Publications

a highly divergent archaeo-eukaryotic primase from the thermococcus nautilus plasmid, ptn2.	we report the characterization of a dna primase/polymerase protein (polptn2) encoded by the ptn2 plasmid from thermococcus nautilus. sequence analysis revealed that this protein corresponds to a fusion between an n-terminal domain homologous to the small catalytic subunit pris of heterodimeric archaeal and eukaryotic primases (aep) and a c-terminal domain related to their large regulatory subunit pril. this unique domain configuration is not found in other virus- and plasmid-encoded primases in ...	2014	24445805
structural and functional analyses of a sterol carrier protein in spodoptera litura.	in insects, cholesterol is one of the membrane components in cells and a precursor of ecdysteroid biosynthesis. because insects lack two key enzymes, squalene synthase and lanosterol synthase, in the cholesterol biosynthesis pathway, they cannot autonomously synthesize cholesterol de novo from simple compounds and therefore have to obtain sterols from their diet. sterol carrier protein (scp) is a cholesterol-binding protein responsible for cholesterol absorption and transport.	2014	24454688
context of action of proline dehydrogenase (prodh) in the hypersensitive response of arabidopsis.	proline (pro) dehydrogenase (prodh) potentiates the oxidative burst and cell death of the plant hypersensitive response (hr) by mechanisms not yet elucidated. prodh converts pro into ∆1 pyrroline-5-carboxylate (p5c) and can act together with p5c dehydrogenase (p5cdh) to produce glu, or with p5c reductase (p5cr) to regenerate pro and thus stimulate the pro/p5c cycle. to better understand the effects of prodh in hr, we studied the enzyme at three stages of the defense response differing in their r ...	2014	24410747
the isolated carboxy-terminal domain of human mitochondrial leucyl-trna synthetase rescues the pathological phenotype of mitochondrial trna mutations in human cells.	mitochondrial (mt) diseases are multisystem disorders due to mutations in nuclear or mtdna genes. among the latter, more than 50% are located in transfer rna (trna) genes and are responsible for a wide range of syndromes, for which no effective treatment is available at present. we show that three human mt aminoacyl-trna syntethases, namely leucyl-, valyl-, and isoleucyl-trna synthetase are able to improve both viability and bioenergetic proficiency of human transmitochondrial cybrid cells carry ...	2014	24413190
crystal structures of ispf from plasmodium falciparum and burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment.	2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase (ispf) catalyzes the conversion of 4-diphosphocytidyl-2c-methyl-d-erythritol-2-phosphate to 2c-methyl-d-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. ispf is found in the protozoan plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many gram-negative bacteria such as burkholderia cenocepacia. ispf represents a ...	2014	24410837
mlh1-mlh3, a meiotic crossover and dna mismatch repair factor, is a msh2-msh3-stimulated endonuclease.	crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. in saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. these invasion intermediates are converted into double holliday junctions and then resolved into crossovers that facilitate homolog s ...	2014	24403070
charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms.	ribosomes are large and highly charged macromolecular complexes consisting of rna and proteins. here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. we examined 50 s ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. we found th ...	2014	24398678
comea is essential for the transfer of external dna into the periplasm in naturally transformable vibrio cholerae cells.	the dna uptake of naturally competent bacteria has been attributed to the action of dna uptake machineries resembling type iv pilus complexes. however, the protein(s) for pulling the dna across the outer membrane of gram-negative bacteria remain speculative. here we show that the competence protein comea binds incoming dna in the periplasm of naturally competent vibrio cholerae cells thereby promoting dna uptake, possibly through ratcheting and entropic forces associated with comea binding. usin ...	2014	24391524
clostridium difficile glutamate dehydrogenase is a secreted enzyme that confers resistance to h2o2.	clostridium difficile produces an nad-specific glutamate dehydrogenase (gdh), which converts l-glutamate into α-ketoglutarate through an irreversible reaction. the enzyme gdh is detected in the stool samples of patients with c. difficile-associated disease and serves as one of the diagnostic tools to detect c. difficile infection (cdi). we demonstrate here that supernatant fluids of c. difficile cultures contain gdh. to understand the role of gdh in the physiology of c. difficile, an isogenic in ...	2014	24145018
ultradeep pyrosequencing and molecular modeling identify key structural features of hepatitis b virus rnase h, a putative target for antiviral intervention.	last-generation nucleoside/nucleotide analogues are potent against hepatitis b virus (hbv) and have a high barrier to resistance. however, delayed responses have been observed in patients previously exposed to other drugs of the same class, long-term resistance is possible, and cure of infection cannot be achieved with these therapies, emphasizing the need for alternative therapeutic approaches. the hbv rnase h represents an interesting target because its enzyme activity is essential to the hbv ...	2014	24173223
iodotyrosine deiodinase: a unique flavoprotein present in organisms of diverse phyla.	iodide is required for thyroid hormone synthesis in mammals and other vertebrates. the role of both iodide and iodinated tyrosine derivatives is currently unknown in lower organisms, yet the presence of a key enzyme in iodide conservation, iodotyrosine deiodinase (iyd), is suggested by genomic data from a wide range of multicellular organisms as well as some bacteria. a representative set of these genes has now been expressed, and the resulting enzymes all catalyze reductive deiodination of diio ...	2014	24153409
mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card.	escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ...	2014	25510492
mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card.	escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ...	2014	25510492
evolution and diversity of the ras superfamily of small gtpases in prokaryotes.	the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ...	2014	25480683
evolution and diversity of the ras superfamily of small gtpases in prokaryotes.	the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ...	2014	25480683
the predatory bacterium bdellovibrio bacteriovorus aspartyl-trna synthetase recognizes trnaasn as a substrate.	the predatory bacterium bdellovibrio bacteriovorus preys on other gram-negative bacteria and was predicted to be an asparagine auxotroph. however, despite encoding asparaginyl-trna synthetase and glutaminyl-trna synthetase, b. bacteriovorus also contains the amidotransferase gatcab. deinococcus radiodurans, and thermus thermophilus also encode both of these aminoacyl-trna synthetases with gatcab. both also code for a second aspartyl-trna synthetase and use the additional aspartyl-trna synthetase ...	2014	25338061
zinc and atp binding of the hexameric aaa-atpase pilf from thermus thermophilus: role in complex stability, piliation, adhesion, twitching motility, and natural transformation.	the traffic aaa-atpase pilf is essential for pilus biogenesis and natural transformation of thermus thermophilus hb27. recently, we showed that pilf forms hexameric complexes containing six zinc atoms coordinated by conserved tetracysteine motifs. here we report that zinc binding is essential for complex stability. however, zinc binding is neither required for pilus biogenesis nor natural transformation. a number of the mutants did not exhibit any pili during growth at 64 °c but still were trans ...	2014	25202014
a review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories.	microbial cell factories (mcfs) are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. this review highlights the progress of computational models for the rational design of an mcf to produce a target bio-commodity. in particular, the rational design of an mcf involves: (i) product selection, (ii) de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial), (iii) mcf chassis selection, (iv) enzyme engineering of ...	2014	25379147
molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix.	tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ...	2014	25108393
multiple regulatory mechanisms control the expression of the geobacillus stearothermophilus gene for extracellular xylanase.	geobacillus stearothermophilus t-6 produces a single extracellular xylanase (xyn10a) capable of producing short, decorated xylo-oligosaccharides from the naturally branched polysaccharide, xylan. gel retardation assays indicated that the master negative regulator, xylr, binds specifically to xylr operators in the promoters of xylose and xylan-utilization genes. this binding is efficiently prevented in vitro by xylose, the most likely molecular inducer. expression of the extracellular xylanase is ...	2014	25070894
outside-in assembly pathway of the type iv pilus system in myxococcus xanthus.	type iv pili (t4p) are ubiquitous bacterial cell surface structures that undergo cycles of extension, adhesion, and retraction. t4p function depends on a highly conserved envelope-spanning macromolecular machinery consisting of 10 proteins that localizes polarly in myxococcus xanthus. using this localization, we investigated the entire t4p machinery assembly pathway by systematically profiling the stability of all and the localization of eight of these proteins in the absence of other t4p machin ...	2014	24187092
type iv pilus biogenesis, twitching motility, and dna uptake in thermus thermophilus: discrete roles of antagonistic atpases pilf, pilt1, and pilt2.	natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species. thermus thermophilus hb27 has emerged as the leading model organism for studies of dna transporters in thermophilic bacteria. recently, we identified a zinc-binding polymerization nucleoside triphosphatase (ntpase), pilf, which is essential for the transport of dna through the outer membrane. here, we present genetic evidence that ...	2014	24212586
nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells.	legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ...	2014	25547789
nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells.	legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ...	2014	25547789
uracil-dna glycosylases-structural and functional perspectives on an essential family of dna repair enzymes.	uracil-dna glycosylases (udgs) are evolutionarily conserved dna repair enzymes that initiate the base excision repair pathway and remove uracil from dna. the udg superfamily is classified into six families based on their substrate specificity. this review focuses on the family i enzymes since these are the most extensively studied members of the superfamily. the structural basis for substrate specificity and base recognition as well as for dna binding, nucleotide flipping and catalytic mechanism ...	2014	25252105
effect of the l499m mutation of the ascomycetous botrytis aclada laccase on redox potential and catalytic properties.	laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. these enzymes contain four cu atoms per molecule organized into three sites: t1, t2 and t3. in all laccases, the t1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. the redox potential of ...	2014	25372682
structural and biochemical characterization of chlamydia trachomatis hypothetical protein ct263 supports that menaquinone synthesis occurs through the futalosine pathway.	the obligate intracellular human pathogen chlamydia trachomatis is the etiological agent of blinding trachoma and sexually transmitted disease. genomic sequencing of chlamydia indicated this medically important bacterium was not exclusively dependent on the host cell for energy. in order for the electron transport chain to function, electron shuttling between membrane-embedded complexes requires lipid-soluble quinones (e.g. menaquionone or ubiquinone). the sources or biosynthetic pathways requir ...	2014	25253688
