Publications

correlations between shine-dalgarno sequences and gene features such as predicted expression levels and operon structures.	this work assesses relationships for 30 complete prokaryotic genomes between the presence of the shine-dalgarno (sd) sequence and other gene features, including expression levels, type of start codon, and distance between successive genes. a significant positive correlation of the presence of an sd sequence and the predicted expression level of a gene based on codon usage biases was ascertained, such that predicted highly expressed genes are more likely to possess a strong sd sequence than avera ...	2002	12270832
evidence for strong selective constraint acting on the nucleotide composition of 16s ribosomal rna genes.	previous studies have shown that the guanine plus cytosine (g+c) content of ribosomal rnas (rrnas) is highly correlated with bacterial growth temperatures. this correlation is strongest in the double-stranded stem regions of the rrna, a fact that can be explained by selection for increased structural stability at high growth temperatures. in this study, we examined the single-stranded regions of 16s rrnas. we reasoned that, since these regions of the molecule are subject to less structural const ...	2002	12034839
detailed analysis of rna-protein interactions within the bacterial ribosomal protein l5/5s rrna complex.	the crystal structure of ribosomal protein l5 from thermus thermophilus complexed with a 34-nt fragment comprising helix iii and loop c of escherichia coli 5s rrna has been determined at 2.5 a resolution. the protein specifically interacts with the bulged nucleotides at the top of loop c of 5s rrna. the rrna and protein contact surfaces are strongly stabilized by intramolecular interactions. charged and polar atoms forming the network of conserved intermolecular hydrogen bonds are located in two ...	2002	12515387
diversity of ribosomal mutations conferring resistance to macrolides, clindamycin, streptogramin, and telithromycin in streptococcus pneumoniae.	mechanisms of resistance were studied in 22 macrolide-resistant mutants selected in vitro from 5 parental strains of macrolide-susceptible streptococcus pneumoniae by serial passage in various macrolides (t. a. davies, b. e. dewasse, m. r. jacobs, and p. c. appelbaum, antimicrob. agents chemother., 44:414-417, 2000). portions of genes encoding ribosomal proteins l22 and l4 and 23s rrna (domains ii and v) were amplified by pcr and analyzed by single-strand conformational polymorphism analysis to ...	2002	11751122
complete polar lipid composition of thermoplasma acidophilum ho-62 determined by high-performance liquid chromatography with evaporative light-scattering detection.	polar ether lipids of thermoplasma acidophilum ho-62 were purified by high-performance liquid chromatography with an evaporative light-scattering detector. structures of purified lipids were investigated by capillary gas chromatography, mass spectrometry, and nuclear magnetic resonance. three types of ether lipids were found: phospholipids, glycolipids, and phosphoglycolipids. the two phospholipids had glycerophosphate as the phosphoester moiety. the seven glycolipids had different combinations ...	2002	11751835
cloning, sequencing, and expression of the cold-inducible hutu gene from the antarctic psychrotrophic bacterium pseudomonas syringae.	a promoter-fusion study with a tn 5-based promoter probe vector had earlier found that the hutu gene which encodes the enzyme urocanase for the histidine utilization pathway is upregulated at a lower temperature (4 degrees c) in the antarctic psychrotrophic bacterium pseudomonas syringae. to examine the characteristics of the urocanase gene and its promoter elements from the psychrotroph, the complete hutu and its upstream region from p. syringae were cloned, sequenced, and analyzed in the prese ...	2002	11772602
simultaneous detection of measles virus, rubella virus, and parvovirus b19 by using multiplex pcr.	we describe here a multiplex reverse transcription-pcr (rtmnpcr) assay designed to detect and differentiate measles virus, rubella virus, and parvovirus b19. serial dilution experiments with vaccine strains that compared cell culture isolation of measles in b95 cells and rubella in rk13 cells showed sensitivity rates of 0.004 50% tissue culture infective dose (tcid(50)) for measles virus and 0.04 tcid(50) for rubella virus. this rtmnpcr can detect as few as 10 molecules for measles virus and rub ...	2002	11773102
cooperative kinetics of both hsp104 atpase domains and interdomain communication revealed by aaa sensor-1 mutants.	aaa proteins share a conserved active site for atp hydrolysis and regulate many cellular processes. aaa proteins are oligomeric and often have multiple atpase domains per monomer, which is suggestive of complex allosteric kinetics of atp hydrolysis. here, using wild-type hsp104 in the hexameric state, we demonstrate that its two aaa modules (nbd1 and nbd2) have very different catalytic activities, but each displays cooperative kinetics of hydrolysis. using mutations in the aaa sensor-1 motif of ...	2002	11782421
blocking site-to-site translocation of a misactivated amino acid by mutation of a class i trna synthetase.	the genetic code is established by the aminoacylation reactions of trna synthetases. its accuracy depends on editing reactions that prevent amino acids from being assigned to incorrect codons. a group of class i synthetases share a common insertion that encodes a distinct site for editing that is about 30 a from the active site. both misactivated aminoacyl adenylates and mischarged amino acids attached to trna are translocated to this site, which, in turn, is divided into subsites--one for the a ...	2002	11782529
contributions of folding cores to the thermostabilities of two ribonucleases h.	to investigate the contribution of the folding cores to the thermodynamic stability of rnases h, we used rational design to create two chimeras composed of parts of a thermophilic and a mesophilic rnase h. each chimera combines the folding core from one parent protein and the remaining parts of the other. both chimeras form active, well-folded rnases h. stability curves, based on cd-monitored chemical denaturations, show that the chimera with the thermophilic core is more stable, has a higher mi ...	2002	11790848
cell-surface-anchoring role of n-terminal surface layer homology domains of clostridium cellulovorans enge.	enge, coding for endoglucanase e, one of the three major subunits of the clostridium cellulovorans cellulosome, has been cloned and sequenced (y. tamaru and r. h. doi, j. bacteriol. 181:3270-3276, 1999). the n-terminal-half region of enge possesses three repeated surface layer homology (slh) domains, which are homologous to those of some bacterial s-layer proteins. also, the c-terminal-half region consists of a catalytic domain of glycosyl hydrolase family 5 and a duplicated sequence (dockerin) ...	2002	11807046
tetracycline induces stabilization of mrna in bacillus subtilis.	the tet(l) gene of bacillus subtilis confers low-level tetracycline (tc) resistance. previous work examining the >20-fold-inducible expression of tet(l) by tc demonstrated a 12-fold translational induction. here we show that the other component of tet(l) induction is at the level of mrna stabilization. addition of a subinhibitory concentration of tc results in a two- to threefold increase in tet(l) mrna stability. using a plasmid-borne derivative of tet(l) with a large in-frame deletion of the c ...	2002	11807047
