Publications
| Title | Abstract | Year(sorted descending) Filter | PMID Filter |
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| specific interaction between the ribosome recycling factor and the elongation factor g from mycobacterium tuberculosis mediates peptidyl-trna release and ribosome recycling in escherichia coli. | once the translating ribosomes reach a termination codon, the nascent polypeptide chain is released in a factor-dependent manner. however, the p-site-bound deacylated trna and the ribosomes themselves remain bound to the mrna (post-termination complex). the ribosome recycling factor (rrf) plays a vital role in dissociating this complex. here we show that the mycobacterium tuberculosis rrf (mturrf) fails to rescue escherichia coli lj14, a strain temperature-sensitive for rrf (frr(ts)). more inter ... | 2001 | 11387230 |
| spontaneous erythromycin resistance mutation in a 23s rrna gene, rrla, of the extreme thermophile thermus thermophilus ib-21. | spontaneous, erythromycin-resistant mutants of thermus thermophilus ib-21 were isolated and found to carry the mutation a2058g in one of two 23s rrna operons. the heterozygosity of these mutants indicates that a2058g confers a dominant or codominant phenotype in this organism. this mutation provides a valuable tool for the genetic manipulation of the 23s rrna genes of thermus. | 2001 | 11418580 |
| using surface-bound rubidium ions for protein phasing. | rubidium is a monovalent metal that can be used as a counterion in protein solutions. x-ray anomalous scattering from rubidium ions bound to the protein surface was used for phasing of the crystal structure of the hsp60 apical domain from thermus thermophilus. multiple-wavelength anomalous dispersion (mad) data were collected from a crystal obtained from a solution containing 0.2 m rubidium salt. one molecule of protein (147 amino acids) binds one well ordered and one poorly ordered rb atom. pha ... | 2001 | 11418770 |
| characterization of a heme-dependent catalase from methanobrevibacter arboriphilus. | recently it was reported that methanogens of the genus methanobrevibacter exhibit catalase activity. this was surprising, since methanobrevibacter species belong to the order methanobacteriales, which are known not to contain cytochromes and to lack the ability to synthesize heme. we report here that methanobrevibacter arboriphilus strains az and dh1 contained catalase activity only when the growth medium was supplemented with hemin. the heme catalase was purified and characterized, and the enco ... | 2001 | 11425719 |
| natural transformation in mesophilic and thermophilic bacteria: identification and characterization of novel, closely related competence genes in acinetobacter sp. strain bd413 and thermus thermophilus hb27. | the mesophile acinetobacter sp. strain bd413 and the extreme thermophile thermus thermophilus hb27 display high frequencies of natural transformation. in this study we identified and characterized a novel competence gene in acinetobacter sp. strain bd413, coma, whose product displays significant similarities to the competence proteins coma and comec in neisseria and bacillus species. transcription of coma correlated with growth phase-dependent transcriptional regulation of the recently identifie ... | 2001 | 11425734 |
| molecular characterization of desulfovibrio gigas neelaredoxin, a protein involved in oxygen detoxification in anaerobes. | desulfovibrio gigas neelaredoxin is an iron-containing protein of 15 kda, having a single iron site with a his(4)cys coordination. neelaredoxins and homologous proteins are widespread in anaerobic prokaryotes and have superoxide-scavenging activity. to further understand its role in anaerobes, its genomic organization and expression in d. gigas were studied and its ability to complement escherichia coli superoxide dismutase deletion mutant was assessed. in d. gigas, neelaredoxin is transcribed a ... | 2001 | 11443075 |
| rad54 protein stimulates the postsynaptic phase of rad51 protein-mediated dna strand exchange. | rad54 and rad51 are important proteins for the repair of double-stranded dna breaks by homologous recombination in eukaryotes. as previously shown, rad51 protein forms nucleoprotein filaments on single-stranded dna, and rad54 protein directly interacts with such filaments to enhance synapsis, the homologous pairing with a double-stranded dna partner. here we demonstrate that saccharomyces cerevisiae rad54 protein has an additional role in the postsynaptic phase of dna strand exchange by stimulat ... | 2001 | 11459988 |
| high stability of a ferredoxin from the hyperthermophilic archaeon a. ambivalens: involvement of electrostatic interactions and cofactors. | the ferredoxin from the thermophilic archaeon acidianus ambivalens is a small monomeric seven-iron protein with a thermal midpoint (t(m)) of 122 degrees c (ph 7). to gain insight into the basis of its thermostability, we have characterized unfolding reactions induced chemically and thermally at various phs. thermal unfolding of this ferredoxin, in the presence of various guanidine hydrochloride (guhcl) concentrations, yields a linear correlation between unfolding enthalpies (deltah[t(m)]) and t( ... | 2001 | 11468351 |
| assessment, by transcription-mediated amplification, of virologic response in patients with chronic hepatitis c virus treated with peginterferon alpha-2a. | transcription-mediated amplification (tma) is an isothermal, autocatalytic target amplification method which has the potential to detect less than 50 hepatitis c virus (hcv) rna copies/ml (10 iu/ml). the tma assay was used to assess the presence of residual hcv rna in plasma from patients treated with polyethylene glycol-modified interferon alpha-2a (peginterferon alpha-2a) who showed a virologic relapse after the end of therapy. stored end-of-treatment and end-of-follow-up plasma samples from 1 ... | 2001 | 11474002 |
| the kink-turn: a new rna secondary structure motif. | analysis of the haloarcula marismortui large ribosomal subunit has revealed a common rna structure that we call the kink-turn, or k-turn. the six k-turns in h.marismortui 23s rrna superimpose with an r.m.s.d. of 1.7 a. there are two k-turns in the structure of thermus thermophilus 16s rrna, and the structures of u4 snrna and l30e mrna fragments form k-turns. the structure has a kink in the phosphodiester backbone that causes a sharp turn in the rna helix. its asymmetric internal loop is flanked ... | 2001 | 11483524 |
| functional and evolutionary relationship between arginine biosynthesis and prokaryotic lysine biosynthesis through alpha-aminoadipate. | our previous studies revealed that lysine is synthesized through alpha-aminoadipate in an extremely thermophilic bacterium, thermus thermophilus hb27. sequence analysis of a gene cluster involved in the lysine biosynthesis of this microorganism suggested that the conversion from alpha-aminoadipate to lysine proceeds in a way similar to that of arginine biosynthesis. in the present study, we cloned an argd homolog of t. thermophilus hb27 which was not included in the previously cloned lysine bios ... | 2001 | 11489859 |
