a) polymerase i (pap i) of escherichia coli is a member of the nucleotidyltransferase (ntr) family that includes the functionally related trna cca-adding enzymes. thirty members of the ntr family were detected in a search of the current database of eubacterial genomic sequences. gram-negative organisms from the beta and gamma subdivisions of the ...	1998	9829937
gene cloning and characterization of recombinant rnase hii from a hyperthermophilic archaeon.	we have cloned the gene encoding rnase hii (rnase hiipk) from the hyperthermophilic archaeon pyrococcus kodakaraensis kod1 by screening of a library for clones that suppressed the temperature-sensitive growth phenotype of an rnh mutant strain of escherichia coli. this gene was expressed in an rnh mutant strain of e. coli, the recombinant enzyme was purified, and its biochemical properties were compared with those of e. coli rnases hi and hii. rnase hiipk is composed of 228 amino acid residues (m ...	1998	9829929
quantification of 16s rrnas in complex bacterial communities by multiple competitive reverse transcription-pcr in temperature gradient gel electrophoresis fingerprints.	a novel approach was developed to quantify rrna sequences in complex bacterial communities. the main bacterial 16s rrnas in drentse a grassland soils (the netherlands) were amplified by reverse transcription (rt)-pcr with bacterium-specific primers and were separated by temperature gradient gel electrophoresis (tgge). the primer pair used (primers u968-gc and l1401) was found to amplify with the same efficiency 16s rrnas from bacterial cultures containing different taxa and cloned 16s ribosomal ...	1998	9797325
construction of a proline-producing mutant of the extremely thermophilic eubacterium thermus thermophilus hb27.	growth of thermus thermophilus hb27 was inhibited by a proline analog, 3,4-dehydroproline (dhp). this result suggested that the gamma-glutamyl kinase (the product of the prob gene) was inhibited by feedback inhibition in t. thermophilus. dhp-resistant mutants were reported previously for escherichia coli (a. m. dandekar and s. l. uratsu, j. bacteriol. 170:5943-5945, 1988) and serratia marcescens (k. omori, s. suzuki, y. imai, and s. komatsubara, j. gen. microbiol. 138:693-699, 1992), and their m ...	1998	9797285
oxygen-insensitive nitroreductases: analysis of the roles of nfsa and nfsb in development of resistance to 5-nitrofuran derivatives in escherichia coli.	nitroheterocyclic and nitroaromatic compounds constitute an enormous range of chemicals whose potent biological activity has significant human health and environmental implications. the biological activity of nitro-substituted compounds is derived from reductive metabolism of the nitro moiety, a process catalyzed by a variety of nitroreductase activities. resistance of bacteria to nitro-substituted compounds is believed to result primarily from mutations in genes encoding oxygen-insensitive nitr ...	1998	9791100
glutamyl-trna(gln) amidotransferase in deinococcus radiodurans may be confined to asparagine biosynthesis.	asparaginyl-trna (asn-trna) and glutaminyl-trna (gln-trna) are essential components of protein synthesis. they can be formed by direct acylation by asparaginyl-trna synthetase (asnrs) or glutaminyl-trna synthetase (glnrs). the alternative route involves transamidation of incorrectly charged trna. examination of the preliminary genomic sequence of the radiation-resistant bacterium deinococcus radiodurans suggests the presence of both direct and indirect routes of asn-trna and gln-trna formation. ...	1998	9789001
thermus thermophilus: a link in evolution of the trna-dependent amino acid amidation pathways.	thermus thermophilus possesses an aspartyl-trna synthetase (asprs2) able to aspartylate efficiently trnaasp and trnaasn. aspartate mischarged on trnaasn then is converted into asparagine by an omega amidase that differs structurally from all known asparagine synthetases. however, aspartate is not misincorporated into proteins because the binding capacity of aminoacylated trnaasn to elongation factor tu is only conferred by conversion of aspartate into asparagine. t. thermophilus additionally con ...	1998	9789000
lactone-ring-cleaving enzyme: genetic analysis, novel rna editing, and evolutionary implications.	a lactonohydrolase from fusarium oxysporum aku 3702 is an enzyme catalyzing the hydrolysis of aldonate lactones to the corresponding aldonic acids. the amino acid sequences of the nh2 terminus and internal peptide fragments of the enzyme were determined to prepare synthetic oligonucleotides as primers for the pcr. an approximate 1, 000-base genomic dna fragment thus amplified was used as the probe to clone both genomic dna and cdna for the enzyme. the lactonohydrolase genomic gene consists of si ...	1998	9788992
