Publications

sortase b, a new class of sortase in listeria monocytogenes.	sortases are transamidases that covalently link proteins to the peptidoglycan of gram-positive bacteria. the genome of the pathogenic bacterium listeria monocytogenes encodes two sortases genes, srta and srtb. the srta gene product anchors internalin and some other lpxtg-containing proteins to the listerial surface. here, we focus on the role of the second sortase, srtb. whereas srta acts on most of the proteins in the peptidoglycan fraction, srtb appears to target minor amounts of surface polyp ...	2004	15028680
reconstruction of the central carbohydrate metabolism of thermoproteus tenax by use of genomic and biochemical data.	the hyperthermophilic, facultatively heterotrophic crenarchaeum thermoproteus tenax was analyzed using a low-coverage shotgun-sequencing approach. a total of 1.81 mbp (representing 98.5% of the total genome), with an average gap size of 100 bp and 5.3-fold coverage, are reported, giving insights into the genome of t. tenax. genome analysis and biochemical studies enabled us to reconstruct its central carbohydrate metabolism. t. tenax uses a variant of the reversible embden-meyerhof-parnas (emp) ...	2004	15028704
the arabidopsis cytochrome p450 cyp707a encodes aba 8'-hydroxylases: key enzymes in aba catabolism.	the hormonal action of abscisic acid (aba) in plants is controlled by the precise balance between its biosynthesis and catabolism. in plants, aba 8'-hydroxylation is thought to play a predominant role in aba catabolism. aba 8'-hydroxylase was shown to be a cytochrome p450 (p450); however, its corresponding gene had not been identified. through phylogenetic and dna microarray analyses during seed imbibition, the candidate genes for this enzyme were narrowed down from 272 arabidopsis p450 genes. t ...	2004	15044947
methionine sulfoxide reductases protect ffh from oxidative damages in escherichia coli.	in proteins, methionine residues are primary targets for oxidation. methionine oxidation is reversed by methionine sulfoxide reductases a and b, a class of highly conserved enzymes. ffh protein, a component of the ubiquitous signal recognition particle, contains a methionine-rich domain, interacting with a small 4.5s rna. in vitro analyses reported here show that: (i) oxidized ffh is unable to bind 4.5s rna, (ii) oxidized ffh contains methionine sulfoxide residues, (iii) oxidized ffh is a substr ...	2004	15057280
crystallographic snapshots of a replicative dna polymerase encountering an abasic site.	abasic sites are common dna lesions, which are strong blocks to replicative polymerases and are potentially mutagenic when bypassed. we report here the 2.8 a structure of the bacteriophage rb69 replicative dna polymerase attempting to process an abasic site analog. four different complexes were captured in the crystal asymmetric unit: two have dna in the polymerase active site whereas the other two molecules are in the exonuclease mode. when compared to complexes with undamaged dna, the dna surr ...	2004	15057283
the role of rna polymerase sigma subunit in promoter-independent initiation of transcription.	in bacteria, initiation of transcription depends on the rna polymerase sigma subunit, which brings catalytically proficient rna polymerase core to promoters by binding to specific dna elements located upstream of the transcription start point. here, we study sigma-dependent synthesis of a transcript that is used to prime replication of the single-stranded genome of bacteriophage m13. we show that, in this system, sigma plays no role in dna recognition, which is accomplished solely through rna po ...	2004	15070729
identification of the xpg region that causes the onset of cockayne syndrome by using xpg mutant mice generated by the cdna-mediated knock-in method.	in addition to xeroderma pigmentosum (xp), mutations in the human xpg gene cause early onset of cockayne syndrome (cs) in some patients (xpg/cs). the cs-causing mutations in such patients all produce truncated xpg proteins. to test the hypothesis that the cs phenotype, with characteristics such as growth retardation and a short life span in xpg/cs patients, results from c-terminal truncations, we constructed mutants with c-terminal truncations in mouse xpg (xpg) (from residue d811 to the stop co ...	2004	15082767
functional interaction between tfiib and the rpb2 subunit of rna polymerase ii: implications for the mechanism of transcription initiation.	the general transcription factor tfiib is required for accurate initiation, although the mechanism by which rna polymerase ii (rnap ii) identifies initiation sites is not well understood. here we describe results from genetic and biochemical analyses of an altered form of yeast tfiib containing an arginine-78 --> cysteine (r78c) replacement in the "b-finger" domain. tfiib r78c shifts start site selection downstream of normal and confers a cold-sensitive growth defect (csm(-)). suppression of the ...	2004	15082791
distinctive protein signatures provide molecular markers and evidence for the monophyletic nature of the deinococcus-thermus phylum.	the deinococcus-thermus group of species is currently recognized as a distinct phylum solely on the basis of their branching in 16s rrna trees. no unique biochemical or molecular characteristics that can distinguish this group from all other bacteria are known at present. in this work, we describe eight conserved indels (viz., inserts or deletions) in seven widely distributed proteins that are distinctive characteristics of the deinococcus-thermus phylum but are not found in any other group of b ...	2004	15126471
a new method for detection of pfmdr1 mutations in plasmodium falciparum dna using real-time pcr.	surveillance for drug-resistant plasmodium falciparum should be a component of malaria control programmes. real-time pcr methods for the detection of parasite single-nucleotide polymorphisms (snps) and gene amplification could be useful survellance tools.	2004	15132750
topology of the substrate-binding site of a lys49-phospholipase a2 influences ca2+-independent membrane-damaging activity.	bthtx-i (bothropstoxin-i) is a myotoxic lys49-pla2 (phospholipase a2 with lys49) isolated from bothrops jararacussu venom, which damages liposome membranes by a ca2+-independent mechanism. the highly conserved phe5/ala102/phe106 motif in the hydrophobic substrate-binding site of the asp49-pla2s is substituted by leu5/val102/leu106 in the lys49-pla2s. the leu5/val102/leu106 triad in bthtx-i was sequentially mutated via all single- and double-mutant combinations to the phe5/ala102/phe106 mutant. a ...	2004	15147240
crystal structure of the deinococcus radiodurans single-stranded dna-binding protein suggests a mechanism for coping with dna damage.	single-stranded dna (ssdna)-binding (ssb) proteins are uniformly required to bind and protect single-stranded intermediates in dna metabolic pathways. all bacterial and eukaryotic ssb proteins studied to date oligomerize to assemble four copies of a conserved domain, called an oligonucleotide/oligosaccharide-binding (ob) fold, that cooperate in nonspecific ssdna binding. the vast majority of bacterial ssb family members function as homotetramers, with each monomer contributing a single ob fold. ...	2004	15159541
