Publications

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
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
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
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
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
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
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
calibrating bacterial evolution.	attempts to calibrate bacterial evolution have relied on the assumption that rates of molecular sequence divergence in bacteria are similar to those of higher eukaryotes, or to those of the few bacterial taxa for which ancestors can be reliably dated from ecological or geological evidence. despite similarities in the substitution rates estimated for some lineages, comparisons of the relative rates of evolution at different classes of nucleotide sites indicate no basis for their universal applica ...	1999	10535975
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
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
detection of human herpesvirus 6 by reverse transcription-pcr.	the role of human herpesvirus 6 (hhv-6) in disease beyond primary infection remains unclear. we have developed and validated a new reverse transcription-pcr (rt-pcr) assay for hhv-6 that can determine the presence of hhv-6 in clinical specimens and differentiate between latent and replicating virus. peripheral blood mononuclear cells from 109 children were evaluated for hhv-6 by rt-pcr, dna pcr, and viral culture. of these samples, 106 were suitable for analysis. a total of 20 samples were posit ...	1999	10523572
loss of cytochrome c oxidase activity and acquisition of resistance to quinone analogs in a laccase-positive variant of azospirillum lipoferum.	laccase, a p-diphenol oxidase typical of plants and fungi, has been found recently in a proteobacterium, azospirillum lipoferum. laccase activity was detected in both a natural isolate and an in vitro-obtained phase variant that originated from the laccase-negative wild type. in this study, the electron transport systems of the laccase-positive variant and its parental laccase-negative forms were compared. during exponential (but not stationary) growth under fully aerobic (but not under microaer ...	1999	10542175
specific inhibition of the eubacterial dna ligase by arylamino compounds.	all known dna ligases catalyze the formation of a phosphodiester linkage between adjacent termini in double-stranded dna via very similar mechanisms. the ligase family can, however, be divided into two classes: eubacterial ligases, which require nad(+) as a cofactor, and other ligases, from viruses, archaea, and eukaryotes, which use atp. drugs that discriminate between dna ligases from different sources may have antieubacterial activity. we now report that a group of arylamino compounds, includ ...	1999	10543760
improving proteolytic cleavage at the 3a/3b site of the hepatitis a virus polyprotein impairs processing and particle formation, and the impairment can be complemented in trans by 3ab and 3abc.	the orchestrated liberation of viral proteins by 3c(pro)-mediated proteolysis is pivotal for gene expression by picornaviruses. proteolytic processing is regulated either by the amino acid sequence at the cleavage site of the substrate or by cofactors covalently or noncovalently linked to the viral proteinase. to determine the role of the amino acid sequence at cleavage sites 3a/3b and 3b/3c that are essential for the liberation of 3c(pro) from its precursors and to assess the function of the st ...	1999	10559299
determination of bovine rotavirus g and p serotypes in italy by pcr.	determination of the g and p serotypes of group a bovine rotaviruses from 149 samples of feces or intestinal contents collected from calves showing clinical signs of neonatal diarrhea was performed by a nested reverse transcription-pcr typing assay. the g6 serotype was the most prevalent, accounting for viruses in 55.7% of the samples; viruses of the g10 and g8 serotypes were found in 34.9 and 4.7% of the samples, respectively. the virus in one sample (0.7%) was not classified due to concomitant ...	1999	10565900
genome sequence of the radioresistant bacterium deinococcus radiodurans r1.	the complete genome sequence of the radiation-resistant bacterium deinococcus radiodurans r1 is composed of two chromosomes (2,648,638 and 412,348 base pairs), a megaplasmid (177,466 base pairs), and a small plasmid (45,704 base pairs), yielding a total genome of 3,284, 156 base pairs. multiple components distributed on the chromosomes and megaplasmid that contribute to the ability of d. radiodurans to survive under conditions of starvation, oxidative stress, and high amounts of dna damage were ...	1999	10567266
