| 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 |
| structure of the topoisomerase vi-b subunit: implications for type ii topoisomerase mechanism and evolution. | type iia and type iib topoisomerases each possess the ability to pass one dna duplex through another in an atp-dependent manner. the role of atp in the strand passage reaction is poorly understood, particularly for the type iib (topoisomerase vi) family. we have solved the structure of the atp-binding subunit of topoisomerase vi (topovi-b) in two states: an unliganded monomer and a nucleotide-bound dimer. we find that topovi-b is highly structurally homologous to the entire 40-43 kda atpase regi ... | 2003 | 12505993 |
| role of ctc from listeria monocytogenes in osmotolerance. | listeria monocytogenes is a food-borne pathogen with the ability to grow under conditions of high osmolarity. in a previous study, we reported the identification of 12 proteins showing high induction after salt stress. one of these proteins is highly similar to the general stress protein ctc of bacillus subtilis. in this study, induction of ctc after salt stress was confirmed at the transcriptional level by using rna slot blot experiments. to explore the role of the ctc gene product in resistanc ... | 2003 | 12513990 |
| 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 |
| uptake and antifungal activity of oligonucleotides in candida albicans. | candida albicans is a significant cause of disease in immunocompromised humans. because the number of people infected by fungal pathogens is increasing, strategies are being developed to target rnas in fungi. this work shows that oligonucleotides can serve as therapeutics against c. albicans. in particular, oligonucleotides are taken up from cell culture medium in an energy-dependent process. after uptake, oligonucleotides, including rna, remain mostly intact after 12 h in culture. for culture c ... | 2003 | 12552085 |
| atp binding by glutamyl-trna synthetase is switched to the productive mode by trna binding. | aminoacyl-trna synthetases catalyze the formation of an aminoacyl-amp from an amino acid and atp, prior to the aminoacyl transfer to trna. a subset of aminoacyl-trna synthetases, including glutamyl-trna synthetase (glurs), have a regulation mechanism to avoid aminoacyl-amp formation in the absence of trna. in this study, we determined the crystal structure of the 'non-productive' complex of thermus thermophilus glurs, atp and l-glutamate, together with those of the glurs.atp, glurs.trna.atp and ... | 2003 | 12554668 |
| the crystal structure of a 26-nucleotide rna containing a hook-turn. | a crystal structure has been obtained for a 26-nucleotide rna that contains the loop e sequence from chromatium minutissimum. rather than having a loop e-like conformation, it consists of an a-form helix that splits into two separate strands following a sheared a-g base pair. the backbone of the strand containing the g of the a-g pair makes a turn of almost 180 degrees in the space of two nucleotides, and then interacts with the minor groove of the helix from which it originates. similar structu ... | 2003 | 12554875 |
| mechanism of molecular interactions for trna(val) recognition by valyl-trna synthetase. | the molecular interactions between valyl-trna synthetase (valrs) and trna(val), with the c34-a35-c36 anticodon, from thermus thermophilus were studied by crystallographic analysis and structure-based mutagenesis. in the valrs-bound structure of trna(val), the successive a35-c36 residues (the major identity elements) of trna(val) are base-stacked upon each other, and fit into a pocket on the alpha-helix bundle domain of valrs. hydrogen bonds are formed between valrs and a35-c36 of trna(val) in a ... | 2003 | 12554880 |
| the deoxyxylulose phosphate pathway of isoprenoid biosynthesis: studies on the mechanisms of the reactions catalyzed by ispg and isph protein. | earlier in vivo studies have shown that the sequential action of the ispg and isph proteins is essential for the reductive transformation of 2c-methyl-d-erythritol 2,4-cyclodiphosphate into dimethylallyl diphosphate and isopentenyl diphosphate via 1-hydroxy-2-methyl-2-(e)-butenyl 4-diphosphate. a recombinant fusion protein comprising maltose binding protein and ispg protein domains was purified from a recombinant escherichia coli strain. the purified protein failed to transform 2c-methyl-d-eryth ... | 2003 | 12571359 |
| the structural basis of cysteine aminoacylation of trnapro by prolyl-trna synthetases. | cysteinyl-trna synthetase is an essential enzyme required for protein synthesis. genes encoding this protein have not been identified in methanocaldococcus jannaschii, methanothermobacter thermautotrophicus, or methanopyrus kandleri. it has previously been proposed that the prolyl-trna synthetase (prors) enzymes in these organisms recognize either proline or cysteine and can aminoacylate their cognate trnas through a dual-specificity mechanism. we report five crystal structures at resolutions be ... | 2003 | 12578991 |
| evidence for rotation of v1-atpase. | v(o)v(1)-atpase is responsible for acidification of eukaryotic intracellular compartments and atp synthesis of archaea and some eubacteria. from the similarity to f(o)f(1)-atp synthase, v(o)v(1)-atpase has been assumed to be a rotary motor, but to date there are no experimental data to support this. here we visualized the rotation of single molecules of v(1)-atpase, a catalytic subcomplex of v(o)v(1)-atpase. v(1)-atpase from thermus thermophilus was immobilized onto a glass surface, and a bead w ... | 2003 | 12598655 |
| orientation and interactions of an essential tryptophan (trp-38) in the capsid subunit of pf3 filamentous virus. | the filamentous bacteriophage pf3 consists of a covalently closed dna single strand of 5833 nucleotides sheathed by approximately 2500 copies of a 44-residue capsid subunit. the capsid subunit contains a single tryptophan residue (trp-38), which is located within the basic c-terminal sequence (-rwikaqff) and is essential for virion assembly in vivo. polarized raman microspectroscopy has been employed to determine the orientation of the trp-38 side chain in the native virus structure. the polariz ... | 2003 | 12609899 |
| genetic diversity: frameshift mechanisms alter coding of a gene (epstein-barr virus lf3 gene) that contains multiple 102-base-pair direct sequence repeats. | frameshift mutations provide recognized mechanisms for changing the coding potential of an organism. here, multiple frameshifts are identified in repetitive sequences within an epstein-barr virus unspliced early gene, lf3, which is associated with the viral replicative cycle and also transcriptionally expressed in many virally associated tumors. on the dna strand encoding lf3, there are three open reading frames, only one of which contains an initiation codon. most (>95%) of the gene consists of ... | 2003 | 12612089 |
| the feci extracytoplasmic-function sigma factor of escherichia coli interacts with the beta' subunit of rna polymerase. | transcription of the ferric citrate transport system of escherichia coli k-12 is mediated by the extracytoplasmic-function (ecf) sigma factor feci, which is activated by ferric citrate in the growth medium. by using a bacterial two-hybrid system, it was shown in vivo that feci binds to the beta' subunit of rna polymerase. the inactive mutant protein feci(k155e) displayed reduced binding to beta', and small deletions along the entire feci protein led to total impairment of beta' binding. in vitro ... | 2003 | 12618442 |