| peplomycin, a bleomycin derivative, induces myofibroblasts in pulmonary fibrosis. | to analyse the mechanism by which a bleomycin derivative, peplomycin (plm) induces pulmonary fibrosis, we investigated differentiation of rat pulmonary fibroblasts to myofibroblasts (mf). in intraperitoneally plm (5 mg/kg/day)-injected rats, the peripheries of lungs adjacent to the pleura revealed advanced fibrosis with a small number of alpha-smooth muscle actin (alpha-sma)-positive mf, which ultrastructurally possessed abundant microfilaments and cellular organelles. in the fibrotic tissue, th ... | 2001 | 11493347 |
| resistance of streptococcus pneumoniae to deformylase inhibitors is due to mutations in defb. | resistance to peptide deformylase inhibitors in escherichia coli or staphylococcus aureus is due to inactivation of transformylase activity. knockout experiments in streptococcus pneumoniae r6x indicate that the transformylase (fmt) and deformylase (defb) genes are essential and that a def paralog (defa) is not. actinonin-resistant mutants of s. pneumoniae atcc 49619 harbor mutations in defb but not in fmt. reintroduction of the mutated defb gene into wild-type s. pneumoniae r6x recreates the re ... | 2001 | 11502510 |
| high-throughput genotyping of single nucleotide polymorphisms with rolling circle amplification. | single nucleotide polymorphisms (snps) are the foundation of powerful complex trait and pharmacogenomic analyses. the availability of large snp databases, however, has emphasized a need for inexpensive snp genotyping methods of commensurate simplicity, robustness, and scalability. we describe a solution-based, microtiter plate method for snp genotyping of human genomic dna. the method is based upon allele discrimination by ligation of open circle probes followed by rolling circle amplification o ... | 2001 | 11511324 |
| hybrid protein between ribosomal protein s16 and rimm of escherichia coli retains the ribosome maturation function of both proteins. | the rimm protein in escherichia coli is associated with free 30s ribosomal subunits but not with 70s ribosomes and is important for efficient maturation of the 30s subunits. a mutant lacking rimm shows a sevenfold-reduced growth rate and a reduced translational efficiency. here we show that a double alanine-for-tyrosine substitution in rimm prevents it from associating with the 30s subunits and reduces the growth rate of e. coli approximately threefold. several faster-growing derivatives of the ... | 2001 | 11514519 |
| recombinational transfer of 100-kilobase genomic dna to plasmid in bacillus subtilis 168. | transformation of bacillus subtilis by a plasmid requires a circular multimeric form. in contrast, linearized plasmids can be circularized only when homologous sequences are present in the host genome. a recombinational transfer system was constructed with this intrinsic b. subtilis recombinational repair pathway. the vector, pgets103, a derivative of the theta-type replicating plasmid ptb19 of thermophilic bacillus, had the full length of escherichia coli plasmid pbr322. a multimeric form of pg ... | 2001 | 11514534 |
| a conformational change in the ribosomal peptidyl transferase center upon active/inactive transition. | the ribosome is a dynamic particle that undergoes many structural changes during translation. we show through chemical probing with dimethyl sulfate (dms) that conformational changes occur at several nucleotides in the peptidyl transferase center upon alterations in ph, temperature, and monovalent ion concentration, consistent with observations made by elson and coworkers over 30 years ago. moreover, we have found that the ph-dependent dms reactivity of a2451 in the center of the 23s rrna peptid ... | 2001 | 11517305 |
| production of recombinant alpha-galactosidases in thermus thermophilus. | a thermus thermophilus selector strain for production of thermostable and thermoactive alpha-galactosidase was constructed. for this purpose, the native alpha-galactosidase gene (agat) of t. thermophilus th125 was inactivated to prevent background activity. in our first attempt, insertional mutagenesis of agat by using a cassette carrying a kanamycin resistance gene led to bacterial inability to utilize melibiose (alpha-galactoside) and galactose as sole carbohydrate sources due to a polar effec ... | 2001 | 11526023 |
| xylulokinase overexpression in two strains of saccharomyces cerevisiae also expressing xylose reductase and xylitol dehydrogenase and its effect on fermentation of xylose and lignocellulosic hydrolysate. | fermentation of the pentose sugar xylose to ethanol in lignocellulosic biomass would make bioethanol production economically more competitive. saccharomyces cerevisiae, an efficient ethanol producer, can utilize xylose only when expressing the heterologous genes xyl1 (xylose reductase) and xyl2 (xylitol dehydrogenase). xylose reductase and xylitol dehydrogenase convert xylose to its isomer xylulose. the gene xks1 encodes the xylulose-phosphorylating enzyme xylulokinase. in this study, we determi ... | 2001 | 11526030 |
| the structure of an asprs-trna(asp) complex reveals a trna-dependent control mechanism. | the 2.6 a resolution crystal structure of an inactive complex between yeast trna(asp) and escherichia coli aspartyl-trna synthetase reveals the molecular details of a trna-induced mechanism that controls the specificity of the reaction. the dimer is asymmetric, with only one of the two bound trnas entering the active site cleft of its subunit. however, the flipping loop, which controls the proper positioning of the amino acid substrate, acts as a lid and prevents the correct positioning of the t ... | 2001 | 11566892 |
| multiple lateral transfers of dissimilatory sulfite reductase genes between major lineages of sulfate-reducing prokaryotes. | a large fragment of the dissimilatory sulfite reductase genes (dsrab) was pcr amplified and fully sequenced from 30 reference strains representing all recognized lineages of sulfate-reducing bacteria. in addition, the sequence of the dsrab gene homologs of the sulfite reducer desulfitobacterium dehalogenans was determined. in contrast to previous reports, comparative analysis of all available dsrab sequences produced a tree topology partially inconsistent with the corresponding 16s rrna phylogen ... | 2001 | 11567003 |
| characterization of a highly thermostable alkaline phosphatase from the euryarchaeon pyrococcus abyssi. | this work reports the first isolation and characterization of an alkaline phosphatase (ap) from a hyperthermophilic archaeon. an ap gene from pyrococcus abyssi, a euryarchaeon isolated from a deep-sea hydrothermal vent, was cloned and the enzyme expressed in escherichia coli. analysis of the sequence showed conservation of the active site and structural elements of the e. coli ap. the recombinant ap was purified and characterized. monomeric and homodimeric active forms were detected, with a mono ... | 2001 | 11571149 |
| mutations in the listerial prob gene leading to proline overproduction: effects on salt tolerance and murine infection. | the observed sensitivity of listeria monocytogenes to the toxic proline analogue l-azetidine-2-carboxylic acid (az) suggested that proline synthesis in listeria may be regulated by feedback inhibition of gamma-glutamyl kinase (gk), the first enzyme of the proline biosynthesis pathway, encoded by the prob gene. taking advantage of the epicurian coli mutator strain xl1-red, we performed random mutagenesis of the recently described proba operon and generated three independent mutations in the liste ... | 2001 | 11571156 |