cloning, sequencing, and characterization of a heat- and alkali-stable type i pullulanase from anaerobranca gottschalkii.	the gene encoding a type i pullulanase was identified from the genome sequence of the anaerobic thermoalkaliphilic bacterium anaerobranca gottschalkii. in addition, the homologous gene was isolated from a gene library of anaerobranca horikoshii and sequenced. the proteins encoded by these two genes showed 39% amino acid sequence identity to the pullulanases from the thermophilic anaerobic bacteria fervidobacterium pennivorans and thermotoga maritima. the pullulanase gene from a. gottschalkii (en ...	2004	15184138
protein tolerance to random amino acid change.	mutagenesis of protein-encoding sequences occurs ubiquitously; it enables evolution, accumulates during aging, and is associated with disease. many biotechnological methods exploit random mutations to evolve novel proteins. to quantitate protein tolerance to random change, it is vital to understand the probability that a random amino acid replacement will lead to a protein's functional inactivation. we define this probability as the "x factor." here, we develop a broadly applicable approach to c ...	2004	15197260
efficient and error-free replication past a minor-groove dna adduct by the sequential action of human dna polymerases iota and kappa.	dna polymerase iota (poliota) is a member of the y family of dna polymerases, which promote replication through dna lesions. the role of poliota in lesion bypass, however, has remained unclear. poliota is highly unusual in that it incorporates nucleotides opposite different template bases with very different efficiencies and fidelities. since interactions of dna polymerases with the dna minor groove provide for the nearly equivalent efficiencies and fidelities of nucleotide incorporation opposit ...	2004	15199127
evidence for transcriptional and posttranscriptional alterations of the sodium/iodide symporter expression in hypofunctioning benign and malignant thyroid tumors.	the uptake of iodide by epithelial thyroid cells requires the expression of a specific transporter, the na(+)/i(-) symporter, nis. benign and malignant thyroid tumors of epithelial origin show a decrease up to a loss of iodide uptake activity. previous studies of the human nis (hnis) gene expression in these tumors, based on the amplification of transcripts and/or immunohistochemical detection of the protein, have yielded divergent data; hnis expression was found either increased or decreased. t ...	2004	15215159
bacillus subtilis ydih is a direct negative regulator of the cydabcd operon.	during aerobic respiration, bacillus subtilis utilizes three terminal oxidases, cytochromes aa3, caa3, and bd. cytochrome bd is encoded by the cydabcd operon. we report here the first identification of a regulator for the cydabcd operon, ydih. while working with deltaresde mutant strains, we identified colonies which contained suppressor mutations (cmp) which bypassed the requirement for resd for all phenotypes not associated with cytochrome aa3 or caa3. mapping identified a class of tn10 insert ...	2004	15231791
expression and functional activity of ppargamma in pancreatic beta cells.	rosiglitazone is an agonist of peroxisome proliferator activated receptor-gamma (ppargamma) and ameliorates insulin resistance in type ii diabetes. in addition, it may also promote increased pancreatic beta-cell viability, although it is not known whether this effect is mediated by a direct action on the beta cell. we have investigated this possibility. semiquantitative real-time reverse transcription-polymerase chain reaction analysis (taqman) revealed that freshly isolated rat islets and the c ...	2004	15237101
the strong efficiency of the escherichia coli gapa p1 promoter depends on a complex combination of functional determinants.	the escherichia coli multi-promoter region of the gapa gene ensures a high level of gapdh (glyceraldehyde-3-phosphate dehydrogenase) production under various growth conditions. in the exponential phase of growth, gapa mrnas are mainly initiated at the highly efficient gapa p1 promoter. in the present study, by using site-directed mutagenesis and chemical probing of the rpo (open complex) formed by esigma70 (holoenzyme associated with sigma70) rnap (rna polymerase) at promoter gapa p1, we show th ...	2004	15250823
substrate specificity of helicobacter pylori histone-like hu protein is determined by insufficient stabilization of dna flexure points.	the histone-like hu protein is ubiquitous in the eubacteria. a role for escherichia coli hu in compaction of the bacterial genome has been reported, along with regulatory roles in dna replication, transposition, repair and transcription. we show here that hu from the human pathogen helicobacter pylori, which has been implicated in the development of ulcers and gastric cancer, exhibits enhanced thermal stability and distinct dna substrate specificity. thermal denaturation of hpyhu (h. pylori hu) ...	2004	15255779
construction of a chimeric thermostable pyrophosphatase to facilitate its purification and immobilization by using the choline-binding tag.	the thermophilic inorganic pyrophosphatase (pyr) from thermus thermophilus has been produced in escherichia coli fused to the c terminus of the choline-binding tag (chb tag) derived from the choline-binding domain (chbd) of pneumococcal lyta autolysin. the chimeric chbd-pyr protein retains its thermostable activity and can be purified in a single step by deae-cellulose affinity chromatography. pyr can be further released from the chbd by thrombin, using the specific protease recognition site inc ...	2004	15294797
use of 16s ribosomal dna pcr and denaturing gradient gel electrophoresis for analysis of the microfloras of healing and nonhealing chronic venous leg ulcers.	the bacterial microfloras of 8 healing and 10 nonhealing chronic venous leg ulcers were compared by using a combination of cultural analysis and denaturing gradient gel electrophoresis (dgge) of pcr-amplified 16s rrna gene products. cultural analysis of the microflora revealed that the majority of both wound types carried the aerobes staphylococcus and pseudomonas spp. (89 and 80%, respectively). sequencing of 16s ribosomal dnas selected on the basis of dgge profiling allowed the identification ...	2004	15297496
amino acid contacts between sigma 70 domain 4 and the transcription activators rhas and rhar.	the rhas and rhar proteins are transcription activators that respond to the availability of l-rhamnose and activate transcription of the operons in the escherichia coli l-rhamnose catabolic regulon. rhar activates transcription of rhasr, and rhas activates transcription of the operon that encodes the l-rhamnose catabolic enzymes, rhabad, as well as the operon that encodes the l-rhamnose transport protein, rhat. rhas is 30% identical to rhar at the amino acid level, and both are members of the ar ...	2004	15342598
dependence of dna polymerase replication rate on external forces: a model based on molecular dynamics simulations.	molecular dynamics simulations are presented for a thermus aquaticus (taq) dna polymerase i complex (consisting of the protein, the primer-template dna strands, and the incoming nucleotide) subjected to external forces. the results obtained with a force applied to the dna template strand provide insights into the effect of the tension on the activity of the enzyme. at forces below 30 pn a local model based on the parameters determined from the simulations, including the restricted motion of the ...	2004	15345530