enhancement of the amplicor enterovirus pcr test with a coprecipitant.	the incorporation of a commercially available coprecipitant into the amplicor enterovirus pcr test specimen preparation enhanced the sensitivity and reproducibility of this assay. fifty-five previously tested archived cerebrospinal fluids (csf) specimens were tested in a blind study in duplicate with and without pellet paint coprecipitant (novagen, inc., madison, wis.). of these specimens, 26 had previously been determined to be positive and 29 had previously been determined to be negative. all ...	1998	9774607
comparative analysis of the regulation of expression and structures of two evolutionarily divergent genes for delta1-pyrroline-5-carboxylate synthetase from tomato.	we isolated two tomato (lycopersicon esculentum) cdna clones, tompro1 and tompro2, specifying delta1-pyrroline-5-carboxylate synthetase (p5cs), the first enzyme of proline (pro) biosynthesis. tompro1 is unusual because it resembles prokaryotic polycistronic operons (m.g. garcía-ríos, t. fujita, p.c. larosa, r.d. locy, j.m. clithero, r.a. bressan, l.n. csonka [1997] proc natl acad sci usa 94: 8249-8254), whereas tompro2 encodes a full-length p5cs. we analyzed the accumulation of pro and the tompr ...	1998	9765552
superoxide dismutase in arabidopsis: an eclectic enzyme family with disparate regulation and protein localization.	a number of environmental stresses can lead to enhanced production of superoxide within plant tissues, and plants are believed to rely on the enzyme superoxide dismutase (sod) to detoxify this reactive oxygen species. we have identified seven cdnas and genes for sod in arabidopsis. these consist of three cuznsods (csd1, csd2, and csd3), three fesods (fsd1, fsd2, and fsd3), and one mnsod (msd1). the chromosomal location of these seven sod genes has been established. to study this enzyme family, a ...	1998	9765550
capacity of nine thermostable dna polymerases to mediate dna amplification in the presence of pcr-inhibiting samples.	the pcr is an extremely powerful method for detecting microorganisms. however, its full potential as a rapid detection method is limited by the inhibition of the thermostable dna polymerase from thermus aquaticus by many components found in complex biological samples. in this study, we have compared the effects of known pcr-inhibiting samples on nine thermostable dna polymerases. samples of blood, cheese, feces, and meat, as well as various ions, were added to pcr mixtures containing various the ...	1998	9758794
effects of temperature, salinity, and medium composition on compatible solute accumulation by thermococcus spp	the effects of salinity and growth temperature on the accumulation of intracellular organic solutes were examined by nuclear magnetic resonance spectroscopy (nmr) in thermococcus litoralis, thermococcus celer, thermococcus stetteri, and thermococcus zilligii (strain an1). in addition, the effects of growth stage and composition of the medium were studied in t. litoralis. a novel compound identified as beta-galactopyranosyl-5-hydroxylysine was detected in t. litoralis grown on peptone-containing ...	1998	9758772
translation elongation factor 2 is part of the target for a new family of antifungals.	translation elongation factor 2 (ef2), which in saccharomyces cerevisiae is expressed from the eft1 and eft2 genes, has been found to be targeted by a new family of highly specific antifungal compounds derived from the natural product sordarin. two complementation groups of mutants resistant to the semisynthetic sordarin derivative gm193663 were found. the major one (21 members) consisted of isolates with mutations on eft2. the minor one (four isolates) is currently being characterized but it is ...	1998	9756779
creation of genetic information by dna polymerase of the thermophilic bacterium thermus thermophilus.	genetic information encoded in a template of a genome is replicated in a complementary way by dna polymerase or rna polymerase with high fidelity; no creation of information occurs in this reaction unless an error occurs. we report here that dna polymerase of the thermophilic bacterium thermus thermophilus can synthesize up to 200 kb linear double-stranded dna in vitro in the complete absence of added primer and template dnas, indicating that genetic information is actively created by protein. t ...	1998	9753734