| screening of active lyssavirus infection in wild bat populations by viral rna detection on oropharyngeal swabs. | brain analysis cannot be used for the investigation of active lyssavirus infection in healthy bats because most bat species are protected by conservation directives. consequently, serology remains the only tool for performing virological studies on natural bat populations; however, the presence of antibodies merely reflects past exposure to the virus and is not a valid marker of active infection. this work describes a new nested reverse transcription (rt)-pcr technique specifically designed for ... | 2001 | 11574590 |
| visualization of protein s1 within the 30s ribosomal subunit and its interaction with messenger rna. | s1 is the largest ribosomal protein, present in the small subunit of the bacterial ribosome. it has a pivotal role in stabilizing the mrna on the ribosome. thus far, s1 has eluded structural determination. we have identified the s1 protein mass in the cryo-electron microscopic map of the escherichia coli ribosome by comparing the map with a recent x-ray crystallographic structure of the 30s subunit, which lacks s1. according to our finding, s1 is located at the junction of head, platform, and ma ... | 2001 | 11593008 |
| characterization of a brucella species 25-kilobase dna fragment deleted from brucella abortus reveals a large gene cluster related to the synthesis of a polysaccharide. | in the present study we completed the nucleotide sequence of a brucella melitensis 16m dna fragment deleted from b. abortus that accounts for 25,064 bp and show that the other brucella spp. contain the entire 25-kb dna fragment. two short direct repeats of four nucleotides, detected in the b. melitensis 16m dna flanking both sides of the fragment deleted from b. abortus, might have been involved in the deletion formation by a strand slippage mechanism during replication. in addition to omp31, co ... | 2001 | 11598046 |
| sequence analysis of four shigella boydii o-antigen loci: implication for escherichia coli and shigella relationships. | shigella strains are in reality clones of escherichia coli and are believed to have emerged relatively recently (g. m. pupo, r. lan, and p. r. reeves, proc. natl. acad. sci. usa 97:10567-10572, 2000). there are 33 o-antigen forms in these shigella clones, of which 12 are identical to o antigens of other e. coli strains. we sequenced o-antigen gene clusters from shigella boydii serotypes 4, 5, 6, and 9 and also studied the o53- and o79-antigen gene clusters of e. coli, encoding o antigens identic ... | 2001 | 11598067 |
| the organization of cytoplasmic ribosomal protein genes in the arabidopsis genome. | eukaryotic ribosomes are made of two components, four ribosomal rnas, and approximately 80 ribosomal proteins (r-proteins). the exact number of r-proteins and r-protein genes in higher plants is not known. the strong conservation in eukaryotic r-protein primary sequence allowed us to use the well-characterized rat (rattus norvegicus) r-protein set to identify orthologues on the five haploid chromosomes of arabidopsis. by use of the numerous expressed sequence tag (est) accessions and the complet ... | 2001 | 11598216 |
| influence of a sulfhydryl cross-link across the allosteric-site interface of e. coli phosphofructokinase. | to assess the role of quaternary stability on the properties of escherichia coli phosphofructokinase (pfk), a disulfide bond has been introduced across the subunit interface containing the allosteric binding sites in e. coli phosphofructokinase by changing n288 to cysteine. n288 is located in close proximity to the equivalent residue on an adjacent subunit. although sds-page of oxidized n288c indicates monomeric protein, blocking the six native cysteine residues with n-ethyl maleimide (nem) reve ... | 2001 | 11604525 |
| differential effects of replacing escherichia coli ribosomal protein l27 with its homologue from aquifex aeolicus. | the rpma gene, which encodes 50s ribosomal subunit protein l27, was cloned from the extreme thermophile aquifex aeolicus, and the protein was overexpressed and purified. comparison of the a. aeolicus protein with its homologue from escherichia coli by circular dichroism analysis and proton nuclear magnetic resonance spectroscopy showed that it readily adopts some structure in solution that is very stable, whereas the e. coli protein is unstructured under the same conditions. a mutant of e. coli ... | 2001 | 11673426 |
| clue to damage recognition by uvrb: residues in the beta-hairpin structure prevent binding to non-damaged dna. | uvrb, the ultimate damage-recognizing component of bacterial nucleotide excision repair, contains a flexible beta-hairpin rich in hydrophobic residues. we describe the properties of uvrb mutants in which these residues have been mutated. the results show that y101 and f108 in the tip of the hairpin are important for the strand-separating activity of uvrb, supporting the model that the beta-hairpin inserts between the two dna strands during the search for dna damage. residues y95 and y96 at the b ... | 2001 | 11689453 |
| structural and mutational studies of the recognition of the arginine trna-specific major identity element, a20, by arginyl-trna synthetase. | arginyl-trna synthetase (argrs) recognizes two major identity elements of trna(arg): a20, located at the outside corner of the l-shaped trna, and c35, the second letter of the anticodon. only a few exceptional organisms, such as the yeast saccharomyces cerevisiae, lack a20 in trna(arg). in the present study, we solved the crystal structure of a typical a20-recognizing argrs from thermus thermophilus at 2.3 a resolution. the structure of the t. thermophilus argrs was found to be similar to that o ... | 2001 | 11698642 |
| brucella abortus genes identified following constitutive growth and macrophage infection. | the chronicity of brucella abortus infection in humans and animals depends on the organism's ability to escape host defenses by gaining entry and surviving inside the macrophage. although no human vaccine exists for brucella, vaccine development in other bacteria has been based on deletions of selective nutritional as well as regulatory systems. our goal is to develop a vaccine for brucella. to further this aim, we have used a green fluorescent protein (gfp) reporter system to identify constitut ... | 2001 | 11705955 |
| nog2p, a putative gtpase associated with pre-60s subunits and required for late 60s maturation steps. | eukaryotic ribosome maturation depends on a set of well ordered processing steps. here we describe the functional characterization of yeast nog2p (ynr053cp), a highly conserved nuclear protein. nog2p contains a putative gtp-binding site, which is essential in vivo. kinetic and steady-state measurements of the levels of pre-rrnas in nog2p-depleted cells showed a defect in 5.8s and 25s maturation and a concomitant increase in the levels of both 27sb(s) and 7s(s) precursors. we found nog2p physical ... | 2001 | 11707418 |
