Publications

visualizing the transfer-messenger rna as the ribosome resumes translation.	bacterial ribosomes stalled by truncated mrnas are rescued by transfer-messenger rna (tmrna), a dual-function molecule that contains a trna-like domain (tld) and an internal open reading frame (orf). occupying the empty a site with its tld, the tmrna enters the ribosome with the help of elongation factor tu and a protein factor called small protein b (smpb), and switches the translation to its own orf. in this study, using cryo-electron microscopy, we obtained the first structure of an in vivo-f ...	2010	20940705
the structure of kpn03535 (gi\|152972051), a novel putative lipoprotein from klebsiella pneumoniae, reveals an ob-fold.	kpn03535 (gi\|152972051) is a putative lipoprotein of unknown function that is secreted by klebsiella pneumoniae mgh 78578. the crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the ob-fold and structurally similar to the bacterial cpx-pathway protein nlpe, single-stranded dna-binding (ssb) proteins and toxins. k. pneumoniae mgh 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pat ...	2010	20944219
the structure of kpn03535 (gi\|152972051), a novel putative lipoprotein from klebsiella pneumoniae, reveals an ob-fold.	kpn03535 (gi\|152972051) is a putative lipoprotein of unknown function that is secreted by klebsiella pneumoniae mgh 78578. the crystal structure reveals that despite a lack of any detectable sequence similarity to known structures, it is a novel variant of the ob-fold and structurally similar to the bacterial cpx-pathway protein nlpe, single-stranded dna-binding (ssb) proteins and toxins. k. pneumoniae mgh 78578 forms part of the normal human skin, mouth and gut flora and is an opportunistic pat ...	2010	20944219
biochemical characterization of individual components of the allochromatium vinosum dsrmkjop transmembrane complex aids understanding of complex function in vivo.	the dsrmkjop transmembrane complex has a most important function in dissimilatory sulfur metabolism and consists of cytoplasmic, periplasmic, and membrane integral proteins carrying fes centers and b- and c-type cytochromes as cofactors. in this study, the complex was isolated from the purple sulfur bacterium allochromatium vinosum and individual components were characterized as recombinant proteins. the two integral membrane proteins dsrm and dsrp were successfully produced in escherichia coli ...	2010	20952577
tmrna-smpb: a journey to the centre of the bacterial ribosome.	ribosomes mediate protein synthesis by decoding the information carried by messenger rnas (mrnas) and catalysing peptide bond formation between amino acids. when bacterial ribosomes stall on incomplete messages, the trans-translation quality control mechanism is activated by the transfer-messenger rna bound to small protein b (tmrna-smpb ribonucleoprotein complex). trans-translation liberates the stalled ribosomes and triggers degradation of the incomplete proteins. here, we present the cryo-ele ...	2010	20953161
structure of the mycobacterium tuberculosis d-alanine:d-alanine ligase, a target of the antituberculosis drug d-cycloserine.	d-alanine:d-alanine ligase (ec 6.3.2.4; ddl) catalyzes the atp-driven ligation of two d-alanine (d-ala) molecules to form the d-alanyl:d-alanine dipeptide. this molecule is a key building block in peptidoglycan biosynthesis, making ddl an attractive target for drug development. d-cycloserine (dcs), an analog of d-ala and a prototype ddl inhibitor, has shown promise for the treatment of tuberculosis. here, we report the crystal structure of mycobacterium tuberculosis ddl at a resolution of 2.1 å. ...	2010	20956591
structure of the mycobacterium tuberculosis d-alanine:d-alanine ligase, a target of the antituberculosis drug d-cycloserine.	d-alanine:d-alanine ligase (ec 6.3.2.4; ddl) catalyzes the atp-driven ligation of two d-alanine (d-ala) molecules to form the d-alanyl:d-alanine dipeptide. this molecule is a key building block in peptidoglycan biosynthesis, making ddl an attractive target for drug development. d-cycloserine (dcs), an analog of d-ala and a prototype ddl inhibitor, has shown promise for the treatment of tuberculosis. here, we report the crystal structure of mycobacterium tuberculosis ddl at a resolution of 2.1 å. ...	2010	20956591
modification of 16s ribosomal rna by the ksga methyltransferase restructures the 30s subunit to optimize ribosome function.	all organisms incorporate post-transcriptional modifications into ribosomal rna, influencing ribosome assembly and function in ways that are poorly understood. the most highly conserved modification is the dimethylation of two adenosines near the 3' end of the small subunit rrna. lack of these methylations due to deficiency in the ksga methyltransferase stimulates translational errors during both the initiation and elongation phases of protein synthesis and confers resistance to the antibiotic k ...	2010	20962038
new functional sulfide oxidase-oxygen reductase supercomplex in the membrane of the hyperthermophilic bacterium aquifex aeolicus.	aquifex aeolicus, a hyperthermophilic and microaerophilic bacterium, obtains energy for growth from inorganic compounds alone. it was previously proposed that one of the respiratory pathways in this organism consists of the electron transfer from hydrogen sulfide (h(2)s) to molecular oxygen. h(2)s is oxidized by the sulfide quinone reductase, a membrane-bound flavoenzyme, which reduces the quinone pool. we have purified and characterized a novel membrane-bound multienzyme supercomplex that bring ...	2010	20971847