abnormal t cell receptor v gene usage in myasthenia gravis: prevalence and characterization of expanded t cell populations.	the usage of t cell receptor (tcr) valpha/vbeta chains on cells from 38 patients with myasthenia gravis (mg) was determined by flow cytometry. there was a decreased number of cells expressing vbeta2 in cd8+ and vbeta3 in cd4+ cells in patients compared with healthy individuals. abnormal expansions of t cells using particular tcr valpha/vbeta gene products were found in 18/38 patients. a significantly higher usage of vbeta13 was observed but there was no restriction with regard to other tcr valph ...	1998	9737677
a natural large chromosomal inversion in lactococcus lactis is mediated by homologous recombination between two insertion sequences.	comparative analysis of chromosomal macrorestriction polymorphism of the two closely related lactococcus lactis subsp. cremoris strains mg1363 and ncdo763 revealed the presence of a large inversion covering half of the genome. to determine what kind of genetic element could be implicated in this rearrangement, the two inversion junctions of mg1363 and ncdo763 chromosomes were cloned and characterized. nucleotide sequence analysis showed the presence of one copy of the lactococcal is905 element i ...	1998	9733685
linkage map of escherichia coli k-12, edition 10: the traditional map.	this map is an update of the edition 9 map by berlyn et al. (m. k. b. berlyn, k. b. low, and k. e. rudd, p. 1715-1902, in f. c. neidhardt et al., ed., escherichia coli and salmonella: cellular and molecular biology, 2nd ed., vol. 2, 1996). it uses coordinates established by the completed sequence, expressed as 100 minutes for the entire circular map, and adds new genes discovered and established since 1996 and eliminates those shown to correspond to other known genes. the latter are included as ...	1998	9729611
insertion sequences.	insertion sequences (iss) constitute an important component of most bacterial genomes. over 500 individual iss have been described in the literature to date, and many more are being discovered in the ongoing prokaryotic and eukaryotic genome-sequencing projects. the last 10 years have also seen some striking advances in our understanding of the transposition process itself. not least of these has been the development of various in vitro transposition systems for both prokaryotic and eukaryotic e ...	1998	9729608
fidelity of dna ligation: a novel experimental approach based on the polymerisation of libraries of oligonucleotides.	complete libraries of oligonucleotides were used as substrates for thermus thermophilus dna ligase, on a m13mp18 ssdna template. a 17mer primer was used to start a polymerisation process. ladders of ligation products were analysed by gel electrophoresis. octa-, nona- and decanucleotide libraries were compared. nonanucleotides were optimum for polymerisation and up to 15 monomers were ligated. the fidelity of incorporation was studied by sequencing 28 clones (2268 bases) of nonanucleotide polymer ...	1998	9722647
domain organization and functional analysis of thermus thermophilus muts protein.	muts protein binds to dna and specifically recognizes mismatched or small looped out heteroduplex dna. in order to elucidate its structure-function relationships, the domain structure of thermus thermophilus muts protein was studied by performing denaturation experiments and limited proteolysis. the former suggested that t. thermophilus muts consists of at least three domains with estimated stabilities of 12.3, 22.9 and 30.7 kcal/mol and the latter revealed that it consists of four domains: a1 ( ...	1998	9722634
multicenter evaluation of the amplicor enterovirus pcr test with cerebrospinal fluid from patients with aseptic meningitis. the european union concerted action on viral meningitis and encephalitis.	the amplicor enterovirus pcr test was compared with viral culture for the detection of enteroviruses in cerebrospinal fluid (csf) specimens. in a multicenter study in which nine laboratories participated, a total of 476 csf specimens were collected from patients with suspected aseptic meningitis. sixty-eight samples were positive by pcr (14.4%), whereas 49 samples were positive by culture (10.4%), demonstrating that the amplicor enterovirus pcr test was significantly more sensitive than culture ...	1998	9705409