| crystal structure of thermostable dna photolyase: pyrimidine-dimer recognition mechanism. | dna photolyase is a pyrimidine-dimer repair enzyme that uses visible light. photolyase generally contains two chromophore cofactors. one is a catalytic cofactor directly contributing to the repair of a pyrimidine-dimer. the other is a light-harvesting cofactor, which absorbs visible light and transfers energy to the catalytic cofactor. photolyases are classified according to their second cofactor into either a folate- or deazaflavin-type. the native structures of both types of photolyases have a ... | 2001 | 11707580 |
| the hunt for living gold. the search for organisms in extreme environments yields useful enzymes for industry. | 2001 | 11713183 | |
| saturation mutagenesis of 5s rrna in saccharomyces cerevisiae. | rrnas are the central players in the reactions catalyzed by ribosomes, and the individual rrnas are actively involved in different ribosome functions. our previous demonstration that yeast 5s rrna mutants (called mof9) can impact translational reading frame maintenance showed an unexpected function for this ubiquitous biomolecule. at the time, however, the highly repetitive nature of the genes encoding rrnas precluded more detailed genetic and molecular analyses. a new genetic system allows all ... | 2001 | 11713264 |
| overexpression, purification and characterization of recj protein from thermus thermophilus hb8 and its core domain. | a recj homolog was cloned from the extremely thermophilic bacterium thermus themophilus hb8. it encodes a 527 amino acid protein that has 33% identity to escherichia coli recj protein and includes the characteristic motifs conserved among recj homologs. although t.thermophilus recj protein (ttrecj) was expressed as an inclusion body, it was purified in soluble form through denaturation with urea and subsequent refolding steps. limited proteolysis showed that ttrecj has a protease-resistant core ... | 2001 | 11713311 |
| importance of the conserved nucleotides around the trna-like structure of escherichia coli transfer-messenger rna for protein tagging. | a bacterial rna functioning as both trna and mrna, transfer-messenger rna (tmrna) rescues stalled ribosomes and clears the cell of incomplete polypeptides. for function, escherichia coli tmrna requires an elaborate interplay between a trna-like structure and an internal mrna domain that are connected by a 295 nt long compact secondary structure. the trna-like structure is surrounded by 16 unpaired nt, including 10 residues that are >95% conserved among the known 140 tmrna sequences. all these re ... | 2001 | 11713316 |
| behavior of dna fibers stretched by precise meniscus motion control. | a modified dna combing method, which can precisely locate straightened dna fibers on a substrate, has been developed. precise motion control of a dna solution droplet on hydrophobic surfaces has allowed detailed analyses of dna straightening behavior. our method provides a technique for consistently straightening lambda phage dna on a trace of droplet motion, though the straightened dnas had several variations in their alignments. the dependence of the straightened dna frequency upon motion rate ... | 2001 | 11713329 |
| structure and dynamics of translation initiation factor aif-1a from the archaeon methanococcus jannaschii determined by nmr spectroscopy. | translation initiation factor 1a (aif-1a) from the archaeon methanococcus jannaschii was expressed in escherichia coli, purified, and characterized in terms of its structure and dynamics using multidimensional nmr methods. the protein was found to be a member of the ob-fold family of rna-associated proteins, containing a barrel of five beta-strands, a feature that is shared with the homologous eukaryotic translation initiation factor 1a (eif-1a), as well as the prokaryotic translation initiation ... | 2001 | 11714910 |
| h(2)o(2)-forming nadh oxidase with diaphorase (cytochrome) activity from archaeoglobus fulgidus. | an enzyme exhibiting nadh oxidase (diaphorase) activity was isolated from the hyperthermophilic sulfate-reducing anaerobe archaeoglobus fulgidus. n-terminal sequence of the protein indicates that it is coded for by open reading frame af0395 in the a. fulgidus genome. the gene af0395 was cloned and its product was purified from escherichia coli. like the native nadh oxidase (noxa2), the recombinant noxa2 (rnoxa2) has an apparent molecular mass of 47 kda, requires flavin adenine dinucleotide for a ... | 2001 | 11717257 |
| novel posttranslational activation of the lys2-encoded alpha-aminoadipate reductase for biosynthesis of lysine and site-directed mutational analysis of conserved amino acid residues in the activation domain of candida albicans. | the alpha-aminoadipate pathway for lysine biosynthesis is present only in fungi. the alpha-aminoadipate reductase (aar) of this pathway catalyzes the conversion of alpha-aminoadipic acid to alpha-aminoadipic-delta-semialdehyde by a complex mechanism involving two gene products, lys2p and lys5p. the lys2 and lys5 genes encode, respectively, a 155-kda inactive aar and a 30-kda phosphopantetheinyl transferase (pptase) which transfers a phosphopantetheinyl group from coenzyme a (coa) to lys2p for th ... | 2001 | 11717270 |
| adp-dependent phosphofructokinases in mesophilic and thermophilic methanogenic archaea. | phosphofructokinase (pfk) is a key enzyme of the glycolytic pathway in all domains of life. two related pfks, atp-dependent and pp(i)-dependent pfk, have been distinguished in bacteria and eucarya, as well as in some archaea. hyperthermophilic archaea of the order thermococcales, including pyrococcus and thermococcus spp., have recently been demonstrated to possess a unique adp-dependent pfk (adp-pfk) that appears to be phylogenetically distinct. here, we report the presence of adp-pfks in glyco ... | 2001 | 11717273 |
| different physiological roles of atp- and pp(i)-dependent phosphofructokinase isoenzymes in the methylotrophic actinomycete amycolatopsis methanolica. | cells of the actinomycete amycolatopsis methanolica grown on glucose possess only a single, exclusively pp(i)-dependent phosphofructokinase (pp(i)-pfk) (a. m. c. r. alves, g. j. w. euverink, h. j. hektor, j. van der vlag, w. vrijbloed, d.h.a. hondmann, j. visser, and l. dijkhuizen, j. bacteriol. 176:6827-6835, 1994). when this methylotrophic bacterium is grown on one-carbon (c(1)) compounds (e.g., methanol), an atp-dependent phosphofructokinase (atp-pfk) activity is specifically induced, complet ... | 2001 | 11717283 |
| complex i and its involvement in redox homeostasis and carbon and nitrogen metabolism in rhodobacter capsulatus. | a transposon mutant of rhodobacter capsulatus, strain mal7, that was incapable of photoautotrophic and chemoautotrophic growth and could not grow photoheterotrophically in the absence of an exogenous electron acceptor was isolated. the phenotype of strain mal7 suggested that the mutation was in some gene(s) not previously shown to be involved in co(2) fixation control. the site of transposition in strain mal7 was identified and shown to be in the gene nuof, which encodes one of the 14 subunits f ... | 2001 | 11717288 |