molecular analyses of the natural transformation machinery and identification of pilus structures in the extremely thermophilic bacterium thermus thermophilus strain hb27.	thermus thermophilus hb27, an extremely thermophilic bacterium, exhibits high competence for natural transformation. to identify genes of the natural transformation machinery of t. thermophilus hb27, we performed homology searches in the partially completed t. thermophilus genomic sequence for conserved competence genes. these analyses resulted in the detection of 28 open reading frames (orfs) exhibiting significant similarities to known competence proteins of gram-negative and gram-positive bac ...	2002	11823215
corynebacterium glutamicum utilizes both transsulfuration and direct sulfhydrylation pathways for methionine biosynthesis.	a direct sulfhydrylation pathway for methionine biosynthesis in corynebacterium glutamicum was found. the pathway was catalyzed by mety encoding o-acetylhomoserine sulfhydrylase. the gene mety, located immediately upstream of meta, was found to encode a protein of 437 amino acids with a deduced molecular mass of 46,751 da. in accordance with dna and protein sequence data, the introduction of mety into c. glutamicum resulted in the accumulation of a 47-kda protein in the cells and a 30-fold incre ...	2002	11844756
structural analysis of an escherichia coli endonuclease viii covalent reaction intermediate.	endonuclease viii (nei) of escherichia coli is a dna repair enzyme that excises oxidized pyrimidines from dna. nei shares with formamidopyrimidine-dna glycosylase (fpg) sequence homology and a similar mechanism of action: the latter involves removal of the damaged base followed by two sequential beta-elimination steps. however, nei differs significantly from fpg in substrate specificity. we determined the structure of nei covalently crosslinked to a 13mer oligodeoxynucleotide duplex at 1.25 a re ...	2002	11847126
identification of a mycobacterium tuberculosis putative classical nitroreductase gene whose expression is coregulated with that of the acr aene within macrophages, in standing versus shaking cultures, and under low oxygen conditions.	tuberculosis remains a leading killer worldwide, and new approaches for its treatment and prevention are urgently needed. this effort will benefit greatly from a better understanding of gene regulation in mycobacterium tuberculosis, particularly with respect to this pathogen's response to its host environment. we examined the behavior of two promoters from the divergently transcribed m. tuberculosis genes acr/hspx/rv2031c (alpha-crystallin homolog) and rv2032/acg (acr-coregulated gene) by using ...	2002	11854240
trna-like recognition of group i introns by a tyrosyl-trna synthetase.	the neurospora crassa mitochondrial tyrosyl-trna synthetase (cyt-18 protein) functions in splicing group i introns by promoting the formation of the catalytically active rna structure. previous work suggested that cyt-18 recognizes a conserved trna-like structure of the group i intron catalytic core. here, directed hydroxyl-radical cleavage assays show that the nucleotide-binding fold and c-terminal domains of cyt-18 interact with the expected group i intron cognates of the aminoacyl-acceptor st ...	2002	11854463
polypeptide release at sense and noncognate stop codons by localized charge-exchange alterations in translational release factors.	the mechanism of stop codon recognition during translation has long been a puzzle. only recently has it been established that a tripeptide in the bacterial release factors (rfs) 1 and 2 serves as the "anticodon" in deciphering stop codons in mrna. however, the molecular basis of the accuracy of stop codon recognition is unknown. although specific tripeptides in the rfs are primarily responsible for selective reading of cognate stop codons, charge-flip variant rf proteins, altered at conserved gl ...	2002	11854484
identification and comparative analysis of the chloroplast alpha-subunit gene of dna-dependent rna polymerase from seven euglena species.	when the sequence of the euglena gracilis chloroplast genome was reported in 1993 the alpha-subunit gene (rpoa) of rna polymerase appeared to be missing, based on a comparison of all putative reading frames to the then known rpoa loci. since there has been a large increase in known rpoa sequences, the question of a euglena chloroplast rpoa gene was re-examined. a previously described unknown reading frame of 161 codons was found to be part of an rpoa gene split by a single group iii intron. this ...	2002	11861918
analysis of the aaa sensor-2 motif in the c-terminal atpase domain of hsp104 with a site-specific fluorescent probe of nucleotide binding.	hsp104 from saccharomyces cerevisiae is a hexameric protein with two aaa atpase domains (n- and c-terminal nucleotide-binding domains nbd1 and nbd2, respectively) per monomer. our previous analysis of the hsp104 atp hydrolysis cycle revealed that nbd1 and nbd2 have very different catalytic properties, but each shows positive cooperativity in hydrolysis. there is also communication between the two domains, in that atp hydrolysis at nbd1 depends on the nucleotide that is bound to nbd2. here, we ex ...	2002	11867765
transfer rna-dependent amino acid biosynthesis: an essential route to asparagine formation.	biochemical experiments and genomic sequence analysis showed that deinococcus radiodurans and thermus thermophilus do not possess asparagine synthetase (encoded by asna or asnb), the enzyme forming asparagine from aspartate. instead these organisms derive asparagine from asparaginyl-trna, which is made from aspartate in the trna-dependent transamidation pathway [becker, h. d. & kern, d. (1998) proc. natl. acad. sci. usa 95, 12832-12837; and curnow, a. w., tumbula, d. l., pelaschier, j. t., min, ...	2002	11880622
filamentous phage active on the gram-positive bacterium propionibacterium freudenreichii.	we present the first description of a single-stranded dna filamentous phage able to replicate in a gram-positive bacterium. phage b5 infects propionibacterium freudenreichii and has a genome consisting of 5,806 bases coding for 10 putative open reading frames. the organization of the genome is very similar to the organization of the genomes of filamentous phages active on gram-negative bacteria. the putative coat protein exhibits homology with the coat proteins of phages ph75 and pf3 active on t ...	2002	11889111
the trna specificity of thermus thermophilus ef-tu.	by introducing a gac anticodon, 21 different escherichia coli trnas were misacylated with either phenylalanine or valine and assayed for their affinity to thermus thermophilus elongation factor tu (ef-tu)*gtp by using a ribonuclease protection assay. the presence of a common esterified amino acid permits the thermodynamic contribution of each trna body to the overall affinity to be evaluated. the e. coli elongator trnas exhibit a wide range of binding affinities that varied from -11.7 kcal/mol f ...	2002	11891293
mutations in the 16s rrna genes of helicobacter pylori mediate resistance to tetracycline.	low-cost and rescue treatments for helicobacter pylori infections involve combinations of several drugs including tetracycline. resistance to tetracycline has recently emerged in h. pylori. the 16s rrna gene sequences of two tetracycline-resistant clinical isolates (mic = 64 microg/ml) were determined and compared to the consensus h. pylori 16s rrna sequence. one isolate had four nucleotide substitutions, and the other had four substitutions and two deletions. natural transformation with the 16s ...	2002	11914344
reduced oxidative pentose phosphate pathway flux in recombinant xylose-utilizing saccharomyces cerevisiae strains improves the ethanol yield from xylose.	in recombinant, xylose-fermenting saccharomyces cerevisiae, about 30% of the consumed xylose is converted to xylitol. xylitol production results from a cofactor imbalance, since xylose reductase uses both nadph and nadh, while xylitol dehydrogenase uses only nad(+). in this study we increased the ethanol yield and decreased the xylitol yield by lowering the flux through the nadph-producing pentose phosphate pathway. the pentose phosphate pathway was blocked either by disruption of the gnd1 gene, ...	2002	11916674