influence of the secondary cell wall polymer on the reassembly, recrystallization, and stability properties of the s-layer protein from bacillus stearothermophilus pv72/p2.	the high-molecular-weight secondary cell wall polymer (scwp) from bacillus stearothermophilus pv72/p2 is mainly composed of n-acetylglucosamine (glcnac) and n-acetylmannosamine (mannac) and is involved in anchoring the s-layer protein via its n-terminal region to the rigid cell wall layer. in addition to this binding function, the scwp was found to inhibit the formation of self-assembly products during dialysis of the guanidine hydrochloride (ghcl)-extracted s-layer protein. the degree of assemb ...	1998	9696762
diversity of cytochrome bc complexes: example of the rieske protein in green sulfur bacteria.	the rieske 2fe2s cluster of chlorobium limicola forma thiosulfatophilum strain tassajara was studied by electron paramagnetic resonance spectroscopy. two distinct orientations of its g tensor were observed in oriented samples corresponding to differing conformations of the protein. only one of the two conformations persisted after treatment with 2,5-dibromo-3-methyl-6-isopropyl-p-benzoquinone. a redox midpoint potential (em) of +160 mv in the ph range of 6 to 7.7 and a decreasing em (-60 to -80 ...	1998	9658021
single amino acid substitution in prokaryote polypeptide release factor 2 permits it to terminate translation at all three stop codons.	prokaryotic translational release factors, rf1 and rf2, catalyze polypeptide release at uag/uaa and uga/uaa stop codons, respectively. in this study, we isolated a bacterial rf2 mutant (rf2) containing an e167k substitution that restored the growth of a temperature-sensitive rf1 strain of escherichia coli and the viability of a chromosomal rf1/rf2 double knockout. in both in vivo and in vitro polypeptide termination assays, rf2 catalyzed uag/uaa termination, as does rf1, as well as uga termina ...	1998	9653158
solution structure of the cytohesin-1 (b2-1) sec7 domain and its interaction with the gtpase adp ribosylation factor 1.	cytohesin-1 (b2-1) is a guanine nucleotide exchange factor for human adp ribosylation factor (arf) gtpases, which are important for vesicular protein trafficking and coatamer assembly in the cell. cytohesin-1 also has been reported to promote cellular adhesion via binding to the beta2 integrin cytoplasmic domain. the solution structure of the sec7 domain of cytohesin-1, which is responsible for both the protein's guanine nucleotide exchange factor function and beta2 integrin binding, was determi ...	1998	9653114
thermotoga neapolitana homotetrameric xylose isomerase is expressed as a catalytically active and thermostable dimer in escherichia coli.	the xyla gene from thermotoga neapolitana 5068 was expressed in escherichia coli. gel filtration chromatography showed that the recombinant enzyme was both a homodimer and a homotetramer, with the dimer being the more abundant form. the purified native enzyme, however, has been shown to be exclusively tetrameric. the two enzyme forms had comparable stabilities when they were thermoinactivated at 95 degrees c. differential scanning calorimetry revealed thermal transitions at 99 and 109.5 degrees ...	1998	9647799
does disparate occurrence of autoregulatory programmed frameshifting in decoding the release factor 2 gene reflect an ancient origin with loss in independent lineages?	in escherichia coli an autoregulatory mechanism of programmed ribosomal frameshifting governs the level of polypeptide chain release factor 2. from an analysis of 20 sequences of genes encoding release factor 2, we infer that this frameshift mechanism was present in a common ancestor of a large group of bacteria and has subsequently been lost in three independent lineages.	1998	9642202
adjustment of conformational flexibility is a key event in the thermal adaptation of proteins.	3-isopropylmalate dehydrogenase (ipmdh, e.c. 1.1.1.85) from the thermophilic bacterium thermus thermophilus hb8 is homologous to ipmdh from the mesophilic escherichia coli, but has an approximately 17 degreesc higher melting temperature. its temperature optimum is 22-25 degreesc higher than that of the e. coli enzyme; however, it is hardly active at room temperature. the increased conformational rigidity required to stabilize the thermophilic enzyme against heat denaturation might explain its di ...	1998	9636162