| cysteinyl-trna synthetase is not essential for viability of the archaeon methanococcus maripaludis. | the methanogenic archaea methanocaldococcus jannaschii and methanothermobacter thermautotrophicus contain a dual-specificity prolyl-trna synthetase (procysrs) that accurately forms both prolyl-trna (pro-trna) and cysteinyl-trna (cys-trna) suitable for in vivo translation. this intriguing enzyme may even perform its dual role in organisms that possess a canonical single-specificity cysteinyl-trna synthetase (cysrs), raising the question as to whether this latter aminoacyl-trna synthetase is indee ... | 2001 | 11717392 |
| recognizing the d-loop of transfer rnas. | 2001 | 11717415 | |
| degradation of xylan to d-xylose by recombinant saccharomyces cerevisiae coexpressing the aspergillus niger beta-xylosidase (xlnd) and the trichoderma reesei xylanase ii (xyn2) genes. | the beta-xylosidase-encoding xlnd gene of aspergillus niger 90196 was amplified by the pcr technique from first-strand cdna synthesized on mrna isolated from the fungus. the nucleotide sequence of the cdna fragment was verified to contain a 2,412-bp open reading frame that encodes a 804-amino-acid propeptide. the 778-amino-acid mature protein, with a putative molecular mass of 85.1 kda, was fused in frame with the saccharomyces cerevisiae mating factor alpha1 signal peptide (mfalpha1(s)) to ensu ... | 2001 | 11722900 |
| deletion of the gre3 aldose reductase gene and its influence on xylose metabolism in recombinant strains of saccharomyces cerevisiae expressing the xyla and xks1 genes. | saccharomyces cerevisiae ferments hexoses efficiently but is unable to ferment xylose. when the bacterial enzyme xylose isomerase (xi) from thermus thermophilus was produced in s. cerevisiae, xylose utilization and ethanol formation were demonstrated. in addition, xylitol and acetate were formed. an unspecific aldose reductase (ar) capable of reducing xylose to xylitol has been identified in s. cerevisiae. the gre3 gene, encoding the ar enzyme, was deleted in s. cerevisiae cen.pk2-1c, yielding y ... | 2001 | 11722921 |
| v-shaped structure of glutamyl-trna reductase, the first enzyme of trna-dependent tetrapyrrole biosynthesis. | processes vital to life such as respiration and photosynthesis critically depend on the availability of tetrapyrroles including hemes and chlorophylls. trna-dependent catalysis generally is associated with protein biosynthesis. an exception is the reduction of glutamyl-trna to glutamate-1-semialdehyde by the enzyme glutamyl-trna reductase. this reaction is the indispensable initiating step of tetrapyrrole biosynthesis in plants and most prokaryotes. the crystal structure of glutamyl-trna reducta ... | 2001 | 11726494 |
| mode of dna-protein interaction between the c-terminal domain of escherichia coli rna polymerase alpha subunit and t7d promoter up element. | the c-terminal domain (ctd) downstream from residue 235 of escherichia coli rna polymerase alpha subunit is involved in recognition of the promoter up element. here we have demonstrated, by dnase i and hydroxyl radical mapping, the presence of two up element subsites on the promoter d of phage t7, each located half and one-and-a-half helix turns, respectively, upstream from the promoter -35 element. this non-typical up element retained its alphactd-binding capability when transferred into the ge ... | 2001 | 11812819 |
| a protonated base pair participating in rrna tertiary structural interactions. | in the recently published x-ray crystallographic structure for the 50s subunit of haloarcula marismortui ribosomes, residue u2546 of the 23s rrna forms a non-watson-crick base pair with u2610. the corresponding residues in the secondary structure of the escherichia coli 23s molecule are u2511 and c2575, and it follows that the latter base (c2575) should be protonated in order to form a base pair that is isostructural with its counterpart in h.marismortui. this prediction was demonstrated experim ... | 2001 | 11812838 |
| nmr structure of a ribosomal rna hairpin containing a conserved cucaa pentaloop. | the structure of a 23 nt rna sequence, rggacccgggcucaaccugggucc, was elucidated using homonuclear nmr, distance geometry and restrained molecular dynamics. this rna is analogous to residues 612-628 of the escherichia coli 16s rrna. the structure of the rna reveals the presence of a pentaloop closed by a duplex stem in typical a-form conformation. the loop does not form a u-turn motif, as previously predicted. a non-planar a.c.a triple base interaction (hydrogen bonds a13 nh6-c10 o2 and c10 n3-a1 ... | 2001 | 11812846 |
| recombinant thermus aquaticus rna polymerase, a new tool for structure-based analysis of transcription. | the three-dimensional structure of dna-dependent rna polymerase (rnap) from thermophilic thermus aquaticus has recently been determined at 3.3 a resolution. currently, very little is known about t. aquaticus transcription and no genetic system to study t. aquaticus rnap genes is available. to overcome these limitations, we cloned and overexpressed t. aquaticus rnap genes in escherichia coli. overproduced t. aquaticus rnap subunits assembled into functional rnap in vitro and in vivo when coexpres ... | 2001 | 11114902 |
| rubrerythrin and rubredoxin oxidoreductase in desulfovibrio vulgaris: a novel oxidative stress protection system. | evidence is presented for an alternative to the superoxide dismutase (sod)-catalase oxidative stress defense system in desulfovibrio vulgaris (strain hildenborough). this alternative system consists of the nonheme iron proteins, rubrerythrin (rbr) and rubredoxin oxidoreductase (rbo), the product of the rbo gene (also called desulfoferrodoxin). a deltarbo strain of d. vulgaris was found to be more sensitive to internal superoxide exposure than was the wild type. unlike rbo, expression of plasmid- ... | 2001 | 11114906 |
| characterization and evolution of anthranilate 1,2-dioxygenase from acinetobacter sp. strain adp1. | the two-component anthranilate 1,2-dioxygenase of the bacterium acinetobacter sp. strain adp1 was expressed in escherichia coli and purified to homogeneity. this enzyme converts anthranilate (2-aminobenzoate) to catechol with insertion of both atoms of o(2) and consumption of one nadh. the terminal oxygenase component formed an alpha(3)beta(3) hexamer of 54- and 19-kda subunits. biochemical analyses demonstrated one rieske-type [2fe-2s] center and one mononuclear nonheme iron center in each larg ... | 2001 | 11114907 |
| initiation factor 2 of myxococcus xanthus, a large version of prokaryotic translation initiation factor 2. | we have isolated the structural gene for translation initiation factor if2 (infb) from the myxobacterium myxococcus xanthus. the gene (3.22 kb) encodes a 1,070-residue protein showing extensive homology within its g domain and c terminus to the equivalent regions of if2 from escherichia coli. the protein cross-reacts with antibodies raised against e. coli if2 and was able to complement an e. coli infb mutant. the m. xanthus protein is the largest if2 known to date. this is essentially due to a l ... | 2001 | 11114918 |