cocrystal structures of glycyl-trna synthetase in complex with trna suggest multiple conformational states in glycylation.	aminoacyl-trna synthetases are an ancient enzyme family that specifically charges trna molecules with cognate amino acids for protein synthesis. glycyl-trna synthetase (glyrs) is one of the most intriguing aminoacyl-trna synthetases due to its divergent quaternary structure and abnormal charging properties. in the past decade, mutations of human glyrs (hglyrs) were also found to be associated with charcot-marie-tooth disease. however, the mechanisms of traditional and alternative functions of hg ...	2014	24898252
metalloproteins containing cytochrome, iron-sulfur, or copper redox centers.		2014	24758379
natural competence and the evolution of dna uptake specificity.	many bacteria are naturally competent, able to actively transport environmental dna fragments across their cell envelope and into their cytoplasm. because incoming dna fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular dna. this review starts with an introductory overview of competence and continues with a detailed consideration of the dna ...	2014	24488316
chlamydia exploit the mammalian tryptophan-depletion defense strategy as a counter-defensive cue to trigger a survival state of persistence.	we previously proposed that in chlamydiaceae rapid vegetative growth and a quiescent state of survival (persistence) depend upon alternative protein translational profiles dictated by host tryptophan (trp) availability. these alternative profiles correspond, respectively, with a set of chlamydial proteins having higher-than-predicted contents of trp ("up-trp" selection), or with another set exhibiting lower-than-predicted contents of trp ("down-trp" selection). a comparative evaluation of chlamy ...	2014	24616884
crystal structure and putative substrate identification for the entamoeba histolytica low molecular weight tyrosine phosphatase.	entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. we have characterized the e. histolytica putative low molecular weight protein tyrosine phosphatase (lmw-ptp). the structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. in amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. a mutant lm ...	2014	24548880
origin and evolution of the peptidyl transferase center from proto-trnas.	we tested the hypothesis of tamura (2011) [3] that molecules of trna gave origin to ribosomes, particularly to the peptidyl transferase center (ptc) of the 23s ribosomal rna. we reconstructed the ancestral sequences from all types of trna and compared them in their sequences with the current ptc of 23s ribosomal rna from different organisms. we built an ancestral sequence of proto-trnas that showed a remarkable overall identity of 50.53% with the catalytic site of ptc. we conclude that the pepti ...	2014	24649398
radical s-adenosylmethionine enzymes.		2014	24476342
bacterial genome instability.	bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ...	2014	24600039
evolution of the f0f1 atp synthase complex in light of the patchy distribution of different bioenergetic pathways across prokaryotes.	bacteria and archaea are characterized by an amazing metabolic diversity, which allows them to persist in diverse and often extreme habitats. apart from oxygenic photosynthesis and oxidative phosphorylation, well-studied processes from chloroplasts and mitochondria of plants and animals, prokaryotes utilize various chemo- or lithotrophic modes, such as anoxygenic photosynthesis, iron oxidation and reduction, sulfate reduction, and methanogenesis. most bioenergetic pathways have a similar general ...	2014	25188293
card integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria.	although the basic mechanisms of prokaryotic transcription are conserved, it has become evident that some bacteria require additional factors to allow for efficient gene transcription. card is an rna polymerase (rnap)-binding protein conserved in numerous bacterial species and essential in mycobacteria. despite the importance of card, its function at transcription complexes remains unclear. we have generated a panel of mutations that individually target three independent functional modules of ca ...	2014	24962732
preliminary x-ray crystallographic analysis of an engineered glutamyl-trna synthetase from escherichia coli.	the nature of interaction between glutamyl-trna synthetase (glurs) and its trna substrate is unique in bacteria in that many bacterial glurs are capable of recognizing two trna substrates: trnaglu and trnagln. to properly understand this distinctive glurs-trna interaction it is important to pursue detailed structure-function studies; however, because of the fact that trna-glurs interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure-function correlation stud ...	2014	25005090
ge23077 binds to the rna polymerase 'i' and 'i+1' sites and prevents the binding of initiating nucleotides.	using a combination of genetic, biochemical, and structural approaches, we show that the cyclic-peptide antibiotic ge23077 (ge) binds directly to the bacterial rna polymerase (rnap) active-center 'i' and 'i+1' nucleotide binding sites, preventing the binding of initiating nucleotides, and thereby preventing transcription initiation. the target-based resistance spectrum for ge is unusually small, reflecting the fact that the ge binding site on rnap includes residues of the rnap active center that ...	2014	24755292
superoxide dismutases and superoxide reductases.		2014	24684599
a homolog of glyceraldehyde-3-phosphate dehydrogenase from riemerella anatipestifer is an extracellular protein and exhibits biological activity.	riemerella anatipestifer is the causative agent of septicemia anserum exsudativa in ducks. its pathogenesis and virulence factors are still unclear. the glycolytic enzyme, glyceraldehyde-3-phosphate dehydrogenase (gapdh), an anchorless and multifunctional protein on the surface of several pathogenic microorganisms, is involved in virulence and adhesion. whether homologs of gapdh exist, and display similar characteristics in r. anatipestifer (ragapdh) has not been determined. in our research, the ...	2014	25183032