immunological and molecular characterization of three variant subtype p1.14 strains of neisseria meningitidis.	epidemic outbreaks of group b meningococcal disease exhibit a clonal nature consisting of a common serotype-subtype. subtype-specific monoclonal antibodies (mabs) directed toward two variable regions (vr1 and vr2) of the class 1 protein of neisseria meningitidis are used in this classification scheme. a new mab was developed to classify a nonsubtypeable (nst) strain of n. meningitidis, 7967. this mab bound to both the nst strain and the prototype subtype p1. 14 strain, s3446, by dot blot analysi ...	1998	9632588
identification of the gene encoding the tryptophan synthase beta-subunit from chlamydomonas reinhardtii.	we report the isolation of a chlamydomonas reinhardtii cdna that encodes the beta-subunit of tryptophan synthase (tsb). this cdna was cloned by functional complementation of a trp-operon-deleted strain of escherichia coli. hybridization analysis indicated that the gene exists in a single copy. the predicted amino acid sequence showed the greatest identity to tsb polypeptides from other photosynthetic organisms. with the goal of identifying mutations in the gene encoding this enzyme, we isolated ...	1998	9625698
an autonomously replicating transforming vector for sulfolobus solfataricus.	a plasmid able to transform and to be stably maintained both in sulfolobus solfataricus and in escherichia coli was constructed by insertion into an e. coli plasmid of the autonomously replicating sequence of the virus particle ssv1 and a suitable mutant of the hph (hygromycin phosphotransferase) gene as the transformation marker. the vector suffered no rearrangement and/or chromosome integration, and its copy number in sulfolobus was increased by exposure of the cells to mitomycin c.	1998	9620978
anaerobic growth, a property horizontally transferred by an hfr-like mechanism among extreme thermophiles.	despite the fact that the extreme thermophilic bacteria belonging to the genus thermus are classified as strict aerobes, we have shown that thermus thermophilus hb8 (atcc 27634) can grow anaerobically when nitrate is present in the growth medium. this strain-specific property is encoded by a respiratory nitrate reductase gene cluster (nar) whose expression is induced by anoxia and nitrate (s. ramírez-arcos, l. a. fernández-herrero, and j. berenguer, biochim. biophys. acta, 1396:215-1997). we sho ...	1998	9620963
evaluation of a commercially available reverse transcription-pcr assay for diagnosis of enteroviral infection in archival and prospectively collected cerebrospinal fluid specimens.	a commercially available reverse transcription (rt)-pcr method (amplicor ev; roche diagnostic systems, inc., branchburg, n.j.) was evaluated for detection of enteroviruses in cerebrospinal fluid from patients with neurological disease. this assay was compared with virus isolation in cell culture and an in-house rt-pcr method designed with a nonoverlapping region of the enteroviral genome. a panel of 200 cerebrospinal fluid specimens prospectively collected from patients with a wide variety of ne ...	1998	9620411
secondary absence of mitochondria in giardia lamblia and trichomonas vaginalis revealed by valyl-trna synthetase phylogeny.	nuclear-coded valyl-trna synthetase (valrs) of eukaryotes is regarded of mitochondrial origin. complete valrs sequences obtained by us from two amitochondriate protists, the diplomonad, giardia lamblia and the parabasalid, trichomonas vaginalis were of the eukaryotic type, strongly suggesting an identical history of valrs in all eukaryotes studied so far. the findings indicate that diplomonads are secondarily amitochondriate and give further evidence for such conclusion reached recently concerni ...	1998	9618503
posttranscriptional modifications in 16s and 23s rrnas of the archaeal hyperthermophile sulfolobus solfataricus.	posttranscriptional modification is common to many types of rna, but the majority of information concerning structure and function of modification is derived principally from trna. by contrast, less is known about modification in rrna in spite of accumulating evidence for its direct participation in translation. the structural identities and approximate molar levels of modifications have been established for 16s and 23s rrnas of the archaeal hyperthermophile sulfolobus solfactaricus by using com ...	1998	9603876