use of fe(iii) as an electron acceptor to recover previously uncultured hyperthermophiles: isolation and characterization of geothermobacterium ferrireducens gen. nov., sp. nov.	it has recently been recognized that the ability to use fe(iii) as a terminal electron acceptor is a highly conserved characteristic in hyperthermophilic microorganisms. this suggests that it may be possible to recover as-yet-uncultured hyperthermophiles in pure culture if fe(iii) is used as an electron acceptor. as part of a study of the microbial diversity of the obsidian pool area in yellowstone national park, wyo., hot sediment samples were used as the inoculum for enrichment cultures in med ...	2002	11916691
efficient trans-cleavage by the schistosoma mansoni smalpha1 hammerhead ribozyme in the extreme thermophile thermus thermophilus.	the catalytic hammerhead structure has been found in association with repetitive dna from several animals, including salamanders, crickets and schistosomes, and functions to process in cis the long multimer transcripts into monomer rna in vivo. the cellular role of these repetitive elements and their transcripts is unknown. moreover, none of these natural hammerheads have been shown to trans-cleave a host mrna in vivo. we analyzed the cis- and trans-cleavage properties of the hammerhead ribozyme ...	2002	11917021
tspgwi, a thermophilic class-iis restriction endonuclease from thermus sp., recognizes novel asymmetric sequence 5'-acgga(n11/9)-3'.	a novel prototype class-iis restriction endonuclease, tspgwi, was isolated from the thermophilic bacterium thermus sp. gw. the recognition sequence and cleavage positions have been established: tspgwi recognizes the non-palindromic 5-bp sequence 5'-acgga-3' and cleaves the dna 11 and 9 nt downstream in the top and bottom strand, respectively. in addition, an accompanying endonuclease, tspgwii, an isoschizomer of pst i, was found in thermus sp. gw cells.	2002	11917039
the large subunit of initiation factor aif2 is a close structural homologue of elongation factors.	the heterotrimeric factor e/aif2 plays a central role in eukaryotic/archaeal initiation of translation. by delivering the initiator methionyl-trna to the ribosome, e/aif2 ensures specificity of initiation codon selection. the three subunits of aif2 from the hyperthermophilic archaeon pyrococcus abyssi could be overproduced in escherichia coli. the beta and gamma subunits each contain a tightly bound zinc. the large gamma subunit is shown to form the structural core for trimer assembly. the cryst ...	2002	11927566
the solution structure of ribosomal protein l18 from thermus thermophilus reveals a conserved rna-binding fold.	we have determined the solution structure of ribosomal protein l18 from thermus thermophilus. l18 is a 12.5 kda protein of the large subunit of the ribosome and binds to both 5 s and 23 s rrna. in the uncomplexed state l18 folds to a mixed alpha/beta globular structure with a long disordered n-terminal region. we compared our high-resolution structure with rna-complexed l18 from haloarcula marismortui and t. thermophilus to examine rna-induced as well as species-dependent structural differences. ...	2002	11964156
stability and interactions of the amino-terminal domain of clpb from escherichia coli.	clpb is a member of a multichaperone system in escherichia coli (with dnak, dnaj, and grpe) that reactivates aggregated proteins. the sequence of clpb contains two atp-binding regions that are enclosed between the n- and c-terminal extensions. whereas it has been found that the n-terminal region of clpb is essential for the chaperone activity, the structure of this region is not known, and its biochemical properties have not been studied. we expressed and purified the n-terminal fragment of clpb ...	2002	11967375
the crystal structure of exonuclease recj bound to mn2+ ion suggests how its characteristic motifs are involved in exonuclease activity.	recj, a 5' to 3' exonuclease specific for single-stranded dna, functions in dna repair and recombination systems. we determined the crystal structure of recj bound to mn(2+) ion essential for its activity. recj has a novel fold in which two domains are interconnected by a long helix, forming a central groove. mn(2+) is located on the wall of the groove and is coordinated by conserved residues characteristic of a family of phosphoesterases that includes recj proteins. the groove is composed of re ...	2002	11972066
modulation of trnaala identity by inorganic pyrophosphatase.	a highly sensitive assay of trna aminoacylation was developed that directly measures the fraction of aminoacylated trna by following amino acid attachment to the 3'-(32)p-labeled trna. when applied to escherichia coli alanyl-trna synthetase, the assay allowed accurate measurement of aminoacylation of the most deleterious mutants of trna(ala). the effect of trna(ala) identity mutations on both aminoacylation efficiency (k(cat)/k(m)) and steady-state level of aminoacyl-trna was evaluated in the ab ...	2002	11983895
infection of tick cells and bovine erythrocytes with one genotype of the intracellular ehrlichia anaplasma marginale excludes infection with other genotypes.	anaplasma marginale, a tick-borne rickettsial pathogen of cattle, is endemic in several areas of the united states. many geographic isolates of a. marginale that occur in the united states are characterized by the major surface protein 1a, which varies in sequence and molecular weight due to different numbers of tandem repeats of 28 or 29 amino acids. recent studies (g. h. palmer, f. r. rurangirwa, and t. f. mcelwain, j. clin. microbiol. 39:631-635, 2001) of an a. marginale-infected herd of catt ...	2002	11986275
protein coding palindromes are a unique but recurrent feature in rickettsia.	rickettsia are unique in inserting in-frame a number of palindromic sequences within protein coding regions. in this study, we extensively analyzed repeated sequences in the genome of rickettsia conorii and examined their locations in regard to coding versus noncoding regions. we identified 656 interspersed repeated sequences classified into 10 distinct families. of the 10 families, three palindromic sequence families showed clear cases of insertions into open reading frames (orfs). the location ...	2002	11997347
a novel type of uracil-dna glycosylase mediating repair of hydrolytic dna damage in the extremely thermophilic eubacterium thermus thermophilus.	spontaneous hydrolytic deamination of dna cytosine and 5-methyl-cytosine residues is an abundant source of c/g (5-mec/g) to t/a transition mutations. as a result of this pressure, at least six different families of enzymes have evolved that initiate repair at u/g (t/g) mispairs, the relevant pre-mutagenic intermediates. the necessarily higher rate of the process at elevated temperatures must pose a correspondingly accentuated problem to contemporary thermophilic organisms and may have been a ser ...	2002	12000829
occurrence of leu+ revertants under starvation cultures in escherichia coli is growth-dependent.	many investigations have reported that advantageous mutations occurred more frequently under selective conditions than those under non-selective conditions. this phenomenon is referred to as adaptive mutation. their characteristics are that adaptive mutations are directed and growth-independent. the idea of directed adaptive mutation had been objected by some reports, however, the idea of growth-independent adaptive mutation has been held till today.	2002	12019019