carbohydrate metabolism in archaea: current insights into unusual enzymes and pathways and their regulation.	the metabolism of archaea, the third domain of life, resembles in its complexity those of bacteria and lower eukarya. however, this metabolic complexity in archaea is accompanied by the absence of many "classical" pathways, particularly in central carbohydrate metabolism. instead, archaea are characterized by the presence of unique, modified variants of classical pathways such as the embden-meyerhof-parnas (emp) pathway and the entner-doudoroff (ed) pathway. the pentose phosphate pathway is only ...	2014	24600042
recent advances in in vivo applications of intein-mediated protein splicing.	intein-mediated protein splicing has become an essential tool in modern biotechnology. fundamental progress in the structure and catalytic strategies of cis- and trans-splicing inteins has led to the development of modified inteins that promote efficient protein purification, ligation, modification and cyclization. recent work has extended these in vitro applications to the cell or to whole organisms. we review recent advances in intein-mediated protein expression and modification, post-translat ...	2014	24490831
improved cultivation and metagenomics as new tools for bioprospecting in cold environments.	only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. this resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent dna sequence information can be combined with functional screening. the coupling of these two approaches circumvents the need ...	2014	25399309
improved cultivation and metagenomics as new tools for bioprospecting in cold environments.	only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. this resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent dna sequence information can be combined with functional screening. the coupling of these two approaches circumvents the need ...	2014	25399309
stability curve prediction of homologous proteins using temperature-dependent statistical potentials.	the unraveling and control of protein stability at different temperatures is a fundamental problem in biophysics that is substantially far from being quantitatively and accurately solved, as it requires a precise knowledge of the temperature dependence of amino acid interactions. in this paper we attempt to gain insight into the thermal stability of proteins by designing a tool to predict the full stability curve as a function of the temperature for a set of 45 proteins belonging to 11 homologou ...	2014	25032839
rna-seq-based analysis of cold shock response in thermoanaerobacter tengcongensis, a bacterium harboring a single cold shock protein encoding gene.	although cold shock responses and the roles of cold shock proteins in microorganisms containing multiple cold shock protein genes have been well characterized, related studies on bacteria possessing a single cold shock protein gene have not been reported. thermoanaerobacter tengcongensis mb4, a thermophile harboring only one known cold shock protein gene (ttescpc), can survive from 50° to 80 °c, but has poor natural competence under cold shock at 50 °c. we therefore examined cold shock responses ...	2014	24667527
magnesium-dependent processes are targets of bacterial manganese toxicity.	a bradyrhizobium japonicum mutant defective in the gene encoding the high-affinity mn(2+) transporter mnth has a severe growth phenotype under manganese limitation. here, we isolated suppressor mutants of an mnth strain that grew under manganese limitation, and activities of high-affinity mn(2+) transport and mn(2+) -dependent enzymes were partially rescued. the suppressor strains harbour gain-of-function mutations in the gene encoding the mg(2+) channel mgte. the mgte variants likely allow mn(2 ...	2014	24975873
an archaeal crispr type iii-b system exhibiting distinctive rna targeting features and mediating dual rna and dna interference.	crispr-cas systems provide a small rna-based mechanism to defend against invasive genetic elements in archaea and bacteria. to investigate the in vivo mechanism of rna interference by two type iii-b systems (cmr-α and cmr-β) in sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-crispr (ac) locus with a single spacer. after pac plasmids were introduced into different strains, northern analyses confirmed that mature crrnas were produced from the plasmid ...	2014	25505143
an archaeal crispr type iii-b system exhibiting distinctive rna targeting features and mediating dual rna and dna interference.	crispr-cas systems provide a small rna-based mechanism to defend against invasive genetic elements in archaea and bacteria. to investigate the in vivo mechanism of rna interference by two type iii-b systems (cmr-α and cmr-β) in sulfolobus islandicus, a genetic assay was developed using plasmids carrying an artificial mini-crispr (ac) locus with a single spacer. after pac plasmids were introduced into different strains, northern analyses confirmed that mature crrnas were produced from the plasmid ...	2014	25505143
crystal structure of cas9 in complex with guide rna and target dna.	the crispr-associated endonuclease cas9 can be targeted to specific genomic loci by single guide rnas (sgrnas). here, we report the crystal structure of streptococcus pyogenes cas9 in complex with sgrna and its target dna at 2.5 å resolution. the structure revealed a bilobed architecture composed of target recognition and nuclease lobes, accommodating the sgrna:dna heteroduplex in a positively charged groove at their interface. whereas the recognition lobe is essential for binding sgrna and dna, ...	2014	24529477
structures of cas9 endonucleases reveal rna-mediated conformational activation.	type ii crispr (clustered regularly interspaced short palindromic repeats)-cas (crispr-associated) systems use an rna-guided dna endonuclease, cas9, to generate double-strand breaks in invasive dna during an adaptive bacterial immune response. cas9 has been harnessed as a powerful tool for genome editing and gene regulation in many eukaryotic organisms. we report 2.6 and 2.2 angstrom resolution crystal structures of two major cas9 enzyme subtypes, revealing the structural core shared by all cas9 ...	2014	24505130