| the rhomboids: a nearly ubiquitous family of intramembrane serine proteases that probably evolved by multiple ancient horizontal gene transfers. | the rhomboid family of polytopic membrane proteins shows a level of evolutionary conservation unique among membrane proteins. they are present in nearly all the sequenced genomes of archaea, bacteria and eukaryotes, with the exception of several species with small genomes. on the basis of experimental studies with the developmental regulator rhomboid from drosophila and the aara protein from the bacterium providencia stuartii, the rhomboids are thought to be intramembrane serine proteases whose ... | 2003 | 12620104 |
| in situ accessibility of small-subunit rrna of members of the domains bacteria, archaea, and eucarya to cy3-labeled oligonucleotide probes. | low accessibility of the rrna is together with cell wall impermeability and low cellular ribosome content a frequent reason for failure of whole-cell fluorescence hybridization with fluorescently labeled oligonucleotide probes. in this study we compare accessibility data for the 16s rrna of escherichia coli (gamma proteobacteria, bacteria) with the phylogenetically distantly related organisms pirellula sp. strain 1 (planctomycetes, bacteria) and metallosphaera sedula (crenarchaeota, archaea) and ... | 2003 | 12620867 |
| characterization of a novel thermostable o-acetylserine sulfhydrylase from aeropyrum pernix k1. | an o-acetylserine sulfhydrylase (oass) from the hyperthermophilic archaeon aeropyrum pernix k1, which shares the pyridoxal 5'-phosphate binding motif with both oass and cystathionine beta-synthase (cbs), was cloned and expressed by using escherichia coli rosetta(de3). the purified protein was a dimer and contained pyridoxal 5'-phosphate. it was shown to be an enzyme with cbs activity as well as oass activity in vitro. the enzyme retained 90% of its activity after a 6-h incubation at 100 degrees ... | 2003 | 12644499 |
| antagonistic signals within the cox2 mrna coding sequence control its translation in saccharomyces cerevisiae mitochondria. | translation of the mitochondrially coded cox2 mrna within the organelle in yeast produces the precursor of cox2p (pre-cox2p), which is processed and assembled into cytochrome c oxidase. the mrna sequence of the first 14 cox2 codons, specifying the pre-cox2p leader peptide, was previously shown to contain a positively acting element required for translation of a mitochondrial reporter gene, arg8(m), fused to the 91st codon of cox2. here we show that three relatively short sequences within the cox ... | 2003 | 12649494 |
| the yeast eif3 subunits tif32/a, nip1/c, and eif5 make critical connections with the 40s ribosome in vivo. | initiation factor 3 (eif3) forms a multifactor complex (mfc) with eif1, eif2, and eif5 that stimulates met-trna(i)(met) binding to 40s ribosomes and promotes scanning or aug recognition. we have previously characterized mfc subcomplexes produced in vivo from affinity-tagged eif3 subunits lacking discrete binding domains for other mfc components. here we asked whether these subcomplexes can bind to 40s ribosomes in vivo. we found that the n- and c-terminal domains of nip1/eif3c, the n- and c-term ... | 2003 | 12651896 |
| high-efficiency generation of antibiotic-resistant strains of streptococcus pneumoniae by pcr and transformation. | we designed a method by which to generate antibiotic-resistant strains of streptococcus pneumoniae at frequencies 4 orders of magnitude greater than the spontaneous mutation rate. the method is based on the natural ability of this organism to be genetically transformed with pcr products carrying sequences homologous to its chromosome. the genes encoding the targets of ciprofloxacin (parc, encoding the parc subunit of dna topoisomerase iv), rifampin (rpob, encoding the beta subunit of rna polymer ... | 2003 | 12654655 |
| non-discriminating and discriminating aspartyl-trna synthetases differ in the anticodon-binding domain. | in most organisms, trna aminoacylation is ensured by 20 aminoacyl-trna synthetases (aarss). in eubacteria, however, synthetases can be duplicated as in thermus thermophilus, which contains two distinct asprss. while asprs-1 is specific, asprs-2 is non-discriminating and aspartylates trna(asp) and trna(asn). the structure at 2.3 a resolution of asprs-2, the first of a non-discriminating synthetase, was solved. it differs from that of asprs-1 but has resemblance to that of discriminating and archa ... | 2003 | 12660169 |
| phylogenetic analysis of anaerobic psychrophilic enrichment cultures obtained from a greenland glacier ice core. | the examination of microorganisms in glacial ice cores allows the phylogenetic relationships of organisms frozen for thousands of years to be compared with those of current isolates. we developed a method for aseptically sampling a sediment-containing portion of a greenland ice core that had remained at -9 degrees c for over 100,000 years. epifluorescence microscopy and flow cytometry results showed that the ice sample contained over 6 x 10(7) cells/ml. anaerobic enrichment cultures inoculated w ... | 2003 | 12676695 |
| ribosomal protein s15 represses its own translation via adaptation of an rrna-like fold within its mrna. | the 16s rrna-binding ribosomal protein s15 is a key component in the assembly of the small ribosomal subunit in bacteria. we have shown that s15 from the extreme thermophile thermus thermophilus represses the translation of its own mrna in vitro, by interacting with the leader segment of its mrna. the s15 mrna-binding site was characterized by footprinting experiments, deletion analysis and site-directed mutagenesis. s15 binding triggers a conformational rearrangement of its mrna into a fold tha ... | 2003 | 12682022 |
| a novel uracil-dna glycosylase family related to the helix-hairpin-helix dna glycosylase superfamily. | cytosine bases can be deaminated spontaneously to uracil, causing dna damage. uracil-dna glycosylase (udg), a ubiquitous uracil-excising enzyme found in bacteria and eukaryotes, is one of the enzymes that repair this kind of dna damage. to date, no udg-coding gene has been identified in methanococcus jannaschii, although its entire genome was deciphered. here, we have identified and characterized a novel udg from m.jannaschii designated as mjudg. it efficiently removed uracil from both single- a ... | 2003 | 12682355 |
| cloning and characterization of trna (m1a58) methyltransferase (trmi) from thermus thermophilus hb27, a protein required for cell growth at extreme temperatures. | n1-methyladenosine (m1a) is found at position 58 in the t-loop of many trnas. in yeast, the formation of this modified nucleoside is catalyzed by the essential trna (m1a58) methyltransferase, a tetrameric enzyme that is composed of two types of subunits (gcd14p and gcd10p). in this report we describe the cloning, expression and characterization of a gcd14p homolog from the hyperthermophilic bacterium thermus thermophilus. the purified recombinant enzyme behaves as a homotetramer of 150 kda by ge ... | 2003 | 12682365 |