omnipotent role of archaeal elongation factor 1 alpha (ef1α in translational elongation and termination, and quality control of protein synthesis.	the molecular mechanisms of translation termination and mrna surveillance in archaea remain unclear. in eukaryotes, erf3 and hbs1, which are homologous to the trna carrier gtpase ef1α, respectively bind erf1 and pelota to decipher stop codons or to facilitate mrna surveillance. however, genome-wide searches of archaea have failed to detect any orthologs to both gtpases. here, we report the crystal structure of arf1 from an archaeon, aeropyrum pernix, and present strong evidence that the authenti ...	2010	20974926
genomic adaptation of prokaryotic organisms at high temperature.	one of the central issues of evolutionary genomics is to find out the adaptive strategies of microorganisms to stabilize nucleic acid molecules under high temperature. thermal adaptation hypothesis gives a link between g+c content and growth temperature if there is a considerable variation of guanine and cytosine content between species. however, there has been a long-standing debate regarding the correlations between genomic gc content and optimal growth temperature (topt). we urged that adapta ...	2010	20975899
error-prone translesion dna synthesis by escherichia coli dna polymerase iv (dinb) on templates containing 1,2-dihydro-2-oxoadenine.	escherichia coli dna polymerase iv (pol iv) is involved in bypass replication of damaged bases in dna. reactive oxygen species (ros) are generated continuously during normal metabolism and as a result of exogenous stress such as ionizing radiation. ros induce various kinds of base damage in dna. it is important to examine whether pol iv is able to bypass oxidatively damaged bases. in this study, recombinant pol iv was incubated with oligonucleotides containing thymine glycol (dtg), 5-formyluraci ...	2010	20976264
pivotal roles of three conserved carboxyl residues of the nuoc (30k) segment in the structural integrity of proton-translocating nadh-quinone oxidoreductase from escherichia coli.	the prokaryotic proton-translocating nadh-quinone oxidoreductase (ndh-1) is an l-shaped membrane-bound enzyme that contains 14 subunits (nuoa-nuon or nqo1-nqo14). all subunits have their counterparts in the eukaryotic enzyme (complex i). ndh-1 consists of two domains: the peripheral arm (nuob, -c, -d, -e, -f, -g, and -i) and the membrane arm (nuoa, -h, -j, -k, -l, -m, and -n). in escherichia coli ndh-1, the hydrophilic subunits nuoc/nqo5/30k and nuod/nqo4/49k are fused together in a single polyp ...	2010	20979355
cryo-em structure and rrna model of a translating eukaryotic 80s ribosome at 5.5-a resolution.	protein biosynthesis, the translation of the genetic code into polypeptides, occurs on ribonucleoprotein particles called ribosomes. although x-ray structures of bacterial ribosomes are available, high-resolution structures of eukaryotic 80s ribosomes are lacking. using cryoelectron microscopy and single-particle reconstruction, we have determined the structure of a translating plant (triticum aestivum) 80s ribosome at 5.5-å resolution. this map, together with a 6.1-å map of a saccharomyces cere ...	2010	20980660
molecular mechanisms of the whole dna repair system: a comparison of bacterial and eukaryotic systems.	dna is subjected to many endogenous and exogenous damages. all organisms have developed a complex network of dna repair mechanisms. a variety of different dna repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. recent studies of the fundamental mechanisms for dna repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as f ...	2010	20981145
ph-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase.	p-hydroxyphenylacetate (hpa) 3-hydroxylase (hpah) catalyzes the hydroxylation of hpa at the ortho-position to yield 3,4-dihydroxyphenylacetate. the enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (c(2)). c(2) catalyzes the hydroxylation of hpa using oxygen and reduced fmn as co-substrates. to date, the effects of ph on the oxygenation of the two-component monooxygenases have never been reported. here, we report the reacti ...	2010	21030590
ph-dependent studies reveal an efficient hydroxylation mechanism of the oxygenase component of p-hydroxyphenylacetate 3-hydroxylase.	p-hydroxyphenylacetate (hpa) 3-hydroxylase (hpah) catalyzes the hydroxylation of hpa at the ortho-position to yield 3,4-dihydroxyphenylacetate. the enzyme is a flavin-dependent two-component monooxygenase that consists of a reductase component and an oxygenase component (c(2)). c(2) catalyzes the hydroxylation of hpa using oxygen and reduced fmn as co-substrates. to date, the effects of ph on the oxygenation of the two-component monooxygenases have never been reported. here, we report the reacti ...	2010	21030590
inactivation of the rlud pseudouridine synthase has minimal effects on growth and ribosome function in wild-type escherichia coli and salmonella enterica.	the escherichia coli rlud gene encodes a pseudouridine synthase responsible for the pseudouridine (ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23s rrna. it has been reported that deletion of rlud in k-12 strains of e. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50s ribosomal subunit assembly and 30s-50s subunit association. suppressor mutations in the prfb and prfc genes encoding release factor 2 (rf2) and rf3 that res ...	2010	21037010