crystal structures and kinetic properties of enoyl-acyl carrier protein reductase i from candidatus liberibacter asiaticus.	huanglongbing (hlb) is a destructive citrus disease. the leading cause of hlb is candidatus liberibacter asiaticus. fatty acid biosynthesis is essential for bacterial viability and has been validated as a target for the discovery of novel antibacterial agents. enoyl-acyl carrier protein reductase (also called enr or fabi and a product of the fabi gene) is an enzyme required in a critical step of bacterial fatty acid biosynthesis and has attracted attention as a target of novel antimicrobial agen ...	2014	24407918
the moxr atpase rava and its cofactor viaa interact with the nadh:ubiquinone oxidoreductase i in escherichia coli.	moxr atpases are widespread throughout bacteria and archaea. the experimental evidence to date suggests that these proteins have chaperone-like roles in facilitating the maturation of dedicated protein complexes that are functionally diverse. in escherichia coli, the moxr atpase rava and its putative cofactor viaa are found to exist in early stationary-phase cells at 37 °c at low levels of about 350 and 90 molecules per cell, respectively. both proteins are predominantly localized to the cytopla ...	2014	24454883
evolutionary insights about bacterial glxrs from whole genome analyses: is glurs2 a chimera?	evolutionary histories of glutamyl-trna synthetase (glurs) and glutaminyl-trna synthetase (glnrs) in bacteria are convoluted. after the divergence of eubacteria and eukarya, bacterial glurs glutamylated both trnagln and trnaglu until glnrs appeared by horizontal gene transfer (hgt) from eukaryotes or a duplicate copy of glurs (glurs2) that only glutamylates trnagln appeared. the current understanding is based on limited sequence data and not always compatible with available experimental results. ...	2014	24521160
the crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein cae31940 from proteobacterium bordetella bronchiseptica rb50, and evolutionary insight into the nmt1/thi5 family.	we report a 2.0 å structure of the cae31940 protein, a proteobacterial nmt1/thi5-like domain-containing protein. we also discuss the primary and tertiary structure similarity with its homologs. the highly conserved fggxmp motif was identified in cae31940, which corresponds to the gcccx motif located in the vicinity of the active center characteristic for thi5-like proteins found in yeast. this suggests that the fggxmp motif may be a unique hallmark of proteobacterial nmt1/thi5-like proteins.	2014	24908050
structural basis of thermal stability of the tungsten cofactor synthesis protein moab from pyrococcus furiosus.	molybdenum and tungsten cofactors share a similar pterin-based scaffold, which hosts an ene-dithiolate function being essential for the coordination of either molybdenum or tungsten. the biosynthesis of both cofactors involves a multistep pathway, which ends with the activation of the metal binding pterin (mpt) by adenylylation before the respective metal is incorporated. in the hyperthermophilic organism pyrococcus furiosus, the hexameric protein moab (pfumoab) has been shown to catalyse mpt-ad ...	2014	24465852
dna polymerases engineered by directed evolution to incorporate non-standard nucleotides.	dna polymerases have evolved for billions of years to accept natural nucleoside triphosphate substrates with high fidelity and to exclude closely related structures, such as the analogous ribonucleoside triphosphates. however, polymerases that can accept unnatural nucleoside triphosphates are desired for many applications in biotechnology. the focus of this review is on non-standard nucleotides that expand the genetic "alphabet." this review focuses on experiments that, by directed evolution, ha ...	2014	25400626
new mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.	the acel_2062 protein from acidothermus cellulolyticus is a protein of unknown function. initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines and aspartic acid within the motif (hexxhxxgxxd). the acel_2062 protein was chosen by the joint center for structural genomics for crystal structure determination to explore novel protein seq ...	2014	24383880
s-layers: principles and applications.	monomolecular arrays of protein or glycoprotein subunits forming surface layers (s-layers) are one of the most commonly observed prokaryotic cell envelope components. s-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. the isoporous lattices completely covering the cell surface provide organisms with various selection advantages including ...	2014	24483139
conserved amino acid residues of the nuod segment important for structure and function of escherichia coli ndh-1 (complex i).	the nuod segment (homologue of mitochondrial 49 kda subunit) of the proton-translocating nadh:quinone oxidoreductase (complex i/ndh-1) from escherichia coli is in the hydrophilic domain and bears many highly conserved amino acid residues. the three-dimensional structural model of ndh-1 suggests that the nuod segment, together with the neighboring subunits, constitutes a putative quinone binding cavity. we used the homologous dna recombination technique to clarify the role of selected key amino a ...	2014	25545070
conserved amino acid residues of the nuod segment important for structure and function of escherichia coli ndh-1 (complex i).	the nuod segment (homologue of mitochondrial 49 kda subunit) of the proton-translocating nadh:quinone oxidoreductase (complex i/ndh-1) from escherichia coli is in the hydrophilic domain and bears many highly conserved amino acid residues. the three-dimensional structural model of ndh-1 suggests that the nuod segment, together with the neighboring subunits, constitutes a putative quinone binding cavity. we used the homologous dna recombination technique to clarify the role of selected key amino a ...	2014	25545070
re-evaluation of the near infrared spectra of mitochondrial cytochrome c oxidase: implications for non invasive in vivo monitoring of tissues.	we re-determined the near infrared (nir) spectral signatures (650-980nm) of the different cytochrome c oxidase redox centres, in the process separating them into their component species. we confirm that the primary contributor to the oxidase nir spectrum between 700 and 980nm is cupric cua, which in the beef heart enzyme has a maximum at 835nm. the 655nm band characterises the fully oxidised haem a3/cub binuclear centre; it is bleached either when one or more electrons are added to the binuclear ...	2014	25175349