reverse transcriptase activity innate to dna polymerase i and dna topoisomerase i proteins of streptomyces telomere complex.	replication of streptomyces linear chromosomes and plasmids proceeds bidirectionally from a central origin, leaving recessed 5' termini that are extended by a telomere binding complex. this complex contains both a telomere-protecting terminal protein (tpg) and a telomere-associated protein that interacts with tpg and the dna ends of linear streptomyces replicons. by using histidine-tagged telomere-associated protein (tap) as a scaffold, we identified dna polymerase (pola) and topoisomerase i (to ...	2004	15353591
mechanism of association and reciprocal activation of two gtpases.	the signal recognition particle (srp) mediates the cotranslational targeting of nascent proteins to the eukaryotic endoplasmic reticulum membrane or the bacterial plasma membrane. during this process, two gtpases, one in srp and one in the srp receptor (named ffh and ftsy in bacteria, respectively), form a complex in which both proteins reciprocally activate the gtpase reaction of one another. here, we explore by site-directed mutagenesis the role of 45 conserved surface residues in the ffh-ftsy ...	2004	15383838
the dna primase of sulfolobus solfataricus is activated by substrates containing a thymine-rich bubble and has a 3'-terminal nucleotidyl-transferase activity.	dna primases are responsible for the synthesis of the short rna primers that are used by the replicative dna polymerases to initiate dna synthesis on the leading- and lagging-strand at the replication fork. in this study, we report the purification and biochemical characterization of a dna primase (sso dna primase) from the thermoacidophilic crenarchaeon sulfolobus solfataricus. the sso dna primase is a heterodimer composed of two subunits of 36 kda (small subunit) and 38 kda (large subunit), wh ...	2004	15459292
regulated communication between the upstream face of rna polymerase and the beta' subunit jaw domain.	we used bacteriophage t7-encoded transcription inhibitor gene protein 2 (gp2) as a probe to study the contribution of the escherichia coli rna polymerase (rnap) beta' subunit jaw domain--the site of gp2 binding--to activator and atp hydrolysis-dependent open complex formation by the sigma(54)-rnap. we show that, unlike sigma(70)-dependent transcription, activated transcription by sigma(54)-rnap is resistant to gp2. in contrast, activator and atp hydrolysis-independent transcription by sigma(54)- ...	2004	15470503
reorganisation of an rna polymerase-promoter dna complex for dna melting.	sigma factors, the key regulatory components of the bacterial rna polymerase (rnap), direct promoter dna binding and dna melting. the sigma(54)-rnap forms promoter complexes in which dna melting is only triggered by an activator and atp hydrolysis-driven reorganisation of an initial sigma(54)-rnap-promoter complex. we report that an initial bacterial rnap-dna complex can be reorganised by an activator to form an intermediate transcription initiation complex where full dna melting has not yet occ ...	2004	15470504
asymmetric atp binding and hydrolysis activity of the thermus aquaticus muts dimer is key to modulation of its interactions with mismatched dna.	prokaryotic muts and eukaryotic msh proteins recognize base pair mismatches and insertions or deletions in dna and initiate mismatch repair. these proteins function as dimers (and perhaps higher order oligomers) and possess an atpase activity that is essential for dna repair. previous studies of escherichia coli muts and eukaryotic msh2-msh6 proteins have revealed asymmetry within the dimer with respect to both dna binding and atpase activities. we have found the thermus aquaticus muts protein a ...	2004	15476405
the a2453-c2499 wobble base pair in escherichia coli 23s ribosomal rna is responsible for ph sensitivity of the peptidyltransferase active site conformation.	peptide bond formation, catalyzed by the ribosomal peptidyltransferase, has long been known to be sensitive to monovalent cation concentrations and ph. more recently, we and others have shown that residue a2451 in the peptidyltransferase center of the escherichia coli 50s ribosomal subunit changes conformation in response to alterations in ph, depending on ionic conditions and temperature. two wobble pairs, a2453-c2499 and a2450-c2063, have been proposed as potential candidates to convey ph-depe ...	2004	15479786
high-efficiency bypass of dna damage by human dna polymerase q.	endogenous dna damage arises frequently, particularly apurinic (ap) sites. these must be dealt with by cells in order to avoid genotoxic effects. dna polymerase theta; is a newly identified enzyme encoded by the human polq gene. we find that polq has an exceptional ability to bypass an ap site, inserting a with 22% of the efficiency of a normal template, and continuing extension as avidly as with a normally paired base. polq preferentially incorporates a opposite an ap site and strongly disfavor ...	2004	15496986
measurement of relative copy number of cdkn2a/arf and cdkn2b in bladder cancer by real-time quantitative pcr and multiplex ligation-dependent probe amplification.	many tumors have large homozygous deletions of the cdkn2a locus (encoding p14(arf) and p16) and of cdkn2b (p15). our aim was to determine which gene is the major target in bladder cancer. we used quantitative real-time pcr (rtq-pcr) to determine copy number of p15, of p14(arf) exon 1beta, and p16 exon 2 in 22 tumor cell lines and 83 bladder tumors, some of which had been assessed previously by duplex pcr. titration experiments showed that homozygous deletion could be detected in the presence of ...	2004	15507675
cold sensitivity of thermophilic and mesophilic rna polymerases.	rna polymerase from mesophilic deinococcus radiodurans displays the same cold sensitivity of promoter opening as rna polymerase from the closely related thermophilic thermus aquaticus. this suggests that, contrary to the accepted view, cold sensitivity of promoter opening by thermophilic rna polymerases may not be a consequence of their thermostability.	2004	15516599
unraveling the interface of signal recognition particle and its receptor by using chemical cross-linking and tandem mass spectrometry.	among the methods used to unravel protein interaction surfaces, chemical cross-linking followed by identification of the cross-linked peptides by mass spectrometry has proven especially useful in dynamic and complex systems. during the signal recognition particle (srp)-dependent targeting of proteins to the bacterial plasma membrane, the specific interaction between ffh (the protein component of srp) and ftsy (the srp receptor) is known to be essential for the efficiency and fidelity of this pro ...	2004	15546976
crystallization and preliminary x-ray crystallographic study of disproportionating enzyme from potato.	disproportionating enzyme (d-enzyme; ec 2.4.1.25) is a 59 kda protein that belongs to the alpha-amylase family. d-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of alpha-1,4 glucan. a crystal of the d-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. preliminary x-ray data showed that the crystal diffracts to 2.0 a resolution and belongs to space group c222(1), with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 a.	2004	16508106