mefloquine and new related compounds target the f(0) complex of the f(0)f(1) h(+)-atpase of streptococcus pneumoniae.	the activities of mefloquine (mfl) and related compounds against previously characterized streptococcus pneumoniae strains carrying defined amino acid substitutions in the c subunit of the f(0)f(1) h(+)-atpase were studied. in addition, a series of mfl-resistant (mfl(r)) strains were isolated and characterized. a good correlation was observed between inhibition of growth and inhibition of the membrane-associated f(0)f(1) h(+)-atpase activity. mfl was about 10-fold more active than optochin and a ...	2002	12019076
unique presence of a manganese catalase in a hyperthermophilic archaeon, pyrobaculum calidifontis va1.	we had previously isolated a facultatively anaerobic hyperthermophilic archaeon, pyrobaculum calidifontis strain va1. here, we found that strain va1, when grown under aerobic conditions, harbors high catalase activity. the catalase was purified 91-fold from crude extracts and displayed a specific activity of 23,500 u/mg at 70 degrees c. the enzyme exhibited a k(m) value of 170 mm toward h(2)o(2) and a k(cat) value of 2.9 x 10(4) s(-1).subunit(-1) at 25 degrees c. gel filtration chromatography in ...	2002	12029047
thermoadaptation of alpha-galactosidase agab1 in thermus thermophilus.	the evolutionary potential of a thermostable alpha-galactosidase, with regard to improved catalytic activity at high temperatures, was investigated by employing an in vivo selection system based on thermophilic bacteria. for this purpose, hybrid alpha-galactosidase genes of agaa and agab from bacillus stearothermophilus kve39, designated agaa1 and agab1, were cloned into an autonomously replicating thermus vector and introduced into thermus thermophilus of1053gd (deltaagat) by transformation. th ...	2002	12029056
structural origins of amino acid selection without editing by cysteinyl-trna synthetase.	cysteinyl-trna synthetase (cysrs) is highly specific for synthesis of cysteinyl adenylate, yet does not possess the amino acid editing activity characteristic of many other trna synthetases. to elucidate how cysrs is able to distinguish cysteine from non-cognate amino acids, crystal structures of the escherichia coli enzyme were determined in apo and cysteine-bound states. the structures reveal that the substrate cysteine thiolate forms a single direct interaction with a zinc ion bound at the ba ...	2002	12032090
importance of compartment formation for a self-encoding system.	a self-encoding system designed to have strict "compartition" of the molecules, i.e., to contain only a single molecule of dna in each compartment, was established, and its evolutionary fate was analyzed. the system comprised the thermus thermophilus dna polymerase gene as the informational molecule and its protein product replicating the gene as the functional molecule. imposing strict compartition allows the self-encoding system to last up to at least the tenth generation, whereas the system c ...	2002	12032314
transfer rna determinants for translational editing by escherichia coli valyl-trna synthetase.	valyl-trna synthetase (valrs) has difficulty differentiating valine from structurally similar non-cognate amino acids, most prominently threonine. to minimize errors in aminoacylation and translation the enzyme catalyzes a proofreading (editing) reaction that is dependent on the presence of cognate trna(val). editing occurs at a site functionally distinct from the aminoacylation site of valrs and previous results have shown that the 3'-terminus of trna(val) is recognized differently at the two s ...	2002	12034843
a membrane-bound archaeal lon protease displays atp-independent proteolytic activity towards unfolded proteins and atp-dependent activity for folded proteins.	in contrast to the eucaryal 26s proteasome and the bacterial atp-dependent proteases, little is known about the energy-dependent proteolysis in members of the third domain, archae. we cloned a gene homologous to atp-dependent lon protease from a hyperthermophilic archaeon and observed the unique properties of the archaeal lon. lon from thermococcus kodakaraensis kod1 (lon(tk)) is a 70-kda protein with an n-terminal atpase domain belonging to the aaa(+) superfamily and a c-terminal protease domai ...	2002	12057965
crystal structure of the lactococcus lactis formamidopyrimidine-dna glycosylase bound to an abasic site analogue-containing dna.	the formamidopyrimidine-dna glycosylase (fpg, mutm) is a bifunctional base excision repair enzyme (dna glycosylase/ap lyase) that removes a wide range of oxidized purines, such as 8-oxoguanine and imidazole ring-opened purines, from oxidatively damaged dna. the structure of a non-covalent complex between the lactoccocus lactis fpg and a 1,3-propanediol (pr) abasic site analogue-containing dna has been solved. through an asymmetric interaction along the damaged strand and the intercalation of the ...	2002	12065399
a novel uracil-dna glycosylase with broad substrate specificity and an unusual active site.	uracil-dna glycosylases (udgs) catalyse the removal of uracil by flipping it out of the double helix into their binding pockets, where the glycosidic bond is hydrolysed by a water molecule activated by a polar amino acid. interestingly, the four known udg families differ in their active site make-up. the activating residues in ung and smug enzymes are aspartates, thermostable udgs resemble ung-type enzymes, but carry glutamate rather than aspartate residues in their active sites, and the less ac ...	2002	12065430
resistance to quinupristin-dalfopristin due to mutation of l22 ribosomal protein in staphylococcus aureus.	the mechanism of resistance to the streptogramin antibiotics quinupristin and dalfopristin was studied in a staphylococcus aureus clinical isolate selected under quinupristin-dalfopristin therapy, in four derivatives of s. aureus rn4220 selected in vitro, and in a mutant selected in a model of rabbit aortic endocarditis. for all strains the mics of erythromycin, quinupristin, and quinupristin-dalfopristin were higher than those for the parental strains but the mics of dalfopristin and lincomycin ...	2002	12069975
immunization of rhesus macaques with a dna prime/modified vaccinia virus ankara boost regimen induces broad simian immunodeficiency virus (siv)-specific t-cell responses and reduces initial viral replication but does not prevent disease progression following challenge with pathogenic sivmac239.	producing a prophylactic vaccine for human immunodeficiency virus (hiv) has proven to be a challenge. most biological isolates of hiv are difficult to neutralize, so that conventional subunit-based antibody-inducing vaccines are unlikely to be very effective. in the rhesus macaque model, some protection was afforded by dna/recombinant viral vector vaccines. however, these studies used as the challenge virus shiv-89.6p, which is neutralizable, making it difficult to determine whether the observed ...	2002	12072518
novel dna-binding proteins in the cyanobacterium anabaena sp. strain pcc 7120.	as an approach towards elucidation of the biochemical regulation of the progression of heterocyst differentiation in anabaena sp. strain pcc 7120, we have identified proteins that bind to a 150-bp sequence upstream from hepc, a gene that plays a role in the synthesis of heterocyst envelope polysaccharide. such proteins were purified in four steps from extracts of vegetative cells of anabaena sp. two of these proteins (abp1 and abp2) are encoded by neighboring genes in the anabaena sp. chromosome ...	2002	12081965