| vima gene downstream of reca is involved in virulence modulation in porphyromonas gingivalis w83. | a 0.9-kb open reading frame encoding a unique 32-kda protein was identified downstream of the reca gene of porphyromonas gingivalis. reverse transcription-pcr and northern blot analysis showed that both the reca gene and this open reading frame are part of the same transcriptional unit. this cloned fragment was insertionally inactivated using the ermf-ermam antibiotic resistance cassette to create a defective mutant by allelic exchange. when plated on brucella blood agar, the mutant strain, desi ... | 2001 | 11119521 |
| molecular ecology of tetracycline resistance: development and validation of primers for detection of tetracycline resistance genes encoding ribosomal protection proteins. | phylogenetic analysis of tetracycline resistance genes encoding the ribosomal protection proteins (rpps) revealed the monophyletic origin of these genes. the most deeply branching class, exemplified by tet and otra, consisted of genes from the antibiotic-producing organisms streptomyces rimosus and streptomyces lividans. with a high degree of confidence, the corresponding genes of the other seven classes (tet m, tet s, tet o, tet w, tet q, tet t, and tetb p) formed phylogenetically distinct sepa ... | 2001 | 11133424 |
| ihfa gene of the bacterium myxococcus xanthus and its role in activation of carotenoid genes by blue light. | myxococcus xanthus responds to blue light by producing carotenoids. several regulatory genes are known that participate in the light action mechanism, which leads to the transcriptional activation of the carotenoid genes. we had already reported the isolation of a carotenoid-less, tn5-induced strain (mr508), whose mutant site was unlinked to the indicated regulatory genes. here, we show that omegamr508::tn5 affects all known light-inducible promoters in different ways. it blocks the activation o ... | 2001 | 11133949 |
| gene cluster of rhodothermus marinus high-potential iron-sulfur protein: oxygen oxidoreductase, a caa(3)-type oxidase belonging to the superfamily of heme-copper oxidases. | the respiratory chain of the thermohalophilic bacterium rhodothermus marinus contains an oxygen reductase, which uses hipip (high potential iron-sulfur protein) as an electron donor. the structural genes encoding the four subunits of this hipip:oxygen oxidoreductase were cloned and sequenced. the genes for subunits ii, i, iii, and iv (named rcoxa to rcoxd) are found in this order and seemed to be organized in an operon of at least five genes with a terminator structure a few nucleotides downstre ... | 2001 | 11133964 |
| identification of the outer membrane porin of thermus thermophilus hb8: the channel-forming complex has an unusually high molecular mass and an extremely large single-channel conductance. | the outer membrane of the thermophilic bacterium thermus thermophilus was isolated using sucrose step gradient centrifugation. its detergent extracts contained an ion-permeable channel with an extremely high single-channel conductance of 20 ns in 1 m kcl. the channel protein was purified by preparative sodium dodecyl sulfate (sds)-polyacylamide gel electrophoresis. it has a high molecular mass of 185 kda, and its channel-forming ability resists boiling in sds for 10 min. | 2001 | 11133980 |
| a subunit of human nuclear rnase p has atpase activity. | human nuclear rnase p purified from hela cells has atpase activity. this activity is associated with one of the protein subunits of the enzyme, rpp20. thus, human nuclear rnase p, which contains several proteins and one essential rna, has at least one other enzymatic activity in addition to cleavage of phosphoester bonds in rna. the amino acid sequence of rpp20 has a signature motif found in an atpase-containing subunit of a family of protein complexes (abc transporters) that mediate a variety o ... | 2001 | 11149958 |
| hepatitis c virus 3'x region interacts with human ribosomal proteins. | to identify proteins that can bind the 3' untranslated region (utr) of hepatitis c virus (hcv) we screened human cdna libraries using the saccharomyces cerevisiae three-hybrid system. screening with an rna sequence derived from the 3'-terminal 98 nucleotides (3'x region) of an infectious clone of hcv (h77c) yielded clones of human ribosomal proteins l22, l3, s3, and ml3, a mitochondrial homologue of l3. we performed preliminary characterization of the binding between the 3'x region and these pro ... | 2001 | 11152508 |
| development of a reverse transcription-pcr-dna enzyme immunoassay for detection of "norwalk-like" viruses and hepatitis a virus in stool and shellfish. | outbreaks of food- and waterborne gastroenteritis are being increasingly reported throughout the world. the analysis of environmental samples by newer diagnostic techniques such as reverse transcription-pcr (rt-pcr) amplification of nucleic acid has begun to identify human enteric viruses (predominantly "norwalk-like" viruses [nlvs]) as the cause of many of these outbreaks. to streamline nlv detection from environmental samples such as shellfish, we have developed an rt-pcr-oligoprobe amplificat ... | 2001 | 11157239 |
| the crystal structure of the ttcsaa protein: an export-related chaperone from thermus thermophilus. | the csaa protein was first characterized in bacillus subtilis as a molecular chaperone with export-related activities. here we report the 2.0 angstrom-resolution crystal structure of the thermus thermophilus csaa protein, designated ttcsaa. atomic structure and experiments in solution revealed a homodimer as the functional unit. the structure of the ttcsaa monomer is reminiscent of the well known oligonucleotide-binding fold, with the addition of extensions at the n- and c-termini that form an e ... | 2001 | 11157762 |
| structure of the emapii domain of human aminoacyl-trna synthetase complex reveals evolutionary dimer mimicry. | the emapii (endothelial monocyte-activating polypeptide ii) domain is a trna-binding domain associated with several aminoacyl-trna synthetases, which becomes an independent domain with inflammatory cytokine activity upon apoptotic cleavage from the p43 component of the multisynthetase complex. it comprises a domain that is highly homologous to bacterial trna-binding proteins (trbp), followed by an extra domain without homology to known proteins. trbps, which may represent ancient trna chaperones ... | 2001 | 11157763 |
| cloning of the soda gene from corynebacterium melassecola and role of superoxide dismutase in cellular viability. | the soda gene encoding the corynebacterium melassecola manganese-cofactored superoxide dismutase (sod) has been cloned in escherichia coli and sequenced. the gene is transcribed monocistronically; the predicted polypeptide is 200 amino acids long and associates in a homotetrameric, manganese-dependent form, able to complement an sod-deficient e. coli mutant. a second open reading frame, coding for a putative 217-amino-acid protein with high homology to peptide methionine sulfoxide reductases fro ... | 2001 | 11157941 |
| multiple regulatory mechanisms act on the 5' untranslated region of the s-layer gene from thermus thermophilus hb8. | the role of the 5' untranslated region (5'utr) of the s-layer gene from thermus thermophilus was analyzed through the isolation of delta 5'utr mutants. in these mutants the half-life of spla mrna was strongly reduced and slpa transcription was no longer subjected to growth phase-dependent repression. overproduction and detachment of the external envelopes of the mutants were observed in stationary phase. | 2001 | 11157968 |