structure of the beta-galactosidase gene from thermus sp. strain t2: expression in escherichia coli and purification in a single step of an active fusion protein.	the nucleotide sequence of both the bgaa gene, coding for a thermostable beta-galactosidase of thermus sp. strain t2, and its flanking regions was determined. the deduced amino acid sequence of the enzyme predicts a polypeptide of 645 amino acids (mr, 73,595). comparative analysis of the open reading frames located in the flanking regions of the bgaa gene revealed that they might encode proteins involved in the transport and hydrolysis of sugars. the observed homology between the deduced amino a ...	1998	9603833
genes for 2,4,5-trichlorophenoxyacetic acid metabolism in burkholderia cepacia ac1100: characterization of the tftc and tftd genes and locations of the tft operons on multiple replicons.	burkholderia cepacia ac1100 uses the chlorinated aromatic compound 2, 4,5-trichlorophenoxyacetic acid (2,4,5-t) as a sole source of carbon and energy. the enzyme which converts the first intermediate in the pathway, 2,4,5-trichlorophenol, to 5-chlorohydroquinone has been purified and consists of two subunits of 58 and 22 kda, encoded by the tftc and tftd genes (48). a degenerate primer was designed from the n terminus of the 58-kda polypeptide and used to isolate a clone containing the tftc and ...	1998	9603818
visualization of elongation factor g on the escherichia coli 70s ribosome: the mechanism of translocation.	during protein synthesis, elongation factor g (ef-g) binds to the ribosome and promotes the step of translocation, a process in which trna moves from the a to the p site of the ribosome and the mrna is advanced by one codon. by using three-dimensional cryo-electron microscopy, we have visualized ef-g in a ribosome-ef-g-gdp-fusidic acid complex. fitting the crystal structure of ef-g-gdp into the cryo density map reveals a large conformational change mainly associated with domain iv, the domain th ...	1998	9600930
the crystal structure of asparaginyl-trna synthetase from thermus thermophilus and its complexes with atp and asparaginyl-adenylate: the mechanism of discrimination between asparagine and aspartic acid.	the crystal structure of thermus thermophilus asparaginyl-trna synthetase has been solved by multiple isomorphous replacement and refined at 2.6 a resolution. this is the last of the three class iib aminoacyl-trna synthetase structures to be determined. as expected from primary sequence comparisons, there are remarkable similarities between the tertiary structures of asparaginyl-trna synthetase and aspartyl-trna synthetase, and most of the active site residues are identical except for three key ...	1998	9582288
association of ferredoxin-nadp oxidoreductase with the chloroplastic pyridine nucleotide dehydrogenase complex in barley leaves	barley (hordeum vulgare l.) leaves were used to isolate and characterize the chloroplast nad(p)h dehydrogenase complex. the stroma fraction and the thylakoid fraction solubilized with sodium deoxycholate were analyzed by native polyacrylamide gel electrophoresis, and the enzymes detected with nadh and nitroblue tetrazolium were electroeluted. the enzymes electroeluted from band s from the stroma fraction and from bands t1 (et1) and t2 from the thylakoid fraction solubilized with sodium deoxychol ...	1998	9576793
control of 5',5'-dinucleoside triphosphate catabolism by aph1, a saccharomyces cerevisiae analog of human fhit.	the putative human tumor suppressor gene fhit (fragile histidine triad) (m. ohta et al., cell 84:587-597, 1996) encodes a protein behaving in vitro as a dinucleoside 5',5"'-p1,p3-triphosphate (ap3a) hydrolase. in this report, we show that the saccharomyces cerevisiae aph1 gene product, which resembles human fhit protein, also hydrolyzes dinucleoside 5',5'-polyphosphates, with ap3a being the preferred substrate. accordingly, disruption of the aph1 gene produced viable s. cerevisiae cells containi ...	1998	9573184
acquired thermotolerance and temperature-induced protein accumulation in the extremely thermophilic bacterium rhodothermus obamensis.	temperature-induced changes in thermotolerance and protein composition were examined in heat-shocked cells and high-temperature-grown cells of the extremely thermophilic bacterium rhodothermus obamensis. the survival at temperatures superoptimal for growth (90 and 95 degrees c) was enhanced in both heat-shocked cells and high-temperature-grown cells relative to that of cells grown at optimal temperatures. in a comparison of protein composition using two-dimensional gel electrophoresis, putative ...	1998	9573167