crystallization and preliminary x-ray crystallographic study of disproportionating enzyme from potato.	disproportionating enzyme (d-enzyme; ec 2.4.1.25) is a 59 kda protein that belongs to the alpha-amylase family. d-enzyme catalyses intramolecular and intermolecular transglycosylation reactions of alpha-1,4 glucan. a crystal of the d-enzyme from potato was obtained by the hanging-drop vapour-diffusion method. preliminary x-ray data showed that the crystal diffracts to 2.0 a resolution and belongs to space group c222(1), with unit-cell parameters a = 69.7, b = 120.3, c = 174.2 a.	2004	16508106
distance-restrained docking of rifampicin and rifamycin sv to rna polymerase using systematic fret measurements: developing benchmarks of model quality and reliability.	we are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (fret) measurements. in this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. using simulated fret data, we have generated a series of benchmarks that permit estimation of model accura ...	2004	15542547
distance-restrained docking of rifampicin and rifamycin sv to rna polymerase using systematic fret measurements: developing benchmarks of model quality and reliability.	we are developing distance-restrained docking strategies for modeling macromolecular complexes that combine available high-resolution structures of the components and intercomponent distance restraints derived from systematic fluorescence resonance energy transfer (fret) measurements. in this article, we consider the problem of docking small-molecule ligands within macromolecular complexes. using simulated fret data, we have generated a series of benchmarks that permit estimation of model accura ...	2004	15542547
crystal structures of 2-acetylaminofluorene and 2-aminofluorene in complex with t7 dna polymerase reveal mechanisms of mutagenesis.	the carcinogen 2-acetylaminofluorene forms two major dna adducts: n-(2'-deoxyguanosin-8-yl)-2-acetylaminofluorene (dg-aaf) and its deacetylated derivative, n-(2'-deoxyguanosin-8-yl)-2-aminofluorene (dg-af). although the dg-aaf and dg-af adducts are distinguished only by the presence or absence of an acetyl group, they have profoundly different effects on dna replication. dg-aaf poses a strong block to dna synthesis and primarily induces frameshift mutations in bacteria, resulting in the loss of ...	2004	15528277
reverse transcriptase at bacterial telomeres.		2004	15454610
reverse gyrase has heat-protective dna chaperone activity independent of supercoiling.	hyperthermophilic organisms must protect their constituent macromolecules from heat-induced degradation. a general mechanism for thermoprotection of dna in active cells is unknown. we show that reverse gyrase, the only protein that is both specific and common to all hyperthermophiles, reduces the rate of double-stranded dna breakage approximately 8-fold at 90 degrees c. this activity does not require atp hydrolysis and is independent of the positive supercoiling activity of the enzyme. reverse g ...	2004	15247343
antibacterial peptide microcin j25 inhibits transcription by binding within and obstructing the rna polymerase secondary channel.	the antibacterial peptide microcin j25 (mccj25) inhibits transcription by bacterial rna polymerase (rnap). biochemical results indicate that inhibition of transcription occurs at the level of ntp uptake or ntp binding by rnap. genetic results indicate that inhibition of transcription requires an extensive determinant, comprising more than 50 amino acid residues, within the rnap secondary channel (also known as the "ntp-uptake channel" or "pore"). biophysical results indicate that inhibition of t ...	2004	15200952
poliovirus rna-dependent rna polymerase (3dpol): kinetic, thermodynamic, and structural analysis of ribonucleotide selection.	we have performed a kinetic and thermodynamic analysis of 3d(pol) derivatives containing substitutions in the ribose-binding pocket with atp analogues containing correct and incorrect sugar configurations. we find that asp-238, a residue in structural motif a that is conserved in all rna-dependent rna polymerases, is a key determinant of polymerase fidelity. alterations in the position of the asp-238 side chain destabilize the catalytically competent 3d(pol)-primer/template-ntp complex and reduc ...	2004	15122880
structure and mechanism of the rna polymerase ii transcription machinery.	advances in structure determination of the bacterial and eukaryotic transcription machinery have led to a marked increase in the understanding of the mechanism of transcription. models for the specific assembly of the rna polymerase ii transcription machinery at a promoter, conformational changes that occur during initiation of transcription, and the mechanism of initiation are discussed in light of recent developments.	2004	15114340
a third base pair for the polymerase chain reaction: inserting isoc and isog.	two additional bases (isoguanosine and isocytosine), generating a third base pair, have been implemented in pcr. enzyme fidelity for the third base pair is demonstrated using molecular thermodynamic melting, chemical cleavage and molecular beacons. when amplifying as few as 15 targets containing multiple non-natural base pairs with 40 cycles of amplification, our results confirm sequence conservation. the additional sequence space provided by three base pairs allows for the construction of molec ...	2004	15051811
snpwave: a flexible multiplexed snp genotyping technology.	scalable multiplexed amplification technologies are needed for cost-effective large-scale genotyping of genetic markers such as single nucleotide polymorphisms (snps). we present snpwave, a novel snp genotyping technology to detect various subsets of sequences in a flexible fashion in a fixed detection format. snpwave is based on highly multiplexed ligation, followed by amplification of up to 20 ligated probes in a single pcr. depending on the multiplexing level of the ligation reaction, the lat ...	2004	15004220
rapid transcriptome responses of maize (zea mays) to uv-b in irradiated and shielded tissues.	depletion of stratospheric ozone has raised terrestrial levels of ultraviolet-b radiation (uv-b), an environmental change linked to an increased risk of skin cancer and with potentially deleterious consequences for plants. to better understand the processes of uv-b acclimation that result in altered plant morphology and physiology, we investigated gene expression in different organs of maize at several uv-b fluence rates and exposure times.	2004	15003119
in vitro mutation artifacts after formalin fixation and error prone translesion synthesis during pcr.	background: clinical specimens are routinely fixed in 10% buffered formalin and paraffin embedded. although dna is commonly extracted from fixed tissues and amplified by pcr, the effects of formalin fixation are relatively unknown. formalin fixation is known to impair pcr, presumably through damage that blocks polymerase elongation, but an insidious possibility is error prone translesion synthesis across sites of damage, producing in vitro artifactual mutations during pcr. methods: to better und ...	2004	15028125
impact of virioplankton on archaeal and bacterial community richness as assessed in seawater batch cultures.	during cruises in the tropical atlantic ocean (january to february 2000) and the southern north sea (december 2000), experiments were conducted to monitor the impact of virioplankton on archaeal and bacterial community richness. prokaryotic cells equivalent to 10 to 100% of the in situ abundance were inoculated into virus-free seawater, and viruses equivalent to 35 to 360% of the in situ abundance were added. batch cultures with microwave-inactivated viruses and without viruses served as control ...	2004	14766558