the identification of spermine binding sites in 16s rrna allows interpretation of the spermine effect on ribosomal 30s subunit functions.	a photoreactive analogue of spermine, n1-azidobenzamidino (aba)-spermine, was covalently attached after irradiation to escherichia coli 30s ribosomal subunits or naked 16s rrna. by means of rnase h digestion and primer extension, the cross-linking sites of aba-spermine in naked 16s rrna were characterised and compared with those identified in 30s subunits. the 5' domain, the internal and terminal loops of helix h24, as well as the upper part of helix h44 in naked 16s rrna, were found to be prefe ...	2002	12087167
molecular characterization of the s-layer gene, sbpa, of bacillus sphaericus ccm 2177 and production of a functional s-layer fusion protein with the ability to recrystallize in a defined orientation while presenting the fused allergen.	the nucleotide sequence encoding the crystalline bacterial cell surface (s-layer) protein sbpa of bacillus sphaericus ccm 2177 was determined by a pcr-based technique using four overlapping fragments. the entire sbpa sequence indicated one open reading frame of 3,804 bp encoding a protein of 1,268 amino acids with a theoretical molecular mass of 132,062 da and a calculated isoelectric point of 4.69. the n-terminal part of sbpa, which is involved in anchoring the s-layer subunits via a distinct t ...	2002	12089001
stress-inducible protein 1 is a cell surface ligand for cellular prion that triggers neuroprotection.	prions are composed of an isoform of a normal sialoglycoprotein called prp(c), whose physiological role has been under investigation, with focus on the screening for ligands. our group described a membrane 66 kda prp(c)-binding protein with the aid of antibodies against a peptide deduced by complementary hydropathy. using these antibodies in western blots from two-dimensional protein gels followed by sequencing the specific spot, we have now identified the molecule as stress-inducible protein 1 ...	2002	12093732
the unique tuf2 gene from the kirromycin producer streptomyces ramocissimus encodes a minor and kirromycin-sensitive elongation factor tu.	streptomyces ramocissimus, the producer of elongation factor tu (ef-tu)-targeted antibiotic kirromycin, contains three divergent tuf-like genes, with tuf1 encoding regular kirromycin-sensitive ef-tu1; the functions of tuf2 and tuf3 are unknown. analysis of the tuf gene organization in nine producers of kirromycin-type antibiotics revealed that they all contain homologues of tuf1 and sometimes of tuf3 but that tuf2 was found in s. ramocissimus only. the tuf2-flanking regions were sequenced, and t ...	2002	12107139
genomic and functional analyses of sxt, an integrating antibiotic resistance gene transfer element derived from vibrio cholerae.	sxt is representative of a family of conjugative-transposon-like mobile genetic elements that encode multiple antibiotic resistance genes. in recent years, sxt-related conjugative, self-transmissible integrating elements have become widespread in asian vibrio cholerae. we have determined the 100-kb dna sequence of sxt. this element appears to be a chimera composed of transposon-associated antibiotic resistance genes linked to a variety of plasmid- and phage-related genes, as well as to many gene ...	2002	12107144
mutant analysis shows that alanine racemases from pseudomonas aeruginosa and escherichia coli are dimeric.	alanine racemases are ubiquitous prokaryotic enzymes providing the essential peptidoglycan precursor d-alanine. we present evidence that the enzymes from pseudomonas aeruginosa and escherichia coli function exclusively as homodimers. moreover, we demonstrate that expression of a k35a y235a double mutation of dadx in e. coli suppresses bacterial growth in a dominant negative fashion.	2002	12107154
class i tyrosyl-trna synthetase has a class ii mode of cognate trna recognition.	bacterial tyrosyl-trna synthetases (tyrrs) possess a flexibly linked c-terminal domain of approximately 80 residues, which has hitherto been disordered in crystal structures of the enzyme. we have determined the structure of thermus thermophilus tyrrs at 2.0 a resolution in a crystal form in which the c-terminal domain is ordered, and confirm that the fold is similar to part of the c-terminal domain of ribosomal protein s4. we have also determined the structure at 2.9 a resolution of the complex ...	2002	12110594
pcr-based ordered genomic libraries: a new approach to drug target identification for streptococcus pneumoniae.	described here are the development and validation of a novel approach to identify genes encoding drug targets in streptococcus pneumoniae. the method relies on the use of an ordered genomic library composed of pcr amplicons that were generated under error-prone conditions so as to introduce random mutations into the dna. since some of the mutations occur in drug target-encoding genes and subsequently affect the binding of the drug to its respective cellular target, amplicons containing drug targ ...	2002	12121925
regulation of riboflavin biosynthesis and transport genes in bacteria by transcriptional and translational attenuation.	the riboflavin biosynthesis in bacteria was analyzed using comparative analysis of genes, operons and regulatory elements. a model for regulation based on formation of alternative rna structures involving the rfn elements is suggested. in gram-positive bacteria including actinomycetes, thermotoga, thermus and deinococcus, the riboflavin metabolism and transport genes are predicted to be regulated by transcriptional attenuation, whereas in most gram-negative bacteria, the riboflavin biosynthesis ...	2002	12136096
functional annotation of class i lysyl-trna synthetase phylogeny indicates a limited role for gene transfer.	functional and comparative genomic studies have previously shown that the essential protein lysyl-trna synthetase (lysrs) exists in two unrelated forms. most prokaryotes and all eukaryotes contain a class ii lysrs, whereas most archaea and a few bacteria contain a less common class i lysrs. in bacteria the class i lysrs is only found in the alpha-proteobacteria and a scattering of other groups, including the spirochetes, while the class i protein is by far the most common form of lysrs in archae ...	2002	12142429
biodiversity of denitrifying and dinitrogen-fixing bacteria in an acid forest soil.	isolated soil dna from an oak-hornbeam forest close to cologne, germany, was suitable for pcr amplification of gene segments coding for the 16s rrna and nitrogenase reductase (nifh), nitrous oxide reductase (nosz), cytochrome cd(1)-containing nitrite reductase (nirs), and cu-containing nitrite reductase (nirk) of denitrification. for each gene segment, diverse pcr products were characterized by cloning and sequencing. none of the 16s rrna gene sequences was identical to any deposited in the data ...	2002	12147477
experimental evaluation of topological parameters determining protein-folding rates.	recent work suggests that structural topology plays a key role in determining protein-folding rates and pathways. the refolding rates of small proteins that fold without intermediates are found to correlate with simple structural parameters such as relative contact order, long-range order, or the fraction of short-range contacts. to test and evaluate the role of structural topology experimentally, a set of circular permutants of the ribosomal protein s6 from thermus thermophilus was analyzed. de ...	2002	12149462
the methanobacterium thermoautotrophicum mcm protein can form heptameric rings.	mini-chromosome maintenance (mcm) proteins form a conserved family found in all eukaryotes and are essential for dna replication. they exist as heteromultimeric complexes containing as many as six different proteins. these complexes are believed to be the replicative helicases, functioning as hexameric rings at replication forks. in most archaea a single mcm protein exists. the protein from methanobacterium thermoautotrophicum (mtmcm) has been reported to assemble into a large complex consistent ...	2002	12151340