how periplasmic thioredoxin tlpa reduces bacterial copper chaperone scoi and cytochrome oxidase subunit ii (coxb) prior to metallation.	two critical cysteine residues in the copper-a site (cu(a)) on subunit ii (coxb) of bacterial cytochrome c oxidase lie on the periplasmic side of the cytoplasmic membrane. as the periplasm is an oxidizing environment as compared with the reducing cytoplasm, the prediction was that a disulfide bond formed between these cysteines must be eliminated by reduction prior to copper insertion. we show here that a periplasmic thioredoxin (tlpa) acts as a specific reductant not only for the cu(2+) transfe ...	2014	25274631
a third subunit in ancestral cytochrome c-dependent nitric oxide reductases.	reduction of no to n2o by denitrifiying bacteria is catalyzed either by a monomeric quinol-nitric oxide reductase (qnor) or by a heterodimeric cytochrome c-dependent nitric oxide reductase (cnor). in ancient thermophilic bacteria belonging to the thermales and aquificales phylogenetic groups, the cluster encoding the cnor includes a small third gene (norh), in addition to those encoding homologues to the subunits of a typical cnor (norc and norb). we show in thermus thermophilus that the three g ...	2014	24907324
evidence for distinct electron transfer processes in terminal oxidases from different origin by means of protein film voltammetry.	cytochrome aa3 from paracoccus denitrificans and cytochrome ba3 from thermus thermophilus, two distinct members of the heme-copper oxidase superfamily, were immobilized on electrodes modified with gold nanoparticles. this procedure allowed us to achieve direct electron transfer between the enzyme and the gold nanoparticles and to obtain evidence for different electrocatalytic properties of the two enzymes. the ph dependence and thermostability reveal that the enzymes are highly adapted to their ...	2014	25054669
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
characterisation of the active/de-active transition of mitochondrial complex i.	oxidation of nadh in the mitochondrial matrix of aerobic cells is catalysed by mitochondrial complex i. the regulation of this mitochondrial enzyme is not completely understood. an interesting characteristic of complex i from some organisms is the ability to adopt two distinct states: the so-called catalytically active (a) and the de-active, dormant state (d). the a-form in situ can undergo de-activation when the activity of the respiratory chain is limited (i.e. in the absence of oxygen). the m ...	2014	24569053
linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry dft exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.	after a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear fe-a3-cub reaction center in this enzyme. a specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. a larger family of tautomers/protonation states is generate ...	2014	24960612
conserved glycine 232 in the ligand channel of ba3 cytochrome oxidase from thermus thermophilus.	knowing how the protein environment modulates ligand pathways and redox centers in the respiratory heme-copper oxidases is fundamental for understanding the relationship between the structure and function of these enzymes. in this study, we investigated the reactions of o2 and no with the fully reduced g232v mutant of ba3 cytochrome c oxidase from thermus thermophilus (tt ba3) in which a conserved glycine residue in the o2 channel of the enzyme was replaced with a bulkier valine residue. previou ...	2014	24937405
molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.	pyridoxal-5'-phosphate or plp, the active form of vitamin b6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. plp-dependent enzymes account for ∼1.5% of most prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes. here, we structurally and functionally characterize three novel plp-dependent enzymes from bacteria in the human microbiome: ...	2014	24888348
parallel pathways for nitrite reduction during anaerobic growth in thermus thermophilus.	respiratory reduction of nitrate and nitrite is encoded in thermus thermophilus by the respective transferable gene clusters. nitrate is reduced by a heterotetrameric nitrate reductase (nar) encoded along transporters and regulatory signal transduction systems within the nitrate respiration conjugative element (nce). the nitrite respiration cluster (nic) encodes homologues of nitrite reductase (nir) and nitric oxide reductase (nor). the expression and role of the nirsjm genes in nitrite respirat ...	2014	24443532
a sco protein among the hypothetical proteins of bacillus lehensis g1: its 3d macromolecular structure and association with cytochrome c oxidase.	at least a quarter of any complete genome encodes for hypothetical proteins (hps) which are largely non-similar to other known, well-characterized proteins. predicting and solving their structures and functions is imperative to aid understanding of any given organism as a complete biological system. the present study highlights the primary effort to classify and cluster 1202 hps of bacillus lehensis g1 alkaliphile to serve as a platform to mine and select specific hp(s) to be studied further in ...	2014	24641837
crystal structure of an (r)-selective ω-transaminase from aspergillus terreus.	chiral amines are important building blocks for the synthesis of pharmaceutical products, fine chemicals, and agrochemicals. ω-transaminases are able to directly synthesize enantiopure chiral amines by catalysing the transfer of an amino group from a primary amino donor to a carbonyl acceptor with pyridoxal 5'-phosphate (plp) as cofactor. in nature, (s)-selective amine transaminases are more abundant than the (r)-selective enzymes, and therefore more information concerning their structures is av ...	2014	24498081
the mononuclear molybdenum enzymes.		2014	24467397