structural distribution of stability in a thermophilic enzyme.	stability parameters for individual residues in thermus thermophilus cysteine-free rnase h were determined by native state hydrogen exchange, thus providing a unique comparison of regional thermodynamics between thermophilic and mesophilic homologues. the general distribution of stability in the thermophilic protein is similar to that of its mesophilic homologue, with a proportional increase in stability for almost all residues. as a consequence, the residue-specific stabilities of the two prote ...	1999	10570131
sequential mechanism of solubilization and refolding of stable protein aggregates by a bichaperone network.	a major activity of molecular chaperones is to prevent aggregation and refold misfolded proteins. however, when allowed to form, protein aggregates are refolded poorly by most chaperones. we show here that the sequential action of two escherichia coli chaperone systems, clpb and dnak-dnaj-grpe, can efficiently solubilize excess amounts of protein aggregates and refold them into active proteins. measurements of aggregate turbidity, congo red, and 4,4'-dianilino-1, 1'-binaphthyl-5,5'-disulfonic ac ...	1999	10570141
ligase-based detection of mononucleotide repeat sequences.	up to 15% of all colorectal cancers are considered to be replication error positive (rer(+)) and contain mutations at hundreds of thousands of microsatellite repeat sequences. recently, a number of intragenic mononucleotide repeat sequences have been demonstrated to be targets for inactivating genes in rer(+)colorectal tumors. in this study, thermostable dna ligases were tested for the ability to detect alterations in microsatellite sequences in colon tumor samples. ligation profiles on mononucl ...	1999	10572192
cloning, overexpression, and mutagenesis of the sporobolomyces salmonicolor aku4429 gene encoding a new aldehyde reductase, which catalyzes the stereoselective reduction of ethyl 4-chloro-3-oxobutanoate to ethyl (s)-4-chloro-3-hydroxybutanoate.	we cloned and sequenced the gene encoding an nadph-dependent aldehyde reductase (arii) in sporobolomyces salmonicolor aku4429, which reduces ethyl 4-chloro-3-oxobutanoate (4-cobe) to ethyl (s)-4-chloro-3-hydroxybutanoate. the arii gene is 1,032 bp long, is interrupted by four introns, and encodes a 37,315-da polypeptide. the deduced amino acid sequence exhibited significant levels of similarity to the amino acid sequences of members of the mammalian 3beta-hydroxysteroid dehydrogenase-plant dihyd ...	1999	10583966
stress genes and proteins in the archaea.	the field covered in this review is new; the first sequence of a gene encoding the molecular chaperone hsp70 and the first description of a chaperonin in the archaea were reported in 1991. these findings boosted research in other areas beyond the archaea that were directly relevant to bacteria and eukaryotes, for example, stress gene regulation, the structure-function relationship of the chaperonin complex, protein-based molecular phylogeny of organisms and eukaryotic-cell organelles, molecular ...	1999	10585970
the small ribosomal subunit from thermus thermophilus at 4.5 a resolution: pattern fittings and the identification of a functional site.	the electron density map of the small ribosomal subunit from thermus thermophilus, constructed at 4.5 a resolution, shows the recognizable morphology of this particle, as well as structural features that were interpreted as ribosomal rna and proteins. unbiased assignments, carried out by quantitative covalent binding of heavy atom compounds at predetermined sites, led to the localization of the surface of the ribosomal protein s13 at a position compatible with previous assignments, whereas the s ...	1999	10588692
structural and functional analyses of the secondary cell wall polymer of bacillus sphaericus ccm 2177 that serves as an s-layer-specific anchor.	sacculi of bacillus sphaericus ccm 2177 contain a secondary cell wall polymer which was completely extracted with 48% hydrofluoric acid. nuclear magnetic resonance analysis showed that the polymer is composed of repeating units, as follows: -->3)-[4, 6-o-(1-carboxyethylidene)]( approximately 0. 5)-beta-d-manpnac-(1-->4)-beta-d-glcpnac-(1-->. the n-terminal part of the s-layer protein carrying s-layer homologous motifs recognizes this polymer as a binding site.	1999	10601228
the heme-copper oxidases of thermus thermophilus catalyze the reduction of nitric oxide: evolutionary implications.	we show that the heme-copper terminal oxidases of thermus thermophilus (called ba(3) and caa(3)) are able to catalyze the reduction of nitric oxide (no) to nitrous oxide (n(2)o) under reducing anaerobic conditions. the rate of no consumption and n(2)o production were found to be linearly dependent on enzyme concentration, and activity was abolished by enzyme denaturation. thus, contrary to the eukaryotic enzyme, both t. thermophilus oxidases display a no reductase activity (3.0 +/- 0.7 mol no/mo ...	1999	10611279
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
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