maize mutants lacking chloroplast ftsy exhibit pleiotropic defects in the biogenesis of thylakoid membranes.	a chloroplast signal recognition particle (srp) that is related to the srp involved in secretion in bacteria and eukaryotic cells is used for the insertion of light-harvesting chlorophyll proteins (lhcps) into the thylakoid membranes. a conserved component of the srp mechanism is a membrane-bound srp receptor, denoted ftsy in bacteria. plant genomes encode ftsy homologs that are targeted to the chloroplast (cpftsy). to investigate the in vivo roles of cpftsy, we characterized maize cpftsy and ma ...	2004	14688289
predicting transmembrane beta-barrels in proteomes.	very few methods address the problem of predicting beta-barrel membrane proteins directly from sequence. one reason is that only very few high-resolution structures for transmembrane beta-barrel (tmb) proteins have been determined thus far. here we introduced the design, statistics and results of a novel profile-based hidden markov model for the prediction and discrimination of tmbs. the method carefully attempts to avoid over-fitting the sparse experimental data. while our model training and sc ...	2004	15141026
extremophiles and their application to veterinary medicine.	: extremophiles are organisms that can grow and thrive in harsh conditions, e.g., extremes of temperature, ph, salinity, radiation, pressure and oxygen tension. thermophilic, halophilic and radiation-resistant organisms are all microbes, some of which are able to withstand multiple extremes. psychrophiles, or cold-loving organisms, include not only microbes, but fish that live in polar waters and animals that can withstand freezing. extremophiles are structurally adapted at a molecular level to ...	2004	21851659
inhibition of bacterial rna polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation.	we define the target, mechanism, and structural basis of inhibition of bacterial rna polymerase (rnap) by the tetramic acid antibiotic streptolydigin (stl). stl binds to a site adjacent to but not overlapping the rnap active center and stabilizes an rnap-active-center conformational state with a straight-bridge helix. the results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix rnap-active-center conformations exist and that cycling between st ...	2005	16122422
structural, functional, and genetic analysis of sorangicin inhibition of bacterial rna polymerase.	a combined structural, functional, and genetic approach was used to investigate inhibition of bacterial rna polymerase (rnap) by sorangicin (sor), a macrolide polyether antibiotic. sor lacks chemical and structural similarity to the ansamycin rifampicin (rif), an rnap inhibitor widely used to treat tuberculosis. nevertheless, structural analysis revealed sor binds in the same rnap beta subunit pocket as rif, with almost complete overlap of rnap binding determinants, and functional analysis revea ...	2005	15692574
comparative genomics of thermus thermophilus and deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance.	thermus thermophilus and deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. t. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas d. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria.	2005	16242020
clinical and molecular findings in osteoporosis-pseudoglioma syndrome.	mutations in the low-density lipoprotein receptor-related protein 5 gene (lrp5) cause autosomal recessive osteoporosis-pseudoglioma syndrome (oppg). we sequenced the coding exons of lrp5 in 37 probands suspected of having oppg on the basis of the co-occurrence of severe congenital or childhood-onset visual impairment with bone fragility or osteoporosis recognized by young adulthood. we found two putative mutant alleles in 26 probands, only one mutant allele in 4 probands, and no mutant alleles i ...	2005	16252235
structural basis for transcription inhibition by tagetitoxin.	tagetitoxin (tgt) inhibits transcription by an unknown mechanism. a structure at a resolution of 2.4 a of the thermus thermophilus rna polymerase (rnap)-tgt complex revealed that the tgt-binding site within the rnap secondary channel overlaps that of the stringent control effector ppgpp, which partially protects rnap from tgt inhibition. tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to tgt in vitro. important ...	2005	16273103
the aauaaa motif of bamboo mosaic virus rna is involved in minus-strand rna synthesis and plus-strand rna polyadenylation.	bamboo mosaic virus (bamv) has a single-stranded positive-sense rna genome with a 5'-cap structure and a 3' poly(a) tail. deleting the internal loop that contains the putative polyadenylation signal (aauaaa) in the 3' untranslated region (utr) of bamv genomic rna appeared to diminish coat protein accumulation to 2% (c. p. cheng and c. h. tsai, j. mol. biol. 288:555-565, 1999). to investigate the function of the aauaaa motif, mutations were introduced into an infectious bamv cdna at each residue ...	2005	16282455
efficient isothermal expansion of human telomeric and minisatellite repeats by thermococcus litoralis dna polymerase.	repeating dna sequences, such as telomeres, centromeres, and micro- and mini-satellites, comprise 50% of the genome and play important roles in regulatory and pathogenic mechanisms. in order to study structures and functions of such repeating sequences, it is important to have simple and efficient methods for making them in vitro. here, we describe the efficient and convenient expansion of repetitive telomeric and minisatellite dna sequences starting from small synthetic templates to final produ ...	2005	16284196
coupled protein domain motion in taq polymerase revealed by neutron spin-echo spectroscopy.	long-range conformational changes in proteins are ubiquitous in biology for the transmission and amplification of signals; such conformational changes can be triggered by small-amplitude, nanosecond protein domain motion. understanding how conformational changes are initiated requires the characterization of protein domain motion on these timescales and on length scales comparable to protein dimensions. using neutron spin-echo spectroscopy (nse), normal mode analysis, and a statistical-mechanica ...	2005	16306270
allele-specific amplification in cancer revealed by snp array analysis.	amplification, deletion, and loss of heterozygosity of genomic dna are hallmarks of cancer. in recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. similarly, loss-of-heterozygosity events have been finely mapped using high-throughput genotyping technologies. we have developed a probe-level allele-specific quantitation procedure that extracts both copy number and allelotype information from single nucleotide polymorphism (snp) ar ...	2005	16322765
the database of macromolecular motions: new features added at the decade mark.	the database of molecular motions, molmovdb (http://molmovdb.org), has been in existence for the past decade. it classifies macromolecular motions and provides tools to interpolate between two conformations (the morph server) and predict possible motions in a single structure. in 2005, we expanded the services offered on molmovdb. in particular, we further developed the morph server to produce improved interpolations between two submitted structures. we added support for multiple chains to the o ...	2005	16381870