| role of the tat ransport system in nitrous oxide reductase translocation and cytochrome cd1 biosynthesis in pseudomonas stutzeri. | by transforming n2o to n2, the multicopper enzyme nitrous oxide reductase provides a periplasmic electron sink for a respiratory chain that is part of denitrification. the signal sequence of the enzyme carries the heptameric twin-arginine consensus motif characteristic of the tat pathway. we have identified tat genes of pseudomonas stutzeri and functionally analyzed the unlinked tatc and tate loci. a tatc mutant retained n2o reductase in the cytoplasm in the unprocessed form and lacking the meta ... | 2001 | 11160097 |
| new host-vector system for thermus spp. based on the malate dehydrogenase gene. | a thermus thermophilus hb27 strain was constructed in which the malate dehydrogenase (mdh) gene was deleted. the deltamdh colonies are recognized by a small-colony phenotype. wild-type phenotype is restored by transformation with thermus plasmids or integration vector containing an intact mdh gene. the wild-type phenotype provides a positive selection tool for the introduction of plasmid dna into thermus spp., and because mdh levels can be readily quantified, this host-vector system is a conveni ... | 2001 | 11160114 |
| kh domain: one motif, two folds. | the k homology (kh) module is a widespread rna-binding motif that has been detected by sequence similarity searches in such proteins as heterogeneous nuclear ribonucleoprotein k (hnrnp k) and ribosomal protein s3. analysis of spatial structures of kh domains in hnrnp k and s3 reveals that they are topologically dissimilar and thus belong to different protein folds. thus kh motif proteins provide a rare example of protein domains that share significant sequence similarity in the motif regions but ... | 2001 | 11160884 |
| characterization of rnase p from thermotoga maritima. | the protein subunit of rnase p from a thermophilic bacterium, thermotoga maritima, was overexpressed in and purified from escherichia coli. the cloned protein was reconstituted with the rna subunit transcribed in vitro. the temperature optimum of the holoenzyme is near 50 degrees c, with no enzymatic activity at 65 degrees c or above. this finding is in sharp contrast to the optimal growth temperature of t.maritima, which is near 80 degrees c. however, in heterologous reconstitution experiments ... | 2001 | 11160919 |
| crystal structure of the holliday junction migration motor protein ruvb from thermus thermophilus hb8. | we report here the crystal structure of the ruvb motor protein from thermus thermophilus hb8, which drives branch migration of the holliday junction during homologous recombination. ruvb has a crescent-like architecture consisting of three consecutive domains, the first two of which are involved in atp binding and hydrolysis. dna is likely to interact with a large basic cleft, which encompasses the atp-binding pocket and domain boundaries, whereas the junction-recognition protein ruva may bind a ... | 2001 | 11171970 |
| connection between poly-beta-hydroxybutyrate biosynthesis and growth on c(1) and c(2) compounds in the methylotroph methylobacterium extorquens am1. | several dna regions containing genes involved in poly-beta-hydroxybutyrate (phb) biosynthesis and degradation and also in fatty acid degradation were identified from genomic sequence data and have been characterized in the serine cycle facultative methylotroph methylobacterium extorquens am1. genes involved in phb biosynthesis include those encoding beta-ketothiolase (phaa), nadph-linked acetoacetyl coenzyme a (acetyl-coa) reductase (phab), and phb synthase (phac). phaa and phab are closely link ... | 2001 | 11208803 |
| experimental evolution of enzyme temperature activity profile: selection in vivo and characterization of low-temperature-adapted mutants of pyrococcus furiosus ornithine carbamoyltransferase. | we have obtained mutants of pyrococcus furiosus ornithine carbamoyltransferase active at low temperatures by selecting for complementation of an appropriate yeast mutant after in vivo mutagenesis. the mutants were double ones, still complementing at 15 degrees c, a temperature already in the psychrophilic range. their kinetic analysis is reported. | 2001 | 11208811 |
| occurrence of transsulfuration in synthesis of l-homocysteine in an extremely thermophilic bacterium, thermus thermophilus hb8. | a cell extract of an extremely thermophilic bacterium, thermus thermophilus hb8, cultured in a synthetic medium catalyzed cystathionine gamma-synthesis with o-acetyl-l-homoserine and l-cysteine as substrates but not beta-synthesis with dl-homocysteine and l-serine (or o-acetyl-l-serine). the amounts of synthesized enzymes metabolizing sulfur-containing amino acids were estimated by determining their catalytic activities in cell extracts. the syntheses of cystathionine beta-lyase (ec 4.4.1.8) and ... | 2001 | 11222609 |
| crystal structure of the lrp-like transcriptional regulator from the archaeon pyrococcus furiosus. | the lrpa protein from the hyperthermophilic archaeon pyrococcus furiosus belongs to the lrp/asnc family of transcriptional regulatory proteins, of which the escherichia coli leucine-responsive regulatory protein is the archetype. its crystal structure has been determined at 2.9 a resolution and is the first for a member of the lrp/asnc family, as well as one of the first for a transcriptional regulator from a hyperthermophile. the structure consists of an n-terminal domain containing a helix-tur ... | 2001 | 11230123 |
| genome of the extremely radiation-resistant bacterium deinococcus radiodurans viewed from the perspective of comparative genomics. | the bacterium deinococcus radiodurans shows remarkable resistance to a range of damage caused by ionizing radiation, desiccation, uv radiation, oxidizing agents, and electrophilic mutagens. d. radiodurans is best known for its extreme resistance to ionizing radiation; not only can it grow continuously in the presence of chronic radiation (6 kilorads/h), but also it can survive acute exposures to gamma radiation exceeding 1,500 kilorads without dying or undergoing induced mutation. these characte ... | 2001 | 11238985 |
| crystal structure of hiv-1 reverse transcriptase in complex with a polypurine tract rna:dna. | we have determined the 3.0 a resolution structure of wild-type hiv-1 reverse transcriptase in complex with an rna:dna oligonucleotide whose sequence includes a purine-rich segment from the hiv-1 genome called the polypurine tract (ppt). the ppt is resistant to ribonuclease h (rnase h) cleavage and is used as a primer for second dna strand synthesis. the 'rnase h primer grip', consisting of amino acids that interact with the dna primer strand, may contribute to rnase h catalysis and cleavage spec ... | 2001 | 11250910 |