| glycyl trna synthetase mutations in charcot-marie-tooth disease type 2d and distal spinal muscular atrophy type v. | charcot-marie-tooth disease type 2d (cmt2d) and distal spinal muscular atrophy type v (dsma-v) are axonal peripheral neuropathies inherited in an autosomal dominant fashion. our previous genetic and physical mapping efforts localized the responsible gene(s) to a well-defined region on human chromosome 7p. here, we report the identification of four disease-associated missense mutations in the glycyl trna synthetase gene in families with cmt2d and dsma-v. this is the first example of an aminoacyl ... | 2003 | 12690580 |
| structure-function studies of escherichia coli rpoh (sigma32) by in vitro linker insertion mutagenesis. | the sigma factor rpoh (sigma(32)) is the key regulator of the heat shock response in escherichia coli. many structural and functional properties of the sigma factor are poorly understood. to gain further insight into rpoh regions that are either important or dispensable for its cellular activity, we generated a collection of tetrapeptide insertion variants by a recently established in vitro linker insertion mutagenesis technique. thirty-one distinct insertions were obtained, and their sigma fact ... | 2003 | 12700252 |
| involvement of the adc operon and manganese homeostasis in streptococcus gordonii biofilm formation. | pioneer oral bacteria, including streptococcus gordonii, initiate the formation of oral biofilms on tooth surfaces, which requires differential expression of genes that recognize unique environmental cues. an s. gordonii::tn917-lac biofilm-defective mutant was isolated by using an in vitro biofilm formation assay. subsequent inverse pcr and sequence analyses identified the transposon insertion to be near the 3' end of an open reading frame (orf) encoding a protein homologous to a streptococcus p ... | 2003 | 12700268 |
| role of 16s rrna helix 44 in ribosomal resistance to hygromycin b. | hygromycin b is an aminoglycoside antibiotic active against prokaryotic and eukaryotic ribosomes. ribosomal alterations in bacteria conferring resistance to hygromycin b have not been described, prompting us to use a single rrna allelic derivative of the gram-positive bacterium mycobacterium smegmatis for investigation of the molecular mechanisms involved in ribosomal resistance to hygromycin b in eubacteria. resistance mutations were found to localize exclusively in 16s rrna. the mutations obse ... | 2003 | 12709313 |
| the versatile thymine dna-glycosylase: a comparative characterization of the human, drosophila and fission yeast orthologs. | human thymine-dna glycosylase (tdg) is well known to excise thymine and uracil from g.t and g.u mismatches, respectively, and was therefore proposed to play a central role in the cellular defense against genetic mutation through spontaneous deamination of 5-methylcytosine and cytosine. in this study, we characterized two newly discovered orthologs of tdg, the drosophila melanogaster thd1p and the schizosaccharomyces pombe thp1p proteins, with an objective to address the function of this subfamil ... | 2003 | 12711670 |
| involvement of conserved asparagine and arginine residues from the n-terminal region in the catalytic mechanism of rat liver and trypanosoma cruzi tyrosine aminotransferases. | rat liver and trypanosoma cruzi tyrosine aminotransferases (tats) share over 40% sequence identity, but differ in their substrate specificities. to explore the molecular features related to these differences, comparative mutagenesis studies were conducted on full length t. cruzi tat and n-terminally truncated rat tat recombinant enzymes. the functionality of arg315 and arg417 in rat tat was investigated for comparison with the conserved arg292 and arg386 in aspartate and bacterial aromatic amino ... | 2003 | 12717026 |
| an unusual mechanism of bacterial gene expression revealed for the rnase p protein of thermus strains. | the rnase p protein gene (rnpa) completely overlaps the rpmh gene (encoding ribosomal protein l34) out of frame in the thermophilic bacterium thermus thermophilus. this results in the synthesis of an extended rnase p protein (c5) of 163 aa and, by inference, of 240 aa in the related strain thermus filiformis. start codons of rnpa and rpmh, apparently governed by the same ribosome binding site, are separated by only 4 nt, which suggests a regulatory linkage between l34 and c5 translation and, acc ... | 2003 | 12719542 |
| expanding trna recognition of a trna synthetase by a single amino acid change. | aspartyl-trna synthetase (asprs) occurs in two types: the discriminating enzyme (d-asprs) forms only asp-trna(asp), whereas the nondiscriminating enzyme (nd-asprs) also synthesizes asp-trna(asn), which is a required intermediate for protein synthesis in many organisms. we attempted to expand the trna recognition of the discriminating thermococcus kodakaraensis asprs to that of a nd-asprs by in vitro mutagenesis. an alignment of 26 archaeal asprs proteins revealed two positions (26 and 85 in the ... | 2003 | 12730374 |
| global expression profiling and physiological characterization of corynebacterium glutamicum grown in the presence of l-valine. | addition of l-valine (50 to 200 mm) to glucose minimal medium had no effect on the growth of wild-type corynebacterium glutamicum atcc 13032 but inhibited the growth of the derived valine production strain val1 [13032 deltailva deltapanbc(pjc1ilvbncd)] in a concentration-dependent manner. in order to explore this strain-specific valine effect, genomewide expression profiling was performed using dna microarrays, which showed that valine caused an increased ilvbn mrna level in val1 but not in the ... | 2003 | 12732517 |
| rna polymerase mutations that impair conversion to a termination-resistant complex by q antiterminator proteins. | bacteriophage lambda q-protein stably binds and modifies rna polymerase (rnap) to a termination-resistant form. we describe amino acid substitutions in rnap that disrupt q-mediated antitermination in vivo and in vitro. the positions of these substitutions in the modeled rnap/dna/rna ternary elongation complex, and their biochemical properties, suggest that they do not define a binding site for q in rnap, but instead act by impairing interactions among core rnap subunits and nucleic acids that ar ... | 2003 | 12756229 |
| an intersubunit contact stimulating transcription initiation by e coli rna polymerase: interaction of the alpha c-terminal domain and sigma region 4. | the c-terminal domain of the escherichia coli rna polymerase (rnap) alpha subunit (alphactd) stimulates transcription initiation by interacting with upstream (up) element dna and a variety of transcription activators. here we identify specific substitutions in region 4.2 of sigma 70 (sigma(70)) and in alphactd that decrease transcription initiation from promoters containing some, but not all, up elements. this decrease in transcription derives from a decrease in the initial equilibrium constant ... | 2003 | 12756230 |