human small intestinal mucosa harbours a small population of cytolytically active cd8+ alphabeta t lymphocytes.	intraepithelial lymphocytes (iel) in normal human small intestine exhibit cytotoxicity. this study was undertaken to characterize the effector cells and their mode of action. freshly isolated jejunal iel and lamina propria lymphocytes (lpl), as well as iel and lpl depleted of cd4+, cd8+ and t-cell receptor (tcr)-gammadelta+ cells were used as effector cells in anti-cd3-mediated redirected cytotoxicity against a murine fcgammar-expressing cell line. effector cell frequencies were estimated by eff ...	2002	12153510
16s rrna mutation-mediated tetracycline resistance in helicobacter pylori.	most helicobacter pylori strains are susceptible to tetracycline, an antibiotic commonly used for the eradication of h. pylori. however, an increase in incidence of tetracycline resistance in h. pylori has recently been reported. here the mechanism of tetracycline resistance of the first dutch tetracycline-resistant (tet(r)) h. pylori isolate (strain 181) is investigated. twelve genes were selected from the genome sequences of h. pylori strains 26695 and j99 as potential candidate genes, based o ...	2002	12183259
structural insights into peptide bond formation.	the large ribosomal subunit catalyzes peptide bond formation and will do so by using small aminoacyl- and peptidyl-rna fragments of trna. we have refined at 3-a resolution the structures of both a and p site substrate and product analogues, as well as an intermediate analogue, bound to the haloarcula marismortui 50s ribosomal subunit. a p site substrate, cca-phe-caproic acid-biotin, binds equally to both sites, but in the presence of sparsomycin binds only to the p site. the cca portions of thes ...	2002	12185246
crystal structures of transcription factor nusg in light of its nucleic acid- and protein-binding activities.	microbial transcription modulator nusg interacts with rna polymerase and termination factor rho, displaying striking functional homology to eukaryotic spt5. the protein is also a translational regulator. we have determined crystal structures of aquifex aeolicus nusg showing a modular design: an n-terminal rnp-like domain, a c-terminal element with a kow sequence motif and a species-specific immunoglobulin-like fold. the structures reveal bona fide nucleic acid binding sites, and nucleic acid bin ...	2002	12198166
albidovulum inexpectatum gen. nov., sp. nov., a nonphotosynthetic and slightly thermophilic bacterium from a marine hot spring that is very closely related to members of the photosynthetic genus rhodovulum.	several bacterial isolates, with an optimum growth temperature of about 50 degrees c, were recovered from the marine hot spring at ferraria on the island of são miguel in the azores. the geothermal water emerged from a porous lava flow and rapidly cooled in contact with seawater except at low tide. the bacterial species represented by strains frr-10(t) and frr-11 was nonpigmented, strictly aerobic, and organotrophic. several genes, bchz, pufb, pufa, pufl, or pufm, encoding the photosynthetic rea ...	2002	12200275
novel domains and orthologues of eukaryotic transcription elongation factors.	the passage of rna polymerase ii across eukaryotic genes is impeded by the nucleosome, an octamer of histones h2a, h2b, h3 and h4 dimers. more than a dozen factors in the yeast saccharomyces cerevisiae are known to facilitate transcription elongation through chromatin. in order to better understand the evolution and function of these factors, their sequences have been compared with known protein, est and dna sequences. elongator subcomplex components elp4p and elp6p are shown to be homologues of ...	2002	12202748
site-directed mutagenesis of conserved charged amino acid residues in clpb from escherichia coli.	clpb is a member of a multichaperone system in escherichia coli (with dnak, dnaj, and grpe) that reactivates strongly aggregated proteins. the sequence of clpb contains two atp-binding domains, each containing walker consensus motifs. the n- and c-terminal sequence regions of clpb do not contain known functional motifs. in this study, we performed site-directed mutagenesis of selected charged residues within the walker a motifs (lys212 and lys611) and the c-terminal region of clpb (asp797, arg81 ...	2002	12220194
identification of a streptolysin s-associated gene cluster and its role in the pathogenesis of streptococcus iniae disease.	streptococcus iniae causes meningoencephalitis and death in cultured fish species and soft-tissue infection in humans. we recently reported that s. iniae is responsible for local tissue necrosis and bacteremia in a murine subcutaneous infection model. the ability to cause bacteremia in this model is associated with a genetic profile unique to strains responsible for disease in fish and humans (j. d. fuller, d. j. bast, v. nizet, d. e. low, and j. c. s. de azavedo, infect. immun. 69:1994-2000, 20 ...	2002	12228303
coordinated methyl and rna binding is required for heterochromatin localization of mammalian hp1alpha.	in mammalian cells, as in schizosaccharomyces pombe and drosophila, hp1 proteins bind histone h3 tails methylated on lysine 9 (k9). however, whereas k9-methylated h3 histones are distributed throughout the nucleus, hp1 proteins are enriched in pericentromeric heterochromatin. this observation suggests that the methyl-binding property of hp1 may not be sufficient for its heterochromatin targeting. we show that the association of hp1alpha with pericentromeric heterochromatin depends not only on it ...	2002	12231507
functional expression of enterobacterial o-polysaccharide biosynthesis enzymes in bacillus subtilis.	the expression of heterologous bacterial glycosyltransferases is of interest for potential application in the emerging field of carbohydrate engineering in gram-positive organisms. to assess the feasibility of using enzymes from gram-negative bacteria, the functional expression of the genes wbap (formerly rfbp), weca (formerly rfe), and wbbo (formerly rfbf) from enterobacterial lipopolysaccharide o-polysaccharide biosynthesis pathways was examined in bacillus subtilis. wbap and weca are initiati ...	2002	12324313
having it both ways: transcription factors that bind dna and rna.	multifunctional proteins challenge the conventional 'one protein-one function' paradigm. here we note apparent multifunctional proteins with nucleic acid partners, tabulating eight examples. we then focus on eight additional cases of transcription factors that bind double-stranded dna with sequence specificity, but that also appear to lead alternative lives as rna-binding proteins. exemplified by the prototypic xenopus tfiiia protein, and more recently by mammalian p53, this list of transcriptio ...	2002	12364590
conservation of the biotin regulon and the bira regulatory signal in eubacteria and archaea.	biotin is a necessary cofactor of numerous biotin-dependent carboxylases in a variety of microorganisms. the strict control of biotin biosynthesis in escherichia coli is mediated by the bifunctional bira protein, which acts both as a biotin-protein ligase and as a transcriptional repressor of the biotin operon. little is known about regulation of biotin biosynthesis in other bacteria. using comparative genomics and phylogenetic analysis, we describe the biotin biosynthetic pathway and the bira r ...	2002	12368242
interaction of avilamycin with ribosomes and resistance caused by mutations in 23s rrna.	the antibiotic growth promoter avilamycin inhibits protein synthesis by binding to bacterial ribosomes. here the binding site is further characterized on escherichia coli ribosomes. the drug interacts with domain v of 23s rrna, giving a chemical footprint at nucleotides a2482 and a2534. selection of avilamycin-resistant halobacterium halobium cells revealed mutations in helix 89 of 23s rrna. furthermore, mutations in helices 89 and 91, which have previously been shown to confer resistance to eve ...	2002	12384333