distribution of hepatitis c virus genotypes in canada: results from the lcdc sentinel health unit surveillance system.	in a sentinel hepatitis surveillance study conducted by sentinel health units, 1469 patients were enrolled, and 959 (65.3%) were positive for antibody to hepatitis c virus (hcv). samples from 387 patients (40.4%) were tested for hcv rna, and 289 (74.7%) were positive for rna. the major risk factor for hcv infection was injection drug use, reported in 71% of cases. the genotyping of hcv isolates showed that subtype 1a (48%) was predominant in canada. the other subtypes detected were 1b (19%), 2a ...	1999	22346372
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
prokaryotic nitrate reduction: molecular properties and functional distinction among bacterial nitrate reductases.		1999	10542156
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
s-layer proteins.		2000	10648507
aminoglycosides: perspectives on mechanisms of action and resistance and strategies to counter resistance.		2000	11083623
a new era for the rna world. conference: rna 2000.		2000	11258477
structural and mechanistic conservation in dna ligases.	dna ligases are enzymes required for the repair, replication and recombination of dna. dna ligases catalyse the formation of phosphodiester bonds at single-strand breaks in double-stranded dna. despite their occurrence in all organisms, dna ligases show a wide diversity of amino acid sequences, molecular sizes and properties. the enzymes fall into two groups based on their cofactor specificity, those requiring nad(+) for activity and those requiring atp. the eukaryotic, viral and archael bacteri ...	2000	11058099
tissue-specific and developmental pattern of expression of the rice sps1 gene.	sucrose-phosphate synthase (sps) is one of the key regulatory enzymes in carbon assimilation and partitioning in plants. sps plays a central role in the production of sucrose in photosynthetic cells and in the conversion of starch or fatty acids into sucrose in germinating seeds. to explore the mechanisms that regulate the tissue-specific and developmental distribution of sps, the expression pattern of rice (oryza sativa) sps1 (genbank accession no. u33175) was examined by in situ reverse transc ...	2000	11027714
designed protein tetramer zipped together with a hydrophobic alzheimer homology: a structural clue to amyloid assembly.	limited solubility and precipitation of amyloidogenic sequences such as the alzheimer peptide (beta-ap) are major obstacles to a molecular understanding of protein fibrillation and deposition processes. here we have circumvented the solubility problem by stepwise engineering a beta-ap homology into a soluble scaffold, the monomeric protein s6. the s6 construct with the highest beta-ap homology crystallizes as a tetramer that is linked by the beta-ap residues forming intermolecular antiparallel b ...	2000	10944185
a recurrent rna-binding domain is appended to eukaryotic aminoacyl-trna synthetases.	aminoacyl-trna synthetases of higher eukaryotes possess polypeptide extensions in contrast to their prokaryotic counterparts. these extra domains of poorly understood function are believed to be involved in protein-protein or protein-rna interactions. here we showed by gel retardation and filter binding experiments that the repeated units that build the linker region of the bifunctional glutamyl-prolyl-trna synthetase had a general rna-binding capacity. the solution structure of one of these rep ...	2000	10654942
identification and characterization of immunoglobulin g in blood as a major inhibitor of diagnostic pcr.	a major inhibitor of diagnostic pcr in human plasma was identified and the mechanism of inhibition was characterized. human blood was divided by centrifugation into buffy coat, plasma, platelets, and erythrocytes. all these blood fractions were found to be highly inhibitory to a standardized pcr mixture containing the thermostable dna polymerase amplitaq gold. pcr inhibitors in human plasma were purified by chromatographic procedures and were characterized by a process of elimination, so that th ...	2000	10618113
functional analysis of the small component of the 4-hydroxyphenylacetate 3-monooxygenase of escherichia coli w: a prototype of a new flavin:nad(p)h reductase subfamily.	escherichia coli w uses the aromatic compound 4-hydroxyphenylacetate (4-hpa) as a sole source of carbon and energy for growth. the monooxygenase which converts 4-hpa into 3,4-dihydroxyphenylacetate, the first intermediate of the pathway, consists of two components, hpab (58.7 kda) and hpac (18.6 kda), encoded by the hpab and hpac genes, respectively, that form a single transcription unit. overproduction of the small hpac component in e. coli k-12 cells has facilitated the purification of the pro ...	2000	10633095