| crystal structure of trna(m1g37)methyltransferase: insights into trna recognition. | trna(m(1)g37)methyltransferase (trmd) catalyzes the transfer of a methyl group from s-adenosyl-l- methionine (adomet) to g(37) within a subset of bacterial trna species, which have a g residue at the 36th position. the modified guanosine is adjacent to and 3' of the anticodon and is essential for the maintenance of the correct reading frame during translation. here we report four crystal structures of trmd from haemophilus influenzae, as binary complexes with either adomet or s-adenosyl-l-homocy ... | 2003 | 12773376 |
| protein synthesis in escherichia coli with mischarged trna. | two types of aspartyl-trna synthetase exist: the discriminating enzyme (d-asprs) forms only asp-trna(asp), while the nondiscriminating one (nd-asprs) also synthesizes asp-trna(asn), a required intermediate in protein synthesis in many organisms (but not in escherichia coli). on the basis of the e. coli trpa34 missense mutant transformed with heterologous nd-asps genes, we developed a system with which to measure the in vivo formation of asp-trna(asn) and its acceptance by elongation factor ef-tu ... | 2003 | 12775689 |
| nmr structure of the active conformation of the varkud satellite ribozyme cleavage site. | substrate cleavage by the neurospora varkud satellite (vs) ribozyme involves a structural change in the stem-loop i substrate from an inactive to an active conformation. we have determined the nmr solution structure of a mutant stem-loop i that mimics the active conformation of the cleavage site internal loop. this structure shares many similarities, but also significant differences, with the previously determined structures of the inactive internal loop. the active internal loop displays differ ... | 2003 | 12782785 |
| functional asymmetry in the lysyl-trna synthetase explored by molecular dynamics, free energy calculations and experiment. | charging of transfer-rna with cognate amino acid is accomplished by the aminoacyl-trna synthetases, and proceeds through an aminoacyl adenylate intermediate. the lysyl-trna synthetase has evolved an active site that specifically binds lysine and atp. previous molecular dynamics simulations of the heat-inducible escherichia coli lysyl-trna synthetase, lysu, have revealed differences in the binding of atp and aspects of asymmetry between the nominally equivalent active sites of this dimeric enzyme ... | 2003 | 12787471 |
| the bacterium thermus thermophilus, like hyperthermophilic archaea, uses a two-step pathway for the synthesis of mannosylglycerate. | the biosynthetic pathway for the synthesis of the compatible solute alpha-mannosylglycerate (mg) in the thermophilic bacterium thermus thermophilus hb27 was identified based on the activities of recombinant mannosyl-3-phosphoglycerate synthase (mpgs) (ec 2.4.1.217) and mannosyl-3-phosphoglycerate phosphatase (mpgp) (ec 3.1.3.70). the sequences of homologous genes from the archaeon pyrococcus horikoshii were used to identify mpgs and mpgp genes in t. thermophilus hb27 genome. both genes were sepa ... | 2003 | 12788726 |
| quantitation of human immunodeficiency virus type 1 in breast milk. | the distribution and stability of human immunodeficiency virus type 1 (hiv-1) in breast milk (bm) components remain largely unknown. inhibitory effects, if any, of bm on hiv rna and dna pcr amplification are poorly understood. we have addressed these issues by using virus-spiked bm samples from hiv-negative women. bm samples from hiv-negative women were spiked with hiv-1 virions or cells containing a single integrated copy of hiv dna (8e5/lav). after incubation under different experimental condi ... | 2003 | 12791866 |
| a snorna that guides the two most conserved pseudouridine modifications within rrna confers a growth advantage in yeast. | ribosomal rnas contain a number of modified nucleotides. the most abundant nucleotide modifications found within rrnas fall into two types: 2'-o-ribose methylations and pseudouridylations. in eukaryotes, small nucleolar guide rnas, the snornas that are the rna components of the snornps, specify the position of these modifications. the 2'-o-ribose methylations and pseudouridylations are guided by the box c/d and box h/aca snornas, respectively. the role of these modifications in rrna remains poor ... | 2003 | 12810910 |
| viridans group streptococci are donors in horizontal transfer of topoisomerase iv genes to streptococcus pneumoniae. | a total of 46 ciprofloxacin-resistant (cip(r)) streptococcus pneumoniae strains were isolated from 1991 to 2001 at the hospital of bellvitge. five of these strains showed unexpectedly high rates of nucleotide variations in the quinolone resistance-determining regions (qrdrs) of their parc, pare, and gyra genes. the nucleotide sequence of the full-length parc, pare, and gyra genes of one of these isolates revealed a mosaic structure compatible with an interspecific recombination origin. southern ... | 2003 | 12821449 |
| dissection of the triple tryptophan electron transfer chain in escherichia coli dna photolyase: trp382 is the primary donor in photoactivation. | in escherichia coli photolyase, excitation of the fad cofactor in its semireduced radical state (fadh*) induces an electron transfer over approximately 15 a from tryptophan w306 to the flavin. it has been suggested that two additional tryptophans are involved in an electron transfer chain fadh* <-- w382 <-- w359 <-- w306. to test this hypothesis, we have mutated w382 into redox inert phenylalanine. ultrafast transient absorption studies showed that, in wt photolyase, excited fadh* decayed with a ... | 2003 | 12835419 |
| contribution of structural genomics to understanding the biology of escherichia coli. | | 2003 | 12837772 |
| determinants of the src homology domain 3-like fold. | in eukaryotes, the src homology domain 3 (sh3) is a very important motif in signal transduction. sh3 domains recognize poly-proline-rich peptides and are involved in protein-protein interactions. until now, the existence of sh3 domains has not been demonstrated in prokaryotes. however, the structure of the c-terminal domain of dtxr clearly shows that the fold of this domain is very similar to that of the sh3 domain. in addition, there is evidence that the c-terminal domain of dtxr binds to poly- ... | 2003 | 12837782 |
| crystal structures of the quinone oxidoreductase from thermus thermophilus hb8 and its complex with nadph: implication for nadph and substrate recognition. | the crystal structures of the zeta-crystalline-like soluble quinone oxidoreductase from thermus thermophilus hb8 (qor(tt)) and of its complex with nadph have been determined at 2.3- and 2.8-a resolutions, respectively. qor(tt) is composed of two domains, and its overall fold is similar to the folds of escherichia coli quinone oxidoreductase (qor(ec)) and horse liver alcohol dehydrogenase. qor(tt) forms a homodimer in the crystal by interaction of the betaf-strands in domain ii, forming a large b ... | 2003 | 12837796 |
| structural basis for thermostability of beta-glycosidase from the thermophilic eubacterium thermus nonproteolyticus hg102. | the three-dimensional structure of a thermostable beta-glycosidase (gly(tn)) from the thermophilic eubacterium thermus nonproteolyticus hg102 was determined at a resolution of 2.4 a. the core of the structure adopts the (betaalpha)(8) barrel fold. the sequence alignments and the positions of the two glu residues in the active center indicate that gly(tn) belongs to the glycosyl hydrolases of retaining family 1. we have analyzed the structural features of gly(tn) related to the thermostability an ... | 2003 | 12837801 |