the database of macromolecular motions: new features added at the decade mark.	the database of molecular motions, molmovdb (http://molmovdb.org), has been in existence for the past decade. it classifies macromolecular motions and provides tools to interpolate between two conformations (the morph server) and predict possible motions in a single structure. in 2005, we expanded the services offered on molmovdb. in particular, we further developed the morph server to produce improved interpolations between two submitted structures. we added support for multiple chains to the o ...	2005	16381870
temperature dependence and thermodynamics of klenow polymerase binding to primed-template dna.	dna binding of klenow polymerase has been characterized with respect to temperature to delineate the thermodynamic driving forces involved in the interaction of this polymerase with primed-template dna. the temperature dependence of the binding affinity exhibits distinct curvature, with tightest binding at 25-30 degrees c. nonlinear temperature dependence indicates klenow binds different primed-template constructs with large heat capacity (deltacp) values (-870 to -1220 cal/mole k) and thus exhi ...	2005	16339886
temperature dependence and thermodynamics of klenow polymerase binding to primed-template dna.	dna binding of klenow polymerase has been characterized with respect to temperature to delineate the thermodynamic driving forces involved in the interaction of this polymerase with primed-template dna. the temperature dependence of the binding affinity exhibits distinct curvature, with tightest binding at 25-30 degrees c. nonlinear temperature dependence indicates klenow binds different primed-template constructs with large heat capacity (deltacp) values (-870 to -1220 cal/mole k) and thus exhi ...	2005	16339886
a low-cost open-source snp genotyping platform for association mapping applications.	association mapping aimed at identifying dna polymorphisms that contribute to variation in complex traits entails genotyping a large number of single-nucleotide polymorphisms (snps) in a very large panel of individuals. few technologies, however, provide inexpensive high-throughput genotyping. here, we present an efficient approach developed specifically for genotyping large fixed panels of diploid individuals. the cost-effective, open-source nature of our methodology may make it particularly at ...	2005	16356268
enhancing the efficiency of a pcr using gold nanoparticles.	we found that the pcr could be dramatically enhanced by au nanoparticles. with the addition of 0.7 nm of 13 nm au nanoparticles into the pcr reagent, the pcr efficiency was increased. especially when maintaining the same or higher amplification yields, the reaction time could be shortened, and the heating/cooling rates could be increased. the excellent heat transfer property of the nanoparticles should be the major factor in improving the pcr efficiency. different pcr systems, dna polymerases, d ...	2005	16314298
expressible molecular colonies.	carrying out polymerase chain reaction in a gel layer generates a 2-d pattern of dna colonies comprising pure genetic clones. here we demonstrate that transcription, translation and protein folding can be performed in the same gel. the resulting nucleoprotein colonies mimic living cells by serving as compartments in which the synthesized rnas and proteins co-localize with their templates. yet, due to the absence of penetration barriers, such a molecular colony display allows cloned genes to be d ...	2005	16204448
comprehensive algorithm for quantitative real-time polymerase chain reaction.	quantitative real-time polymerase chain reactions (qrt-pcr) have become the method of choice for rapid, sensitive, quantitative comparison of rna transcript abundance. useful data from this method depend on fitting data to theoretical curves that allow computation of mrna levels. calculating accurate mrna levels requires important parameters such as reaction efficiency and the fractional cycle number at threshold (ct) to be used; however, many algorithms currently in use estimate these important ...	2005	16241897
the use of thymidine analogs to improve the replication of an extra dna base pair: a synthetic biological system.	synthetic biology based on a six-letter genetic alphabet that includes the two non-standard nucleobases isoguanine (isog) and isocytosine (isoc), as well as the standard a, t, g and c, is known to suffer as a consequence of a minor tautomeric form of isoguanine that pairs with thymine, and therefore leads to infidelity during repeated cycles of the pcr. reported here is a solution to this problem. the solution replaces thymidine triphosphate by 2-thiothymidine triphosphate (2-thiottp). because o ...	2005	16192575
polymerase evolution: efforts toward expansion of the genetic code.	genetic information is encoded by, but potentially not limited to, a four-letter alphabet. a variety of predominantly hydrophobic nucleobase analogues that form self-pairs in dna have been examined as third base pair candidates. for example, the pics self-pair is both stable in duplex dna and synthesized by some wild-type polymerases with reasonable efficiency. these efforts to expand the genetic code are expected to be facilitated by optimizing both the unnatural nucleobase analogues and the po ...	2005	16144377
high fidelity tna synthesis by therminator polymerase.	therminator dna polymerase is an efficient dna-dependent tna polymerase capable of polymerizing tna oligomers of at least 80 nt in length. in order for therminator to be useful for the in vitro selection of functional tna sequences, its tna synthesis fidelity must be high enough to preserve successful sequences. we used sequencing to examine the fidelity of therminator-catalyzed tna synthesis at different temperatures, incubation times, tntp ratios and primer/template combinations. tna synthesis ...	2005	16157867
critical factors for assembling a high volume of dna barcodes.	large-scale dna barcoding projects are now moving toward activation while the creation of a comprehensive barcode library for eukaryotes will ultimately require the acquisition of some 100 million barcodes. to satisfy this need, analytical facilities must adopt protocols that can support the rapid, cost-effective assembly of barcodes. in this paper we discuss the prospects for establishing high volume dna barcoding facilities by evaluating key steps in the analytical chain from specimens to barc ...	2005	16214753
cumulative effect of amino acid replacements results in enhanced thermostability of potato type l alpha-glucan phosphorylase.	the thermostability of potato type l alpha-glucan phosphorylase (ec 2.4.1.1) was enhanced by random and site-directed mutagenesis. we obtained three single-residue mutations-phe39-->leu (f39l), asn135-->ser (n135s), and thr706-->ile (t706i)-by random mutagenesis. although the wild-type enzyme was completely inactivated, these mutant enzymes retained their activity even after heat treatment at 60 degrees c for 2 h. combinations of these mutations were introduced by site-directed mutagenesis. the ...	2005	16151135