flexibility, conformational diversity and two dimerization modes in complexes of ribosomal protein l12.	protein l12, the only multicopy component of the ribosome, is presumed to be involved in the binding of translation factors, stimulating factor-dependent gtp hydrolysis. crystal structures of l12 from thermotogamaritima have been solved in two space groups by the multiple anomalous dispersion method and refined at 2.4 and 2.0 a resolution. in both crystal forms, an asymmetric unit comprises two full-length l12 molecules and two n-terminal l12 fragments that are associated in a specific, hetero-t ...	2000	10637222
active site constraints in the hydrolysis reaction catalyzed by bacterial rnase p: analysis of precursor trnas with a single 3'-s-phosphorothiolate internucleotide linkage.	endonucleolytic processing of precursor trnas (ptrnas) by rnase p yields 3'-oh and 5'-phosphate termini, and at least two metal ions are thought to be essential for catalysis. to determine if the hydrolysis reaction catalyzed by bacterial rnase p (rnas) involves stabilization of the 3'-oxyanion leaving group by direct coordination to one of the catalytic metal ions, ptrna substrates with single 3'- s -phosphorothiolate linkages at the rnase p cleavage site were synthesized. with a 3'- s -phospho ...	2000	10637323
optimised ligation of oligonucleotides by thermal ligases: comparison of thermus scotoductus and rhodothermus marinus dna ligases to other thermophilic ligases.	we describe the characterisation of four thermo-stable nad(+)-dependent dna ligases, from thermus thermophilus (tth), thermus scotoductus (ts), rhodothermus marinus (rm) and thermus aquaticus (taq), by an assay which measures ligation rate and mismatch discrimination. complete libraries of octa-, nona- and decanucleotides were used as substrates. the assay comprised the polymerisation of oligo-nucleotides initiated from a 17 base 'primer', using m13mp18 ssdna as template. polymers of ligation pr ...	2000	10637340
structure and expression of the human p68 rna helicase gene.	nuclear dead box protein p68 is immunologically related to sv40 large tumour antigen and both proteins possess rna helicase activity. in this report, we describe the structural organisation of the human p68 gene and aspects of the regulation of its expression. northern blot and primer extension analyses indicate that, although its level is variable, the p68 rna helicase appears to be expressed from a single transcription start site in all tissues tested. sequence analysis revealed that the p68 p ...	2000	10648785
pcr-based assay to quantify human immunodeficiency virus type 1 dna in peripheral blood mononuclear cells.	an assay that quantifies the amount of human immunodeficiency virus type 1 (hiv-1) dna in peripheral blood mononuclear cells has been developed. pcr amplification of the hiv-1 dna is performed in the presence of an internal quantitation standard, and colorimetric detection of the amplified product is performed with microwell plates. the copies of hiv-1 dna are normalized to total genomic dna input. the assay has an analytical sensitivity of 10 input copies per amplification reaction and a three- ...	2000	10655358
protein sequences conserved in prokaryotic aminoacyl-trna synthetases are important for the activity of the processivity factor of human mitochondrial dna polymerase.	previous studies have shown that the small subunit of xenopus dna polymerase gamma (pol gammab) acts as a processivity factor to stimulate the 140 kda catalytic subunit of human dna polymerase gamma. a putative human pol gammab initially identified by analysis of dna sequence had not been shown to be functional, and appeared to be an incomplete clone. in this paper, we report the cloning of full-length human and mouse pol gammab. both human and mouse pol gammab proteins were expressed in their m ...	2000	10666468
cyanobacterial cell walls: news from an unusual prokaryotic envelope.		2000	10671437
effect of temperature on stability and activity of elongation factor 2 proteins from antarctic and thermophilic methanogens.	despite the presence and abundance of archaea in low-temperature environments, little information is available regarding their physiological and biochemical properties. in order to investigate the adaptation of archaeal proteins to low temperatures, we purified and characterized the elongation factor 2 (ef-2) protein from the antarctic methanogen methanococcoides burtonii, which was expressed in escherichia coli, and compared it to the recombinant ef-2 protein from a phylogenetically related the ...	2000	10671454
nonlinearity in genetic decoding: homologous dna replicase genes use alternatives of transcriptional slippage or translational frameshifting.	the tau and gamma subunits of dna polymerase iii are both encoded by a single gene in escherichia coli and thermus thermophilus. gamma is two-thirds the size of tau and shares virtually all its amino acid sequence with tau. e. coli and t. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between tau and gamma. both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller gamma protein. in e. coli ...	2000	10677518