| detecting protein-protein interactions in the intact cell of bacillus subtilis (atcc 6633). | the salt bridge, paired group-specific reagent cyanogen (ethanedinitrile; c(2)n(2)) converts naturally occurring pairs of functional groups into covalently linked products. cyanogen readily permeates cell walls and membranes. when the paired groups are shared between associated proteins, isolation of the covalently linked proteins allows their identity to be assigned. examination of organisms of known genome sequence permits identification of the linked proteins by mass spectrometric techniques ... | 2003 | 12837803 |
| pilin-like proteins in the extremely thermophilic bacterium thermus thermophilus hb27: implication in competence for natural transformation and links to type iv pilus biogenesis. | the extreme thermophile thermus thermophilus hb27 exhibits high frequencies of natural transformation. although we recently reported identification of the first competence genes in thermus, the molecular basis of dna uptake is unknown. a pilus-like structure is assumed to be involved. twelve genes encoding prepilin-like proteins were identified in three loci in the genome of t. thermophilus. mutational analyses, described in this paper, revealed that one locus, which contains four genes that enc ... | 2003 | 12839734 |
| a modified saccharomyces cerevisiae strain that consumes l-arabinose and produces ethanol. | metabolic engineering is a powerful method to improve, redirect, or generate new metabolic reactions or whole pathways in microorganisms. here we describe the engineering of a saccharomyces cerevisiae strain able to utilize the pentose sugar l-arabinose for growth and to ferment it to ethanol. expanding the substrate fermentation range of s. cerevisiae to include pentoses is important for the utilization of this yeast in economically feasible biomass-to-ethanol fermentation processes. after over ... | 2003 | 12839792 |
| development of antibiotic-overproducing strains by site-directed mutagenesis of the rpsl gene in streptomyces lividans. | certain rpsl (which encodes the ribosomal protein s12) mutations that confer resistance to streptomycin markedly activate the production of antibiotics in streptomyces spp. these rpsl mutations are known to be located in the two conserved regions within the s12 protein. to understand the roles of these two regions in the activation of silent genes, we used site-directed mutagenesis to generate eight novel mutations in addition to an already known (k88e) mutation that is capable of activating ant ... | 2003 | 12839808 |
| molecular phylogenetic exploration of bacterial diversity in a bakreshwar (india) hot spring and culture of shewanella-related thermophiles. | the bacterial diversity of a hot spring in bakreshwar, india, was investigated by a culture-independent approach. 16s ribosomal dna clones derived from the sediment samples were found to be associated with gamma-proteobacteria, cyanobacteria, and green nonsulfur and low-gc gram-positive bacteria. the first of the above phylotypes cobranches with shewanella, a well-known iron reducer. this phylogenetic correlation has been exploited to develop culture conditions for thermophilic iron-reducing mic ... | 2003 | 12839826 |
| direct observation of protonation reactions during the catalytic cycle of cytochrome c oxidase. | cytochrome c oxidase, the terminal protein in the respiratory chain, converts oxygen into water and helps generate the electrochemical gradient used in the synthesis of atp. the catalytic action of cytochrome c oxidase involves electron transfer, proton transfer, and o2 reduction. these events trigger specific molecular changes at the active site, which, in turn, influence changes throughout the protein, including alterations of amino acid side chain orientations, hydrogen bond patterns, and pro ... | 2003 | 12851460 |
| x-ray crystal structures of the wt and a hyper-accurate ribosome from escherichia coli. | protein biosynthesis on the ribosome requires accurate reading of the genetic code in mrna. two conformational rearrangements in the small ribosomal subunit, a closing of the head and body around the incoming trna and an rna helical switch near the mrna decoding site, have been proposed to select for complementary base-pairing between mrna codons and trna anticodons. we determined x-ray crystal structures of the wt and a hyper-accurate variant of the escherichia coli ribosome at resolutions of 1 ... | 2003 | 12853578 |
| a new thermus sp. class-iis enzyme sub-family: isolation of a 'twin' endonuclease tspdti with a novel specificity 5'-atgaa(n(11/9))-3', related to tspgwi, taqii and tth111ii. | the tspdti restriction endonuclease, which shows a novel recognition specificity 5'-atgaa(n(11/9))-3', was isolated from thermus sp. dt. tspdti appears to be a 'twin' of restriction endonuclease tspgwi from thermus sp. gw, as we have previously reported. tspgwi was isolated from the same location as tspdti, it recognizes a related sequence 5'-acgga(n(11/9))-3' and has conserved cleavage positions. both enzymes resemble two other class-iis endonucleases from thermus sp.: taqii and tth111ii. n-ter ... | 2003 | 12853651 |
| ribosomal localization of translation initiation factor if2. | bacterial translation initiation factor if2 is a gtp-binding protein that catalyzes binding of initiator fmet-trna in the ribosomal p site. the topographical localization of if2 on the ribosomal subunits, a prerequisite for understanding the mechanism of initiation complex formation, has remained elusive. here, we present a model for the positioning of if2 in the 70s initiation complex as determined by cleavage of rrna by the chemical nucleases cu(ii):1,10-orthophenanthroline and fe(ii):edta tet ... | 2003 | 12869707 |
| when contemporary aminoacyl-trna synthetases invent their cognate amino acid metabolism. | faithful protein synthesis relies on a family of essential enzymes called aminoacyl-trna synthetases, assembled in a piecewise fashion. analysis of the completed archaeal genomes reveals that all archaea that possess asparaginyl-trna synthetase (asnrs) also display a second orf encoding an asnrs truncated from its anticodon binding-domain (asnrs2). we show herein that pyrococcus abyssi asnrs2, in contrast to asnrs, does not sustain asparaginyl-trnaasn synthesis but is instead capable of converti ... | 2003 | 12874385 |
| identification of protein biochemical functions by similarity search using the molecular surface database ef-site. | the identification of protein biochemical functions based on their three-dimensional structures is strongly required in the post-genome-sequencing era. we have developed a new method to identify and predict protein biochemical functions using the similarity information of molecular surface geometries and electrostatic potentials on the surfaces. our prediction system consists of a similarity search method based on a clique search algorithm and the molecular surface database ef-site (electrostati ... | 2003 | 12876308 |