replicative homeostasis ii: influence of polymerase fidelity on rna virus quasispecies biology: implications for immune recognition, viral autoimmunity and other "virus receptor" diseases.	much of the worlds' population is in active or imminent danger from established infectious pathogens, while sporadic and pandemic infections by these and emerging agents threaten everyone. rna polymerases (rnapol) generate enormous genetic and consequent antigenic heterogeneity permitting both viruses and cellular pathogens to evade host defences. thus, rnapol causes more morbidity and premature mortality than any other molecule. the extraordinary genetic heterogeneity defining viral quasispecie ...	2005	16115320
a unique trna recognition mechanism of caenorhabditis elegans mitochondrial ef-tu2.	nematode mitochondria expresses two types of extremely truncated trnas that are specifically recognized by two distinct elongation factor tu (ef-tu) species named ef-tu1 and ef-tu2. this is unlike the canonical ef-tu molecule that participates in the standard protein biosynthesis systems, which basically recognizes all elongator trnas. ef-tu2 specifically recognizes ser-trna(ser) that lacks a d arm but has a short t arm. our previous study led us to speculate the lack of the d arm may be essenti ...	2005	16113240
fidelity of dpo4: effect of metal ions, nucleotide selection and pyrophosphorolysis.	we report the crystal structures of a translesion dna polymerase, dpo4, complexed with a matched or mismatched incoming nucleotide and with a pyrophosphate product after misincorporation. these structures suggest two mechanisms by which dpo4 may reject a wrong incoming nucleotide with its preformed and open active site. first, a mismatched replicating base pair leads to poor base stacking and alignment of the metal ions and as a consequence, inhibits incorporation. by replacing mg2+ with mn2+, w ...	2005	16107880
molecular mimicry: quantitative methods to study structural similarity between protein and rna.	with rapidly increasing availability of three-dimensional structures, one major challenge for the post-genome era is to infer the functions of biological molecules based on their structural similarity. while quantitative studies of structural similarity between the same type of biological molecules (e.g., protein vs. protein) have been carried out intensively, the comparable study of structural similarity between different types of biological molecules (e.g., protein vs. rna) remains unexplored. ...	2005	16043503
nucleotide exchange and excision technology (next) dna shuffling: a robust method for dna fragmentation and directed evolution.	dna shuffling is widely used for optimizing complex properties contained within dna and proteins. demonstrated here is the amplification of a gene library by pcr using uridine triphosphate (dutp) as a fragmentation defining exchange nucleotide with thymidine, together with the three other nucleotides. the incorporated uracil bases were excised using uracil-dna-glycosylase and the dna backbone subsequently cleaved with piperidine. these end-point reactions required no adjustments. polyacrylamide ...	2005	16061932
determination of protein-dna binding constants and specificities from statistical analyses of single molecules: muts-dna interactions.	atomic force microscopy (afm) is a powerful technique for examining the conformations of protein-dna complexes and determining the stoichiometries and affinities of protein-protein complexes. we extend the capabilities of afm to the determination of protein-dna binding constants and specificities. the distribution of positions of the protein on the dna fragments provides a direct measure of specificity and requires no knowledge of the absolute binding constants. the fractional occupancies of the ...	2005	16061937
uracil content of 16s rrna of thermophilic and psychrophilic prokaryotes correlates inversely with their optimal growth temperatures.	we report here the finding of a highly significant inverse correlation of the uracil content of 16s rrna and the optimum growth temperature (t(opt)) of cultured thermophilic and psychrophilic prokaryotes. this correlation was significantly different from the weaker correlations between the contents of other nucleotides and t(opt). analysis of the 16s rrna secondary structure regions revealed a fall in the a:u base-pair content in step with the increase in t(opt) that was much steeper than that o ...	2005	16030352
sequence determination of nucleic acids containing 5-methylisocytosine and isoguanine: identification and insight into polymerase replication of the non-natural nucleobases.	nucleobase analogs 5-methylisocytosine ((me)isoc) and isoguanine (isog) form a non-natural base pair in duplex nucleic acids with base pairing specificity orthogonal to the natural nucleobase pairs. sequencing reactions were conducted with oligodeoxyribonucleotides (odns) containing d(me)isoc and disog using modified pyrosequencing and dye terminator methods. modified dye terminator sequencing was generally useful for the sequence identification of odns containing the non-natural nucleobases. th ...	2005	15933210
piecemaker: selection of dna fragments for selector-guided multiplex amplification.	we describe piecemaker, a software tool for the design of applications of selector probes-oligonucleotide probes that direct circularization of target nucleic acid molecules. such probes can be combined in parallel to circularize a selection of fragments from restriction digested total genomic dna. these fragments can then be amplified in a single pcr using a common primer pair, yielding substrates for subsequent analyses, such as parallel genotyping or sequencing. however, designing multiplex s ...	2005	15860769
surface plasmon field-enhanced fluorescence spectroscopy studies of primer extension reactions.	surface plasmon field-enhanced fluorescence spectroscopy (spfs) utilizes the evanescent electromagnetic field of a surface plasmon to excite chromophors in close proximity to the surface. while conventional surface plasmon resonance spectroscopy allows the observation of surface reactions by means of refractive index changes, spfs additionally provides a channel for the read-out of fluorescence changes. thus, the detection limit for low mass compounds, whose adsorption is only accompanied by sma ...	2005	15849312
correcting errors in synthetic dna through consensus shuffling.	although efficient methods exist to assemble synthetic oligonucleotides into genes and genomes, these suffer from the presence of 1-3 random errors/kb of dna. here, we introduce a new method termed consensus shuffling and demonstrate its use to significantly reduce random errors in synthetic dna. in this method, errors are revealed as mismatches by re-hybridization of the population. the dna is fragmented, and mismatched fragments are removed upon binding to an immobilized mismatch binding prote ...	2005	15800206
chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of a2451.	the main enzymatic reaction of the large ribosomal subunit is peptide bond formation. ribosome crystallography showed that a2451 of 23s rrna makes the closest approach to the attacking amino group of aminoacyl-trna. mutations of a2451 had relatively small effects on transpeptidation and failed to unequivocally identify the crucial functional group(s). here, we employed an in vitro reconstitution system for chemical engineering the peptidyl transferase center by introducing non-natural nucleoside ...	2005	15767286