highly conserved modified nucleosides influence mg2+-dependent trna folding.	transfer rna structure involves complex folding interactions of the tpsic domain with the d domain. however, the role of the highly conserved nucleoside modifications in the tpsic domain, rt54, psi55 and m5c49, in tertiary folding is not understood. to determine whether these modified nucleosides have a role in trna folding, the association of variously modified yeast trna(phe) t-half molecules (nucleosides 40-72) with the corresponding unmodified d-half molecule (nucleosides 1-30) was detected ...	2002	12409466
proteomic characterization of the small subunit of chlamydomonas reinhardtii chloroplast ribosome: identification of a novel s1 domain-containing protein and unusually large orthologs of bacterial s2, s3, and s5.	to understand how chloroplast mrnas are translated into functional proteins, a detailed understanding of all of the components of chloroplast translation is needed. to this end, we performed a proteomic analysis of the plastid ribosomal proteins in the small subunit of the chloroplast ribosome from the green alga chlamydomonas reinhardtii. twenty proteins were identified, including orthologs of escherichia coli s1, s2, s3, s4, s5, s6, s7, s9, s10, s12, s13, s14, s15, s16, s17, s18, s19, s20, and ...	2002	12417713
crystal structure of a human aminoacyl-trna synthetase cytokine.	the 20 aminoacyl-trna synthetases catalyze the first step of protein synthesis and establish the rules of the genetic code through aminoacylation reactions. biological fragments of two human enzymes, tyrosyl-trna synthetase (tyrrs) and tryptophanyl-trna synthetase, connect protein synthesis to cell-signaling pathways including angiogenesis. alternative splicing or proteolysis produces these fragments. the proangiogenic n-terminal fragment mini-tyrrs has il-8-like cytokine activity that, like oth ...	2002	12427973
emergence of tetracycline resistance in helicobacter pylori: multiple mutational changes in 16s ribosomal dna and other genetic loci.	tetracycline is useful in combination therapies against the gastric pathogen helicobacter pylori. we found 6 tetracycline-resistant (tet(r)) strains among 159 clinical isolates (from el salvador, lithuania, and india) and obtained the following four results: (i) 5 of 6 tet(r) isolates contained one or two nucleotide substitutions in one part of the primary tetracycline binding site in 16s rrna (aga(965-967) [escherichia coli coordinates] changed to gga, agc, gua, or ggc [lowercase letters are us ...	2002	12435699
identification and characterization of novel surface proteins in lactobacillus johnsonii and lactobacillus gasseri.	we have identified and sequenced the genes encoding the aggregation-promoting factor (apf) protein from six different strains of lactobacillus johnsonii and lactobacillus gasseri. both species harbor two apf genes, apf1 and apf2, which are in the same orientation and encode proteins of 257 to 326 amino acids. multiple alignments of the deduced amino acid sequences of these apf genes demonstrate a very strong sequence conservation of all of the genes with the exception of their central regions. n ...	2002	12450842
discontinuous and non-discontinuous subgenomic rna transcription in a nidovirus.	arteri-, corona-, toro- and roniviruses are evolutionarily related positive-strand rna viruses, united in the order nidovirales. the best studied nidoviruses, the corona- and arteriviruses, employ a unique transcription mechanism, which involves discontinuous rna synthesis, a process resembling similarity-assisted copy-choice rna recombination. during infection, multiple subgenomic (sg) mrnas are transcribed from a mirror set of sg negative-strand rna templates. the sg mrnas all possess a short ...	2002	12456663
elucidation of structure-function relationships in the protein subunit of bacterial rnase p using a genetic complementation approach.	rnase p is a ribonucleoprotein involved in trna biosynthesis in all living organisms. bacterial rnase p is comprised of a catalytic rna subunit and a lone protein cofactor which plays a supporting, albeit essential, role in the trna processing reaction in vivo. in this study, we have searched various databases to identify homologs of the protein subunit of rnase p from diverse bacteria and used an alignment of their primary sequences to determine the most highly conserved residues, and thereby e ...	2002	12466529
an inserted region of leucyl-trna synthetase plays a critical role in group i intron splicing.	yeast mitochondrial leucyl-trna synthetase (leurs) binds to the bi4 intron and collaborates with the bi4 maturase to aid excision of the group i intron. deletion analysis isolated the inserted leurs cp1 domain as a critical factor in the protein's splicing activity. protein fragments comprised of just the leurs cp1 region rescued complementation of a yeast strain that expressed a splicing-defective leurs. three-hybrid analysis determined that these cp1-containing leurs fragments, ranging from 21 ...	2002	12486008
in vivo selection of spectinomycin-binding rnas.	the folding of even short rna molecules in a random library can produce a huge number of possible macromolecular structures. using this principle, we have designed selections to seek non-coding rna transcripts capable of interfering with specific macromolecules such as transcription factors in living bacterial cells. here we show that such selections can uncover an unexpected class of rnas. in the present case, we report short rna transcripts whose expression confers bacterial resistance to the ...	2002	12490711
characterization of the interaction between the nucleotide exchange factor ef-ts from nematode mitochondria and elongation factor tu.	caenorhabditis elegans mitochondria have two elongation factor (ef)-tu species, denoted ef-tu1 and ef-tu2. recombinant nematode ef-ts purified from escherichia coli bound both of these molecules and also stimulated the translational activity of ef-tu, indicating that the nematode ef-ts homolog is a functional ef-ts protein of mitochondria. complexes formed by the interaction of nematode ef-ts with ef-tu1 and ef-tu2 could be detected by native gel electrophoresis and purified by gel filtration. a ...	2002	12490713
molecular analysis of the role of two aromatic aminotransferases and a broad-specificity aspartate aminotransferase in the aromatic amino acid metabolism of pyrococcus furiosus.	the genes encoding aromatic aminotransferase ii (aroat ii) and aspartate aminotransferase (aspat) from pyrococcus furiosus have been identified, expressed in escherichia coli and the recombinant proteins characterized. the aroat ii enzyme was specific for the transamination reaction of the aromatic amino acids, and uses a-ketoglutarate as the amino acceptor. like the previously characterized aroat i, aroat ii has highest efficiency for phenylalanine (k(cat)/km = 923 s(-1) mm(-1)). northern blot ...	2002	15803651
proteolysis in hyperthermophilic microorganisms.	proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. in this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genus pyrococcus, the crenarchaeote sulfolobus ...	2002	15803660
peptide deformylase as an antibacterial drug target: assays for detection of its inhibition in escherichia coli cell homogenates and intact cells.	an assay was developed to determine the activity of peptide deformylase (pdf) inhibitors under conditions as close as possible to the physiological situation. the assay principle is the detection of n-terminal [35s]methionine labeling of a protein that contains no internal methionine. if pdf is active, the deformylation of the methionine renders the peptide a substrate for methionine aminopeptidase, resulting in the removal of the n-terminal methionine label. in the presence of a pdf inhibitor, ...	2001	11257015