| crystal structure of the conserved protein tt1542 from thermus thermophilus hb8. | the tt1542 protein from thermus thermophilus hb8 is annotated as a conserved hypothetical protein, and belongs to the duf158 family in the pfam database. a blast search revealed that homologs of tt1542 are present in a wide range of organisms. the tt1542 homologs in eukaryotes, pig-l in mammals, and gpi12 in yeast and protozoa, have n-acetylglucosaminylphosphatidylinositol (glcnac-pi) de-n-acetylase activity. although most of the homologs in prokaryotes are hypothetical and have no known functio ... | 2003 | 12876312 |
| dynamic reorganization of the functionally active ribosome explored by normal mode analysis and cryo-electron microscopy. | combining structural data for the ribosome from x-ray crystallography and cryo-electron microscopy with dynamic models based on elastic network normal mode analysis, an atomically detailed picture of functionally important structural rearrangements that occur during translocation is elucidated. the dynamic model provides a near-atomic description of the ratchet-like rearrangement of the 70s ribosome seen in cryo-electron microscopy, and permits the identification of bridging interactions that ei ... | 2003 | 12878726 |
| a novel is element, is621, of the is110/is492 family transposes to a specific site in repetitive extragenic palindromic sequences in escherichia coli. | an escherichia coli strain, ecor28, was found to have insertions of an identical sequence (1,279 bp in length) at 10 loci in its genome. this insertion sequence (named is621) has one large open reading frame encoding a putative protein that is 326 amino acids in length. a computer-aided homology search using the dna sequence as the query revealed that is621 was homologous to the piv genes, encoding pilin gene invertase (piv). a homology search using the amino acid sequence of the putative protei ... | 2003 | 12897009 |
| temperature-dependent hypermutational phenotype in reca mutants of thermus thermophilus hb27. | the reca gene from thermus thermophilus hb27 was cloned and engineered to obtain insertion (reca::kat) and deletion (deltareca) derivatives. transcription of reca in this extreme thermophile was induced by mitomycin c, leading to the synthesis of a monocistronic mrna. this dna damage-mediated induction was dependent on the integrity of reca. in addition to uv sensitivity, the reca mutants of t. thermophilus showed severe pleiotropic defects, ranging from irregular nucleoid condensation and segre ... | 2003 | 12897010 |
| directed evolution of thermus maltogenic amylase toward enhanced thermal resistance. | the thermostability of maltogenic amylase from thermus sp. strain im6501 (thma) was improved greatly by random mutagenesis using dna shuffling. four rounds of dna shuffling and subsequent recombination of the mutations produced the highly thermostable mutant enzyme thma-dm, which had a total of seven individual mutations. the seven amino acid substitutions in thma-dm were identified as r26q, s169n, i333v, m375t, a398v, q411l, and p453l. the optimal reaction temperature of the recombinant enzyme ... | 2003 | 12902281 |
| is the in situ accessibility of the 16s rrna of escherichia coli for cy3-labeled oligonucleotide probes predicted by a three-dimensional structure model of the 30s ribosomal subunit? | systematic studies on the hybridization of fluorescently labeled, rrna-targeted oligonucleotides have shown strong variations in in situ accessibility. reliable predictions of target site accessibility would contribute to more-rational design of probes for the identification of individual microbial cells in their natural environments. during the past 3 years, numerous studies of the higher-order structure of the ribosome have advanced our understanding of its spatial conformation. these studies ... | 2003 | 12902289 |
| comparative genomics of bacterial zinc regulons: enhanced ion transport, pathogenesis, and rearrangement of ribosomal proteins. | zinc is an important component of many proteins, but in large concentrations it is poisonous to the cell. thus its transport is regulated by zinc repressors zur of proteobacteria and gram-positive bacteria from the bacillus group and adcr of bacteria from the streptococcus group. comparative computational analysis allowed us to identify binding signals of zur repressors gaaatgttatantataacatttc for gamma-proteobacteria, gtaatgtaataacattac for the agrobacterium group, gatatgttataacatatc for the rh ... | 2003 | 12904577 |
| glutathione synthetase homologs encode alpha-l-glutamate ligases for methanogenic coenzyme f420 and tetrahydrosarcinapterin biosyntheses. | proteins in the atp-grasp superfamily of amide bond-forming ligases have evolved to function in a number of unrelated biosynthetic pathways. previously identified homologs encoding glutathione synthetase, d-alanine:d-alanine ligase and the bacterial ribosomal protein s6:glutamate ligase have been vertically inherited within certain organismal lineages. although members of this specificity-diverse superfamily share a common reaction mechanism, the nonoverlapping set of amino acid and peptide subs ... | 2003 | 12909715 |
| analysis of the dna joining repertoire of chlorella virus dna ligase and a new crystal structure of the ligase-adenylate intermediate. | chlorella virus dna ligase is the smallest eukaryotic atp-dependent dna ligase known; it suffices for yeast cell growth in lieu of the essential yeast dna ligase cdc9. the chlorella virus ligase-adenylate intermediate has an intrinsic nick sensing function and its dna footprint extends 8-9 nt on the 3'-hydroxyl (3'-oh) side of the nick and 11-12 nt on the 5'-phosphate (5'-po4) side. here we establish the minimal length requirements for ligatable 3'-oh and 5'-po4 strands at the nick (6 nt) and de ... | 2003 | 12930960 |
| mutations in rpobc suppress the defects of a sinorhizobium meliloti rela mutant. | the nitrogen-fixing symbiosis between sinorhizobium meliloti and medicago sativa requires complex physiological adaptation by both partners. one method by which bacteria coordinately control physiological adaptation is the stringent response, which is triggered by the presence of the nucleotide guanosine tetraphosphate (ppgpp). ppgpp, produced by the rela enzyme, is thought to bind to and alter the ability of rna polymerase (rnap) to initiate and elongate transcription and affect the affinity of ... | 2003 | 12949113 |
| inference of protein function and protein linkages in mycobacterium tuberculosis based on prokaryotic genome organization: a combined computational approach. | the genome of mycobacterium tuberculosis was analyzed using recently developed computational approaches to infer protein function and protein linkages. we evaluated and employed a method to infer genes likely to belong to the same operon, as judged by the nucleotide distance between genes in the same genomic orientation, and combined this method with those of the rosetta stone, phylogenetic profile and conserved gene neighbor computational methods for the inference of protein function. | 2003 | 12952538 |
| characterization of microbial communities in gas industry pipelines. | culture-independent techniques, denaturing gradient gel electrophoresis (dgge) analysis, and random cloning of 16s rrna gene sequences amplified from community dna were used to determine the diversity of microbial communities in gas industry pipelines. samples obtained from natural gas pipelines were used directly for dna extraction, inoculated into sulfate-reducing bacterium medium, or used to inoculate a reactor that simulated a natural gas pipeline environment. the variable v2-v3 (average siz ... | 2003 | 12957923 |