| two c or not two c: recurrent disruption of zn-ribbons, gene duplication, lineage-specific gene loss, and horizontal gene transfer in evolution of bacterial ribosomal proteins. | ribosomal proteins are encoded in all genomes of cellular life forms and are, generally, well conserved during evolution. in prokaryotes, the genes for most ribosomal proteins are clustered in several highly conserved operons, which ensures efficient co-regulation of their expression. duplications of ribosomal-protein genes are infrequent, and given their coordinated expression and functioning, it is generally assumed that ribosomal-protein genes are unlikely to undergo horizontal transfer. howe ... | 2001 | 11574053 |
| hyperthermophilic enzymes: sources, uses, and molecular mechanisms for thermostability. | enzymes synthesized by hyperthermophiles (bacteria and archaea with optimal growth temperatures of > 80 degrees c), also called hyperthermophilic enzymes, are typically thermostable (i.e., resistant to irreversible inactivation at high temperatures) and are optimally active at high temperatures. these enzymes share the same catalytic mechanisms with their mesophilic counterparts. when cloned and expressed in mesophilic hosts, hyperthermophilic enzymes usually retain their thermal properties, ind ... | 2001 | 11238984 |
| the renaissance of aminoacyl-trna synthesis. | the role of trna as the adaptor in protein synthesis has held an enduring fascination for molecular biologists. over four decades of study, taking in numerous milestones in molecular biology, led to what was widely held to be a fairly complete picture of how trnas and amino acids are paired prior to protein synthesis. however, recent developments in genomics and structural biology have revealed an unexpected array of new enzymes, pathways and mechanisms involved in aminoacyl-trna synthesis. as a ... | 2001 | 11375928 |
| distribution of substitution rates and location of insertion sites in the tertiary structure of ribosomal rna. | the relative substitution rate of each nucleotide site in bacterial small subunit rrna, large subunit rrna and 5s rrna was calculated from sequence alignments for each molecule. two-dimensional and three-dimensional variability maps of the rrnas were obtained by plotting the substitution rates on secondary structure models and on the tertiary structure of the rrnas available from x-ray diffraction results. this showed that the substitution rates are generally low near the centre of the ribosome, ... | 2001 | 11812832 |
| aaa proteins: in search of a common molecular basis. international meeting on cellular functions of aaa proteins. | 2001 | 11713188 | |
| gene cassette pcr: sequence-independent recovery of entire genes from environmental dna. | the vast majority of bacteria in the environment have yet to be cultured. consequently, a major proportion of both genetic diversity within known gene families and an unknown number of novel gene families reside in these uncultured organisms. isolation of these genes is limited by lack of sequence information. where such sequence data exist, pcr directed at conserved sequence motifs recovers only partial genes. here we outline a strategy for recovering complete open reading frames from environme ... | 2001 | 11679351 |
| electrostatics of nanosystems: application to microtubules and the ribosome. | evaluation of the electrostatic properties of biomolecules has become a standard practice in molecular biophysics. foremost among the models used to elucidate the electrostatic potential is the poisson-boltzmann equation; however, existing methods for solving this equation have limited the scope of accurate electrostatic calculations to relatively small biomolecular systems. here we present the application of numerical methods to enable the trivially parallel solution of the poisson-boltzmann eq ... | 2001 | 11517324 |
| functional relevance of the disulfide-linked complex of the n-terminal pdz domain of inad with norpa. | in drosophila, phototransduction is mediated by g(q)-activation of phospholipase c and is a well studied model system for understanding the kinetics of signal initiation, propagation and termination controlled by g proteins. the proper intracellular targeting and spatial arrangement of most proteins involved in fly phototransduction require the multi-domain scaffolding protein inad, composed almost entirely of five pdz domains, which independently bind various proteins including norpa, the relev ... | 2001 | 11500369 |
| survey and summary: the applications of universal dna base analogues. | a universal base analogue forms 'base pairs' with each of the natural dna/rna bases with little discrimination between them. a number of such analogues have been prepared and their applications as biochemical tools investigated. most of these analogues are non-hydrogen bonding, hydrophobic, aromatic 'bases' which stabilise duplex dna by stacking interactions. this review of the literature of universal bases (to 2000) details the analogues investigated, and their uses and limitations are discusse ... | 2001 | 11410649 |
| enhancing the catalytic repertoire of nucleic acids: a systematic study of linker length and rigidity. | the incorporation of potentially catalytic groups in dna is of interest for the in vitro selection of novel deoxyribozymes. a series of 10 c5-modified analogues of 2'-deoxyuridine triphosphate have been synthesised that possess side chains of differing flexibility and bearing a primary amino or imidazole functionality. for each series of nucleotide analogues differing degrees of flexibility of the c5 side chain was achieved through the use of alkynyl, alkenyl and alkyl moieties. the imidazole fu ... | 2001 | 11266559 |
| chloroplast ribosomal protein s7 of chlamydomonas binds to chloroplast mrna leader sequences and may be involved in translation initiation. | certain mutations isolated in the 5' untranslated region (5'utr) of the chloroplast rps7 gene in chlamydomonas reduce expression of reporter genes. second site suppressors in this 5'utr sequence restore reporter expression. 5'utr sequences with the original mutations fail to bind a 20-kd protein, one of five proteins that bind to leaders of several chloroplast genes. however, 5'utrs from suppressed mutants restore binding to this protein but do not bind a 47-kd protein present on the wild type a ... | 2001 | 11158540 |
| aminoacyl-trna synthetases database. | aminoacyl-trna synthetases (aarss) are at the center of the question of the origin of life. they constitute a family of enzymes integrating the two levels of cellular organization: nucleic acids and proteins. aarss arose early in evolution and are believed to be a group of ancient proteins. they are responsible for attaching amino acid residues to their cognate trna molecules, which is the first step in the protein synthesis. the role they play in a living cell is essential for the precise decip ... | 2001 | 11125115 |
| tmrdb (tmrna database). | the tmrna database (tmrdb) is maintained at the university of texas health science center at tyler, texas, and is accessible on the www at url http://psyche.uthct.edu/dbs/tmrdb/tmrdb.++ +html. a tmrdb mirror site is located on the campus of auburn university, auburn, alabama, reachable at the url http://www.ag.auburn.edu/mirror/tmrdb/. since april 1997, the tmrdb has provided sequences of tmrna (previously called 10sa rna), a molecule present in most bacteria and some organelles. this release ad ... | 2000 | 10592214 |
| 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 |