use of a restriction enzyme-digested pcr product as substrate for helicase assays.	dna helicases play essential roles in many cellular processes. the currently available techniques to generate substrates for helicase assays are fairly complicated and need some expertise not available in all laboratories. here, a pcr-based method to generate a substrate for a helicase assay is described, and its application for several archaeal, bacterial and viral enzymes is demonstrated.	2005	15653629
nucleotide specificity of hiv-1 reverse transcriptases with amino acid substitutions affecting ala-114.	ala-114, together with asp-113, tyr-115 and gln-151, form the pocket that accommodates the 3'-oh of the incoming dntp in the hiv-1 rt (reverse transcriptase). four mutant rts having serine, glycine, threonine or valine instead of ala-114 were obtained by site-directed mutagenesis. while mutants a114s and a114g retained significant dna polymerase activity, a114t and a114v showed very low catalytic efficiency in nucleotide incorporation assays, due to their high apparent k(m) values for dntp. disc ...	2005	15548134
distinct roles for the saccharomyces cerevisiae mismatch repair proteins in heteroduplex rejection, mismatch repair and nonhomologous tail removal.	the saccharomyces cerevisiae mismatch repair (mmr) protein msh6 and the sgs1 helicase were recently shown to play similarly important roles in preventing recombination between divergent dna sequences in a single-strand annealing (ssa) assay. in contrast, mmr factors such as mlh1p, pms1p, and exo1p were shown to not be required or to play only minimal roles. in this study we tested mutations that disrupt sgs1p helicase activity, msh2p-msh6p mismatch recognition, and atp binding and hydrolysis act ...	2005	15489516
presence of beta-lactamase gene tem-1 dna sequence in commercial taq dna polymerase.		2005	15635039
non-cross-linking gold nanoparticle aggregation as a detection method for single-base substitutions.	aggregation of dna-modified gold nanoparticles in a non-cross-linking configuration has extraordinary selectivity against terminal mismatch of the surface-bound duplex. in this paper, we demonstrate the utility of this selectivity for detection of single-base substitutions. the samples were prepared through standard protocols: dna extraction, pcr amplification and single-base primer extension. oligonucleotide-modified nanoparticles correctly responded to the unpurified products from the primer e ...	2005	15640441
mutants with temperature-sensitive defects in the escherichia coli mismatch repair system: sensitivity to mispairs generated in vivo.	we have used direct selections to generate large numbers of mutants of escherichia coli defective in the mismatch repair system and have screened these to identify mutants with temperature-sensitive defects. we detected and sequenced mutations that give rise to temperature-sensitive muts, mutl, and muth proteins. one mutation, muts60, results in almost normal levels of spontaneous mutations at 37 degrees c but above this temperature gives rise to higher and higher levels of mutations, reaching t ...	2005	15659661
identification and characterization of genes involved in the downstream degradation pathway of gamma-hexachlorocyclohexane in sphingomonas paucimobilis ut26.	sphingomonas paucimobilis ut26 utilizes gamma-hexachlorocyclohexane (gamma-hch) as a sole source of carbon and energy. in our previous study, we cloned and characterized genes that are involved in the conversion of gamma-hch to maleylacetate (ma) via chlorohydroquinone (chq) in ut26. in this study, we identified and characterized an ma reductase gene, designated linf, that is essential for the utilization of gamma-hch in ut26. a gene named lineb, whose deduced product showed significant identity ...	2005	15659662
substrate requirements for regulated intramembrane proteolysis of bacillus subtilis pro-sigmak.	during sporulation of bacillus subtilis, pro-sigmak is activated by regulated intramembrane proteolysis (rip) in response to a signal from the forespore. rip of pro-sigmak removes its prosequence (amino acids 1 to 20), releasing sigmak from the outer forespore membrane into the mother cell cytoplasm, in a reaction catalyzed by spoivfb, a metalloprotease in the s2p family of intramembrane-cleaving proteases. the requirements for pro-sigmak to serve as a substrate for rip were investigated by prod ...	2005	15659674
low copy number dna template can render polymerase chain reaction error prone in a sequence-dependent manner.	paraffin-embedded tissue is an important source of material for molecular pathology and genetic investigations. we used dna isolated from microdissected formalin-fixed, paraffin-embedded gastric tumors for mutation analysis of a region of the human gene for uracil-dna glycosylase (ung), encoding the ung catalytic domain, and detected apparent base substitutions which, after further investigation, proved to be polymerase chain reaction (pcr) artifacts. we demonstrate that low dna template input i ...	2005	15681472
rna polymerase mutants defective in the initiation of transcription-coupled dna repair.	the bacterial mfd protein is a transcription-repair coupling factor that performs two key functions during transcription-coupled dna repair. the first is to remove rna polymerase (rnap) complexes that have been stalled by a dna lesion from the site of damage, and the second is to mediate the recruitment of dna repair proteins. mfd also displaces transcription complexes that have been stalled by protein roadblocks, and catalyses the reactivation of transcription complexes that have become 'backtr ...	2005	15687384
pseudomonas aeruginosa mutl protein functions in escherichia coli.	escherichia coli muts, mutl and muth proteins act sequentially in the mmrs (mismatch repair system). muth directs the repair system to the newly synthesized strand due to its transient lack of dam (dna-adenine methylase) methylation. although pseudomonas aeruginosa does not have the corresponding e. coli muth and dam homologues, and consequently the mmrs seems to work differently, we show that the mutl gene from p. aeruginosa is capable of complementing a mutl-deficient strain of e. coli. mutl f ...	2005	15709980
rifampin-resistant rna polymerase mutants of chlamydia trachomatis remain susceptible to the ansamycin rifalazil.	stable, homotypic mutants of chlamydia trachomatis for which mics of rifampin and rifalazil are elevated were isolated by serial passage at sub-mic concentrations of these compounds. an alternative approach, in which chlamydia cells were incubated and subsequently passaged three times, all in the presence of the selective agent at concentrations above the mic, appeared to be a more effective means of selecting for mutants. in every instance where an elevation in the mic occurred, one or more mut ...	2005	15728912
separation of mutation avoidance and antirecombination functions in an escherichia coli muts mutant.	dna mismatch repair in escherichia coli has been shown to be involved in two distinct processes: mutation avoidance, which removes potential mutations arising as replication errors, and antirecombination which prevents recombination between related, but not identical (homeologous), dna sequences. we show that cells with the mutsdelta800 mutation (which removes the c-terminal 53 amino acids of muts) on a multicopy plasmid are proficient for mutation avoidance. in interspecies genetic crosses, how ...	2005	15731339