a biochemical approach to study the role of the terminal oxidases in aerobic respiration in shewanella oneidensis mr-1.	the genome of the facultative anaerobic γ-proteobacterium shewanella oneidensis mr-1 encodes for three terminal oxidases: a bd-type quinol oxidase and two heme-copper oxidases, a a-type cytochrome c oxidase and a cbb 3-type oxidase. in this study, we used a biochemical approach and directly measured oxidase activities coupled to mass-spectrometry analysis to investigate the physiological role of the three terminal oxidases under aerobic and microaerobic conditions. our data revealed that the cbb ...	2014	24466040
transferable denitrification capability of thermus thermophilus.	laboratory-adapted strains of thermus spp. have been shown to require oxygen for growth, including the model strains t. thermophilus hb27 and hb8. in contrast, many isolates of this species that have not been intensively grown under laboratory conditions keep the capability to grow anaerobically with one or more electron acceptors. the use of nitrogen oxides, especially nitrate, as electron acceptors is one of the most widespread capabilities among these facultative strains. in this process, nit ...	2014	24141123
five checkpoints maintaining the fidelity of transcription by rna polymerases in structural and energetic details.	transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in rna, is essential for life. results from molecular dynamics (md) simulations of eukaryotic rna polymerase (rnap) ii and bacterial rnap with experimental data suggest that fidelity may involve as many as five checkpoints. using md simulations, the effects of different active site ntps in both open and closed trigger loop (tl) structures of rnaps are compared. unfavorable initial binding of mism ...	2014	25550432
five checkpoints maintaining the fidelity of transcription by rna polymerases in structural and energetic details.	transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in rna, is essential for life. results from molecular dynamics (md) simulations of eukaryotic rna polymerase (rnap) ii and bacterial rnap with experimental data suggest that fidelity may involve as many as five checkpoints. using md simulations, the effects of different active site ntps in both open and closed trigger loop (tl) structures of rnaps are compared. unfavorable initial binding of mism ...	2014	25550432
the tfe-induced transient native-like structure of the intrinsically disordered σ₄⁷⁰ domain of escherichia coli rna polymerase.	the transient folding of domain 4 of an e. coli rna polymerase σ⁷⁰ subunit (recσ₄⁷⁰) induced by an increasing concentration of 2,2,2-trifluoroethanol (tfe) in an aqueous solution was monitored by means of cd and heteronuclear nmr spectroscopy. nmr data, collected at a 30% tfe, allowed the estimation of the population of a locally folded recσ₄⁷⁰ structure (csi descriptors) and of local backbone dynamics ((15)n relaxation). the spontaneous organization of the helical regions of the initially unfol ...	2014	25261014
dna polymerases as useful reagents for biotechnology - the history of developmental research in the field.	dna polymerase is a ubiquitous enzyme that synthesizes complementary dna strands according to the template dna in living cells. multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. in addition to their fundamental role in maintaining genome integrity during replication and repair, dna polymerases are widely used for dna manipulation in vitro, including dna cloning, sequencing, labeling, mutagenesis, and other purposes. the fu ...	2014	25221550
replication slippage of the thermophilic dna polymerases b and d from the euryarchaeota pyrococcus abyssi.	replication slippage or slipped-strand mispairing involves the misalignment of dna strands during the replication of repeated dna sequences, and can lead to genetic rearrangements such as microsatellite instability. here, we show that polb and pold replicative dna polymerases from the archaeal model pyrococcus abyssi (pab) slip in vitro during replication of a single-stranded dna template carrying a hairpin structure and short direct repeats. we find that this occurs in both their wild-type (exo ...	2014	25177316
from metagenomics to pure culture: isolation and characterization of the moderately halophilic bacterium spiribacter salinus gen. nov., sp. nov.	recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera alkalilimnicola and arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. here we used several strategies and culture media in order to isolate this organism in pure culture. we report the isolatio ...	2014	24747894
inteins as indicators of gene flow in the halobacteria.	this research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the halobacteria. we surveyed 118 genomes representing 26 genera of halobacteria for intein sequences. we then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. we identified 24 proteins in the halobacteria that hav ...	2014	25018750
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant mycobacterium tuberculosis.	rifamycin b, a product of amycolatopsis mediterranei s699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and aids-related mycobacterial infections. however, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of mycobacterium tuberculosis. as part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of ...	2014	24923585
molecular basis of rna polymerase promoter specificity switch revealed through studies of thermus bacteriophage transcription regulator.	transcription initiation is the central point of gene expression regulation. understanding of molecular mechanism of transcription regulation requires, ultimately, the structural understanding of consequences of transcription factors binding to dna-dependent rna polymerase (rnap), the enzyme of transcription. we recently determined a structure of a complex between transcription factor gp39 encoded by a thermus bacteriophage and thermus rnap holoenzyme. in this addendum to the original publicatio ...	2014	25105059
pcr performance of a thermostable heterodimeric archaeal dna polymerase.	dna polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (pcr), cdna cloning, genome sequencing, and nucleic acid based diagnostics. taking into account the multiple dna amplification techniques in use, different dna polymerases must be optimized for each type of application. one of the current tendencies is to reengineer or to discover new dna polymerases with increased performance and broadened substrate ...	2014	24847315