modified constructs of the trna tpsic domain to probe substrate conformational requirements of m(1)a(58) and m(5)u(54) trna methyltransferases.	the tpsic stem and loop (tsl) of trna contains highly conserved nucleoside modifications, m(5)c(49), t(54), psi(55)and m(1)a(58). u(54)is methylated to m(5)u (t) by m(5)u(54)methyltransferase (rumt); a(58)is methylated to m(1)a by m(1)a(58)trna methyltransferase (ramt). rumt recognizes and methylates a minimal tsl heptadecamer and ramt has previously been reported to recognize and methylate the 3'-half of the trna molecule. we report that ramt can recognize and methylate a tsl heptadecamer. to b ...	2000	10684932
ligation reaction specificities of an nad(+)-dependent dna ligase from the hyperthermophile aquifex aeolicus.	an nad(+)-dependent dna ligase from the hyperthermophilic bacterium aquifex aeolicus was cloned, expressed in escherichia coli and purified to homogeneity. the enzyme is most active in slightly alkaline ph conditions with either mg(2+)or mn(2+)as the metal cofactor. ca(2+)and ni(2+)mainly support formation of dna-adenylate intermediates. the catalytic cycle is characterized by a low k (cat)value of 2 min(-1)with concomitant accumulation of the dna - adenylate intermediate when mg(2+)is used as t ...	2000	10684941
evolution of arginine biosynthesis in the bacterial domain: novel gene-enzyme relationships from psychrophilic moritella strains (vibrionaceae) and evolutionary significance of n-alpha-acetyl ornithinase.	in the arginine biosynthetic pathway of the vast majority of prokaryotes, the formation of ornithine is catalyzed by an enzyme transferring the acetyl group of n-alpha-acetylornithine to glutamate (ornithine acetyltransferase [oatase]) (argj encoded). only two exceptions had been reported-the enterobacteriaceae and myxococcus xanthus (members of the gamma and delta groups of the class proteobacteria, respectively)-in which ornithine is produced from n-alpha-acetylornithine by a deacylase, acetyl ...	2000	10692366
crystal structure of nad(+)-dependent dna ligase: modular architecture and functional implications.	dna ligases catalyze the crucial step of joining the breaks in duplex dna during dna replication, repair and recombination, utilizing either atp or nad(+) as a cofactor. despite the difference in cofactor specificity and limited overall sequence similarity, the two classes of dna ligase share basically the same catalytic mechanism. in this study, the crystal structure of an nad(+)-dependent dna ligase from thermus filiformis, a 667 residue multidomain protein, has been determined by the multiwav ...	2000	10698952
metabolic engineering of saccharomyces cerevisiae.	comprehensive knowledge regarding saccharomyces cerevisiae has accumulated over time, and today s. cerevisiae serves as a widley used biotechnological production organism as well as a eukaryotic model system. the high transformation efficiency, in addition to the availability of the complete yeast genome sequence, has facilitated genetic manipulation of this microorganism, and new approaches are constantly being taken to metabolicially engineer this organism in order to suit specific needs. in t ...	2000	10704473
aminoacyl-trna synthetases, the genetic code, and the evolutionary process.	the aminoacyl-trna synthetases (aarss) and their relationship to the genetic code are examined from the evolutionary perspective. despite a loose correlation between codon assignments and aars evolutionary relationships, the code is far too highly structured to have been ordered merely through the evolutionary wanderings of these enzymes. nevertheless, the aarss are very informative about the evolutionary process. examination of the phylogenetic trees for each of the aarss reveals the following. ...	2000	10704480
a missense mutation in the nuclear gene coding for the mitochondrial aspartyl-trna synthetase suppresses a mitochondrial trna(asp) mutation.	the nuclear suppressor allele nsm3 in strain ff1210-6c/170-e22 (e22), which suppresses a mutation of the yeast mitochondrial trna(asp)gene in saccharomyces cerevisiae, was cloned and identified. to isolate the nsm3 allele, a genomic dna library using the vector yep13 was constructed from strain e22. nine yep13 recombinant plasmids were isolated and shown to suppress the mutation in the mitochondrial trna(asp)gene. these nine plasmids carry a common 4. 5-kb chromosomal dna fragment which contains ...	2000	10710420
one tube mutation detection using sensitive fluorescent dyeing of muts protected dna.	a novel, universal method for mutation detection utilising the ability of muts protein to recognise dna incomplementarities is proposed. the examined and reference dna fragments are pcr amplified. the pcr products are purified, mixed, heated and cooled to form heteroduplexes. in the case of mutation the heteroduplex dna containing mismatch is protected against exonuclease digestion by muts, while the dna without mismatches is degraded. the protection effect is visualised by the direct addition o ...	2000	10734213