peptide deformylase as an antibacterial drug target: target validation and resistance development.	new inhibitors of peptide deformylase (pdf) which are very potent against the isolated enzyme and show a certain degree of antibacterial activity have recently been synthesized by our group. several lines of experimental evidence indicate that these inhibitors indeed interfere with the target enzyme in the bacterial cell. (i) the inhibition of escherichia coli growth could be counteracted by overexpression of pdf from different organisms, including e. coli, streptococcus pneumoniae, and haemophi ...	2001	11257016
hydrogen peroxide-forming nadh oxidase belonging to the peroxiredoxin oxidoreductase family: existence and physiological role in bacteria.	amphibacillus xylanus and sporolactobacillus inulinus nadh oxidases belonging to the peroxiredoxin oxidoreductase family show extremely high peroxide reductase activity for hydrogen peroxide and alkyl hydroperoxides in the presence of the small disulfide redox protein, ahpc (peroxiredoxin). in order to investigate the distribution of this enzyme system in bacteria, 15 bacterial strains were selected from typical aerobic, facultatively anaerobic, and anaerobic bacteria. ahpc-linked alkyl hydroper ...	2001	11274101
rac, a stable ribosome-associated complex in yeast formed by the dnak-dnaj homologs ssz1p and zuotin.	the yeast cytosol contains multiple homologs of the dnak and dnaj chaperone family. our current understanding of which homologs functionally interact is incomplete. zuotin is a dnaj homolog bound to the yeast ribosome. we have now identified the dnak homolog ssz1p/pdr13p as zuotin's partner chaperone. zuotin and ssz1p form a ribosome-associated complex (rac) that is bound to the ribosome via the zuotin subunit. rac is unique among the eukaryotic dnak-dnaj systems, as the 1:1 complex is stable, e ...	2001	11274393
bacterial diversity and community structure in an aerated lagoon revealed by ribosomal intergenic spacer analyses and 16s ribosomal dna sequencing.	we investigated the bacterial community structure in an aerated plug-flow lagoon treating pulp and paper mill effluent. for this investigation, we developed a composite method based on analyses of pcr amplicons containing the ribosomal intergenic spacer (ris) and its flanking partial 16s rrna gene. community percent similarity was determined on the basis of ris length polymorphism. a community succession was evident in the lagoon, indicated by a progressive community transition through seven sam ...	2001	11282606
purification and characterization of the recombinant thermus sp. strain t2 alpha-galactosidase expressed in escherichia coli.	the nucleotide sequence of the thermus sp. strain t2 dna coding for a thermostable alpha-galactosidase was determined. the deduced amino acid sequence of the enzyme predicts a polypeptide of 474 amino acids (m(r), 53,514). the observed homology between the deduced amino acid sequences of the enzyme and alpha-galactosidase from thermus brockianus was over 70%. thermus sp. strain t2 alpha-galactosidase was expressed in its active form in escherichia coli and purified. native polyacrylamide gel ele ...	2001	11282611
crystal structures of complexes of the small ribosomal subunit with tetracycline, edeine and if3.	the small ribosomal subunit is responsible for the decoding of genetic information and plays a key role in the initiation of protein synthesis. we analyzed by x-ray crystallography the structures of three different complexes of the small ribosomal subunit of thermus thermophilus with the a-site inhibitor tetracycline, the universal initiation inhibitor edeine and the c-terminal domain of the translation initiation factor if3. the crystal structure analysis of the complex with tetracycline reveal ...	2001	11296217
rna tertiary interactions in the large ribosomal subunit: the a-minor motif.	analysis of the 2.4-a resolution crystal structure of the large ribosomal subunit from haloarcula marismortui reveals the existence of an abundant and ubiquitous structural motif that stabilizes rna tertiary and quaternary structures. this motif is termed the a-minor motif, because it involves the insertion of the smooth, minor groove edges of adenines into the minor groove of neighboring helices, preferentially at c-g base pairs, where they form hydrogen bonds with one or both of the 2' ohs of ...	2001	11296253
conservation of the binding site for the arginine repressor in all bacterial lineages.	the arginine repressor argr/ahrc is a transcription factor universally conserved in bacterial genomes. its recognition signal (the arg box), a weak palindrome, is also conserved between genomes, despite a very low degree of similarity between individual sites within a genome. thus, the arginine repressor is different from two other universal transcription factors - hrca, whose recognition signal is very strongly conserved both within and between genomes, and lexa/dinr, whose signal is strongly c ...	2001	11305941
attached and unattached bacterial communities in a 120-meter corehole in an acidic, crystalline rock aquifer.	the bacteria colonizing geologic core sections (attached) were contrasted with those found suspended in the groundwater (unattached) by examining the microbiology of 16 depth-paired core and groundwater samples using a suite of culture-independent and culture-dependent analyses. one hundred twenty-two meters was continuously cored from a buried chalcopyrite ore hosted in a biotite-quartz-monzonite porphyry at the mineral park mine near kingman, ariz. every fourth 1.5-m core was acquired using mi ...	2001	11319087
cloning and functional characterization of an nad(+)-dependent dna ligase from staphylococcus aureus.	a staphylococcus aureus mutant conditionally defective in dna ligase was identified by isolation of complementing plasmid clones that encode the s. aureus liga gene. orthologues of the putative s. aureus nad(+)-dependent dna ligase could be identified in the genomes of bacillus stearothermophilus and other gram-positive bacteria and confirmed the presence of four conserved amino acid motifs, including motif i, kxdg with lysine 112, which is believed to be the proposed site of adenylation. dna se ...	2001	11325928
evidence against an interaction between the mrna downstream box and 16s rrna in translation initiation.	based on the complementarity of the initial coding region (downstream box [db]) of several bacterial and phage mrnas to bases 1469 to 1483 in helix 44 of 16s rrna (anti-downstream box [adb]), it has been proposed that db-adb base pairing enhances translation in a way that is similar to that of the shine-dalgarno (sd)/anti-shine-dalgarno (asd) interaction. computer modeling of helix 44 on the 30s subunit shows that the topography of the 30s ribosome does not allow a simultaneous db-adb interactio ...	2001	11344158
oxaloacetate synthesis in the methanarchaeon methanosarcina barkeri: pyruvate carboxylase genes and a putative escherichia coli-type bifunctional biotin protein ligase gene (bpl/bira) exhibit a unique organization.	evidence is presented that, in methanosarcina barkeri oxaloacetate synthesis, an essential and major co(2) fixation reaction is catalyzed by an apparent alpha(4)beta(4)-type acetyl coenzyme a-independent pyruvate carboxylase (pyc), composed of 64.2-kda biotinylated and 52.9-kda atp-binding subunits. the purified enzyme was most active at 70 degrees c, insensitive to aspartate and glutamate, mildly inhibited by alpha-ketoglutarate, and severely inhibited by atp, adp, and excess mg(2+). it showed ...	2001	11371547