| molecular analysis of echovirus 13 isolates and aseptic meningitis, spain. | echovirus 13 (ev13), considered rare, was reported worldwide in 2000, mostly related to aseptic meningitis outbreaks. in spain, 135 ev13 isolates were identified. the genetic relationships between 64 representative strains from spain and other reported isolates from the united states, germany, italy, japan, and sweden were described by analyzing the partial sequence of the major capsid protein (vp1) gene. the strains from spain were clearly identified as ev13 (79.5% similarity with the ev13 refe ... | 2003 | 12967490 |
| single-nucleotide polymorphism genotyping on optical thin-film biosensor chips. | single-nucleotide polymorphisms (snps) constitute the bulk of human genetic variation and provide excellent markers to identify genetic factors contributing to complex disease susceptibility. a rapid, sensitive, and inexpensive assay is important for large-scale snp scoring. here we report the development of a multiplex snp detection system using silicon chips coated to create a thin-film optical biosensor. allele-discriminating, aldehyde-labeled oligonucleotides are arrayed and covalently attac ... | 2003 | 12975525 |
| the extended loops of ribosomal proteins l4 and l22 are not required for ribosome assembly or l4-mediated autogenous control. | ribosomal proteins l4 and l22 both have a globular domain that sits on the surface of the large ribosomal subunit and an extended loop that penetrates its core. the tips of both loops contribute to the lining of the peptide exit tunnel and have been implicated in a gating mechanism that might regulate the exit of nascent peptides. also, the extensions of l4 and l22 contact multiple domains of 23s rrna, suggesting they might facilitate rrna folding during ribosome assembly. to learn more about th ... | 2003 | 13130133 |
| a noncognate aminoacyl-trna synthetase that may resolve a missing link in protein evolution. | efforts to delineate the advent of many enzymes essential to protein translation are often limited by the fact that the modern genetic code evolved before divergence of the tree of life. glutaminyl-trna synthetase (glnrs) is one noteworthy exception to the universality of the translation apparatus. in eukaryotes and some bacteria, this enzyme is essential for the biosynthesis of gln-trnagln, an obligate intermediate in translation. glnrs is absent, however, in archaea, and most bacteria, organel ... | 2003 | 13679580 |
| role of residual structure in the unfolded state of a thermophilic protein. | ribonucleases h from the thermophilic bacterium thermus thermophilus and the mesophile escherichia coli demonstrate a dramatic and surprising difference in their change in heat capacity upon unfolding (deltacp degrees ). the lower deltacp degrees of the thermophilic protein directly contributes to its higher thermal denaturation temperature (tm). we propose that this deltacp degrees difference originates from residual structure in the unfolded state of the thermophilic protein; we verify this hy ... | 2003 | 14504401 |
| genetic characterization of optochin-susceptible viridans group streptococci. | two clinical isolates of viridans group streptococci (vs) with different degrees of susceptibility to optochin (opt), i.e., fully opt-susceptible (opt(s)) vs strain 1162/99 (for which the mic was equal to that for streptococcus pneumoniae, 0.75 micro g/ml) and intermediate opt(s) vs strain 1174/97 (mic, 6 micro g/ml) were studied. besides being opt susceptible, they showed characteristics typical of vs, such as bile insolubility; lack of reaction with pneumococcal capsular antibodies; and lack o ... | 2003 | 14506029 |
| osmotic adaptation of thermus thermophilus rq-1: lesson from a mutant deficient in synthesis of trehalose. | strains of thermus thermophilus accumulate primarily trehalose and smaller amounts of mannosylglycerate in response to salt stress in yeast extract-containing media (o. c. nunes, c. m. manaia, m. s. da costa, and h. santos, appl. environ. microbiol. 61:2351-2357, 1995). a 2.4-kbp dna fragment from t. thermophilus strain rq-1 carrying otsa (encoding trehalose-phosphate synthase [tps]), otsb (encoding trehalose-phosphate phosphatase [tpp]), and a short sequence of the 5' end of tres (trehalose syn ... | 2003 | 14526004 |
| atp-bound conformation of topoisomerase iv: a possible target for quinolones in streptococcus pneumoniae. | topoisomerase iv, a c(2)e(2) tetramer, is involved in the topological changes of dna during replication. this enzyme is the target of antibacterial compounds, such as the coumarins, which target the atp binding site in the pare subunit, and the quinolones, which bind, outside the active site, to the quinolone resistance-determining region (qrdr). after site-directed and random mutagenesis, we found some mutations in the atp binding site of pare near the dimeric interface and outside the qrdr tha ... | 2003 | 14526026 |
| the ribosome and yidc. new insights into the biogenesis of escherichia coli inner membrane proteins. | in the bacterium escherichia coli, inner membrane proteins (imps) are generally targeted through the signal recognition particle pathway to the sec translocon, which is capable of both linear transport into the periplasm and lateral transport into the lipid bilayer. lateral transport seems to be assisted by the imp yidc. in this article, we discuss recent observations that point to a key role for the ribosome in imp targeting and to the diverse roles of yidc in imp assembly. | 2003 | 14528263 |
| structures of deacylated trna mimics bound to the e site of the large ribosomal subunit. | during translation, trnas cycle through three binding sites on the ribosome: the a, the p, and the e sites. we have determined the structures of complexes between the haloarcula marismortui large ribosomal subunit and two different e site substrates: a deacylated trna acceptor stem minihelix and a cca-acceptor end. both of these trna mimics contain analogs of adenosine 76, the component responsible for a large proportion of e site binding affinity. they bind in the center of the loop-extension o ... | 2003 | 14561884 |
| the saccharomyces cerevisiae u2 snrna:pseudouridine-synthase pus7p is a novel multisite-multisubstrate rna:psi-synthase also acting on trnas. | the saccharomyces cerevisiae pus7 protein was recently characterized as a novel rna:pseudouridine (psi)-synthase acting at position 35 in u2 snrna. however, u2 snrna was the only potential substrate tested for this enzyme. in this work, we demonstrated that although pus7p is responsible for the formation of only one of the six psi residues present in yeast usnrnas, it catalyzes u to psi conversion at position 13 in cytoplasmic trnas and at position 35 in pre-trna(tyr). sites of rna modification ... | 2003 | 14561887 |