mycobacterial rna polymerase requires a u-tract at intrinsic terminators and is aided by nusg at suboptimal terminators.	intrinsic terminators, which encode gc-rich rna hairpins followed immediately by a 7-to-9-nucleotide (nt) u-rich "u-tract," play principal roles of punctuating and regulating transcription in most bacteria. however, canonical intrinsic terminators with strong u-tracts are underrepresented in some bacterial lineages, notably mycobacteria, leading to proposals that their rna polymerases stop at noncanonical intrinsic terminators encoding various rna structures lacking u-tracts. we generated recomb ...	2014	24713321
the impact of drug resistance on mycobacterium tuberculosis physiology: what can we learn from rifampicin?	the emergence of drug-resistant pathogens poses a major threat to public health. although influenced by multiple factors, high-level resistance is often associated with mutations in target-encoding or related genes. the fitness cost of these mutations is, in turn, a key determinant of the spread of drug-resistant strains. rifampicin (rif) is a frontline anti-tuberculosis agent that targets the rpob-encoded β subunit of the dna-dependent rna polymerase (rnap). in mycobacterium tuberculosis (mtb), ...	2014	26038512
antibiotic streptolydigin requires noncatalytic mg2+ for binding to rna polymerase.	multisubunit rna polymerase, an enzyme that accomplishes transcription in all living organisms, is a potent target for antibiotics. the antibiotic streptolydigin inhibits rna polymerase by sequestering the active center in a catalytically inactive conformation. here, we show that binding of streptolydigin to rna polymerase strictly depends on a noncatalytic magnesium ion which is likely chelated by the aspartate of the bridge helix of the active center. substitutions of this aspartate may explai ...	2014	24342645
structural basis for promoter specificity switching of rna polymerase by a phage factor.	transcription of dna to rna by dna-dependent rna polymerase (rnap) is the first step of gene expression and a major regulation point. bacteriophages hijack their host's transcription machinery and direct it to serve their needs. the gp39 protein encoded by thermus thermophilus phage p23-45 binds the host's rnap and inhibits transcription initiation from its major "-10/-35" class promoters. phage promoters belonging to the minor "extended -10" class are minimally inhibited. we report the crystal ...	2014	24589779
novel highly thermostable endolysin from thermus scotoductus mat2119 bacteriophage ph2119 with amino acid sequence similarity to eukaryotic peptidoglycan recognition proteins.	in this study, we present the discovery and characterization of a highly thermostable endolysin from bacteriophage ph2119 infecting thermus strain mat2119 isolated from geothermal areas in iceland. nucleotide sequence analysis of the 16s rrna gene affiliated the strain with the species thermus scotoductus. bioinformatics analysis has allowed identification in the genome of phage 2119 of an open reading frame (468 bp in length) coding for a 155-amino-acid basic protein with an mr of 17,555. ph211 ...	2014	24271162
structure of the carboxy-terminal domain of mycobacterium tuberculosis card protein: an essential rrna transcriptional regulator.	the card protein is highly expressed in mycobacterial strains under basal conditions and is transcriptionally induced during multiple types of genotoxic stress and starvation. the card protein binds the β subunit of rna polymerase and influences gene expression. the disruption of interactions between card and the β subunit of rna polymerase has a significant effect on mycobacterial survival, resistance to stress and pathogenesis. to understand the structure of card and its interaction with the β ...	2014	24637748
the core of allosteric motion in thermus caldophilus l-lactate dehydrogenase.	for thermus caldophilus l-lactate dehydrogenase (tcldh), fructose 1,6-bisphosphate (fbp) reduced the pyruvate s(0.5) value 10(3)-fold and increased the v(max) value 4-fold at 30 °c and ph 7.0, indicating that tcldh has a much more t state-sided allosteric equilibrium than thermus thermophilus l-lactate dehydrogenase, which has only two amino acid replacements, a154g and h179y. the inactive (t) and active (r) state structures of tcldh were determined at 1.8 and 2.0 å resolution, respectively. the ...	2014	25258319
phylogenetic analysis and evolutionary origins of dna polymerase x-family members.	mammalian dna polymerase (pol) β is the founding member of a large group of dna polymerases now termed the x-family. dna polymerase β has been kinetically, structurally, and biologically well characterized and can serve as a phylogenetic reference. accordingly, we have performed a phylogenetic analysis to understand the relationship between pol β and other members of the x-family of dna polymerases. the bacterial x-family dna polymerases, saccharomyces cerevisiae pol iv, and four mammalian x-fam ...	2014	25112931
intrastrand triplex dna repeats in bacteria: a source of genomic instability.	repetitive nucleic acid sequences are often prone to form secondary structures distinct from b-dna. prominent examples of such structures are dna triplexes. we observed that certain intrastrand triplex motifs are highly conserved and abundant in prokaryotic genomes. a systematic search of 5246 different prokaryotic plasmids and genomes for intrastrand triplex motifs was conducted and the results summarized in the itxf database available online at http://bioinformatics.uni-konstanz.de/utils/itxf/ ...	2015	26450966
molecular mechanism and evolution of guanylate kinase regulation by (p)ppgpp.	the nucleotide (p)ppgpp mediates bacterial stress responses, but its targets and underlying mechanisms of action vary among bacterial species and remain incompletely understood. here, we characterize the molecular interaction between (p)ppgpp and guanylate kinase (gmk), revealing the importance of this interaction in adaptation to starvation. combining structural and kinetic analyses, we show that (p)ppgpp binds the gmk active site and competitively inhibits the enzyme. the (p)ppgpp-gmk interact ...	2015	25661490