| microbial community structure in midgut and hindgut of the humus-feeding larva of pachnoda ephippiata (coleoptera: scarabaeidae). | the guts of soil-feeding macroinvertebrates contain a complex microbial community that is involved in the transformation of ingested soil organic matter. in a companion paper (t. lemke, u. stingl, m. egert, m. w. friedrich, and a. brune, appl. environ. microbiol. 69:6650-6658, 2003), we show that the gut of our model organism, the humivorous larva of the cetoniid beetle pachnoda ephippiata, is characterized by strong midgut alkalinity, high concentrations of microbial fermentation products, and ... | 2003 | 14602626 |
| analysis, characterization, and loci of the tuf genes in lactobacillus and bifidobacterium species and their direct application for species identification. | we analyzed the tuf gene, encoding elongation factor tu, from 33 strains representing 17 lactobacillus species and 8 bifidobacterium species. the tuf sequences were aligned and used to infer phylogenesis among species of lactobacilli and bifidobacteria. we demonstrated that the synonymous substitution affecting this gene renders elongation factor tu a reliable molecular clock for investigating evolutionary distances of lactobacilli and bifidobacteria. in fact, the phylogeny generated by these tu ... | 2003 | 14602655 |
| comparative analysis of editosome proteins in trypanosomatids. | detailed comparisons of 16 editosome proteins from trypanosoma brucei, trypanosoma cruzi and leishmania major identified protein motifs associated with catalysis and protein or nucleic acid interactions that suggest their functions in rna editing. five related proteins with rnase iii-like motifs also contain a u1-like zinc finger and either dsrbm or pumilio motifs. these proteins may provide the endoribonuclease function in editing. two other related proteins, at least one of which is associated ... | 2003 | 14602897 |
| enhancement of dna, cdna synthesis and fidelity at high temperatures by a dimeric single-stranded dna-binding protein. | bacterial single-stranded dna-binding proteins (ssbs) are required for dna replication and repair. we have over-expressed and purified the native form and two his-tagged fusions of the ssb from thermus thermophilus (tthssb). the three proteins were found as dimers in solution. they bound in vitro to single-stranded dna specifically over a temperature range of 4-80 degrees c, and the wild-type protein could withstand incubation at 94 degrees c for 2 min. addition of tthssb to pcr halved the elong ... | 2003 | 14602905 |
| j protein cochaperone of the mitochondrial inner membrane required for protein import into the mitochondrial matrix. | the major hsp70 of the mitochondrial matrix (ssc1 in yeast) is critically important for the translocation of proteins from the cytosol, across the mitochondrial inner membrane, and into the matrix. tim44, a peripheral inner membrane protein with limited sequence similarity to the j domain of j-type cochaperones, tethers ssc1 to the import channel. here we report that, unlike a j protein, tim44 does not stimulate the atpase activity of ssc1, nor does it affect the stimulation by either a known mi ... | 2003 | 14605210 |
| coevolution of an aminoacyl-trna synthetase with its trna substrates. | glutamyl-trna synthetases (glurss) occur in two types, the discriminating and the nondiscriminating enzymes. they differ in their choice of substrates and use either trnaglu or both trnaglu and trnagln. although most organisms encode only one glurs, a number of bacteria encode two different glurs proteins; yet, the trna specificity of these enzymes and the reason for such gene duplications are unknown. a database search revealed duplicated glurs genes in >20 bacterial species, suggesting that th ... | 2003 | 14615592 |
| products transcribed from rearranged rrn genes of escherichia coli can assemble to form functional ribosomes. | to examine the flexibility of rrna operons with respect to fundamental organization, transcription, processing, and assembly of ribosomes, operon variations were introduced by a plasmid into an escherichia coli strain that has deletions of all chromosomal copies of rrna genes. in the reconstructed operons, a salmonella intervening sequence (ivs) from 23s helix 45 was introduced into the e. coli 23s gene at the same position. three different constructs of the e. coli 16s gene were then placed who ... | 2003 | 14617656 |
| quantification of alternatively spliced fgfr2 rnas using the rna invasive cleavage assay. | the regulated splicing of fibroblast growth factor receptor-2 (fgfr2) transcripts leads to tissue-specific expression of distinct receptor isoforms. these isoforms contain two different versions of the ligand binding ig-like domain iii, which are encoded by exon iiib or exon iiic. the mutually exclusive use of exon iiib and exon iiic can be recapitulated in tissue culture using dt3 and at3 rat prostate carcinoma cells. we used this well-characterized system to evaluate the precision and accuracy ... | 2003 | 14624010 |
| solution nmr structure of the 30s ribosomal protein s28e from pyrococcus horikoshii. | we report nmr assignments and solution structure of the 71-residue 30s ribosomal protein s28e from the archaean pyrococcus horikoshii, target jr19 of the northeast structural genomics consortium. the structure, determined rapidly with the aid of automated backbone resonance assignment (autoassign) and automated structure determination (autostructure) software, is characterized by a four-stranded beta-sheet with a classic greek-key topology and an oligonucleotide/oligosaccharide beta-barrel (ob) ... | 2003 | 14627742 |
| an archaebacteria-derived glutamyl-trna synthetase and trna pair for unnatural amino acid mutagenesis of proteins in escherichia coli. | the addition of novel amino acids to the genetic code of escherichia coli involves the generation of an aminoacyl-trna synthetase and trna pair that is 'orthogonal', meaning that it functions independently of the synthetases and trnas endogenous to e.coli. the amino acid specificity of the orthogonal synthetase is then modified to charge the corresponding orthogonal trna with an unnatural amino acid that is subsequently incorporated into a polypeptide in response to a nonsense or missense codon. ... | 2003 | 14627803 |
| regulation of lysine biosynthesis and transport genes in bacteria: yet another rna riboswitch? | comparative analysis of genes, operons and regulatory elements was applied to the lysine biosynthetic pathway in available bacterial genomes. we report identification of a lysine-specific rna element, named the lys element, in the regulatory regions of bacterial genes involved in biosynthesis and transport of lysine. similarly to the previously described rna regulatory elements for three vitamins (riboflavin, thiamin and cobalamin), purine and methionine regulons, this regulatory rna structure i ... | 2003 | 14627808 |
| ribosomal proteins rps0 and rps21 of saccharomyces cerevisiae have overlapping functions in the maturation of the 3' end of 18s rrna. | the rps0 proteins of saccharomyces cerevisiae are components of the 40s ribosomal subunit required for maturation of the 3' end of 18s rrna. drosophila and human homologs of the rps0 proteins physically interact with rps21 proteins, and decreased expression of both proteins in drosophila impairs control of cellular proliferation in hematopoietic organs during larval development. here, we characterize the yeast rps21a/b genes and show that strains where both genes are disrupted are not viable. re ... | 2003 | 14627813 |