inactivation of the rlud pseudouridine synthase has minimal effects on growth and ribosome function in wild-type escherichia coli and salmonella enterica.	the escherichia coli rlud gene encodes a pseudouridine synthase responsible for the pseudouridine (ψ) modifications at positions 1911, 1915, and 1917 in helix 69 of 23s rrna. it has been reported that deletion of rlud in k-12 strains of e. coli is associated with extremely slow growth, increased readthrough of stop codons, and defects in 50s ribosomal subunit assembly and 30s-50s subunit association. suppressor mutations in the prfb and prfc genes encoding release factor 2 (rf2) and rf3 that res ...	2010	21037010
subunit dissociation and metal binding by escherichia coli apo-manganese superoxide dismutase.	metal binding by apo-manganese superoxide dismutase (apo-mnsod) is essential for functional maturation of the enzyme. previous studies have demonstrated that metal binding by apo-mnsod is conformationally gated, requiring protein reorganization for the metal to bind. we have now solved the x-ray crystal structure of apo-mnsod at 1.9å resolution. the organization of active site residues is independent of the presence of the metal cofactor, demonstrating that protein itself templates the unusual m ...	2010	21044611
subunit dissociation and metal binding by escherichia coli apo-manganese superoxide dismutase.	metal binding by apo-manganese superoxide dismutase (apo-mnsod) is essential for functional maturation of the enzyme. previous studies have demonstrated that metal binding by apo-mnsod is conformationally gated, requiring protein reorganization for the metal to bind. we have now solved the x-ray crystal structure of apo-mnsod at 1.9å resolution. the organization of active site residues is independent of the presence of the metal cofactor, demonstrating that protein itself templates the unusual m ...	2010	21044611
structure of dihydroorotase from bacillus anthracis at 2.6 å resolution.	dihydroorotase (ec 3.5.2.3) catalyzes the reversible cyclization of n-carbamoyl-l-aspartate to l-dihydroorotate in the third step of the pyrimidine-biosynthesis pathway in bacillus anthracis. a comparison is made between the structures of dihydroorotase from four different organisms, including b. anthracis dihydroorotase, and reveals substantial variations in the active site, dimer interface and overall tertiary structure. these differences demonstrate the utility of exploring multiple structure ...	2010	21045288
crystallization and preliminary x-ray diffraction analysis of human cytosolic seryl-trna synthetase.	human cytosolic seryl-trna synthetase (hsserrs) is responsible for the covalent attachment of serine to its cognate trna(ser). significant differences between the amino-acid sequences of eukaryotic, prokaryotic and archaebacterial serrss indicate that the domain composition of hsserrs differs from that of its eubacterial and archaebacterial analogues. as a consequence of an n-terminal insertion and a c-terminal extra-sequence, the binding mode of trna(ser) to hsserrs is expected to differ from t ...	2010	21045311
identification, cloning, and characterization of l-phenylserine dehydrogenase from pseudomonas syringae nk-15.	the gene encoding d-phenylserine dehydrogenase from pseudomonas syringae nk-15 was identified, and a 9,246-bp nucleotide sequence containing the gene was sequenced. six orfs were confirmed in the sequenced region, four of which were predicted to form an operon. a homology search of each orf predicted that orf3 encoded l-phenylserine dehydrogenase. hence, orf3 was cloned and overexpressed in escherichia coli cells and recombinant orf3 was purified to homogeneity and characterized. the purified or ...	2010	21048868
temporal regulation of gene expression of the thermus thermophilus bacteriophage p23-45.	regulation of gene expression during infection of the thermophilic bacterium thermus thermophilus hb8 with the bacteriophage p23-45 was investigated. macroarray analysis revealed host transcription shut-off and identified three temporal classes of phage genes; early, middle and late. primer extension experiments revealed that the 5' ends of p23-45 early transcripts are preceded by a common sequence motif that likely defines early viral promoters. t. thermophilus hb8 rna polymerase (rnap) recogni ...	2010	21050864
yaej is a novel ribosome-associated protein in escherichia coli that can hydrolyze peptidyl-trna on stalled ribosomes.	in bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger rna (tmrna). in the absence of tmrna, however, there is evidence that stalled ribosomes are released from non-stop mrnas. here, we show a novel ribosome rescue system mediated by a small basic protein, yaej, from escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (rf). in vitro translation experiments us ...	2010	21051357
yaej is a novel ribosome-associated protein in escherichia coli that can hydrolyze peptidyl-trna on stalled ribosomes.	in bacteria, ribosomes often become stalled and are released by a trans-translation process mediated by transfer-messenger rna (tmrna). in the absence of tmrna, however, there is evidence that stalled ribosomes are released from non-stop mrnas. here, we show a novel ribosome rescue system mediated by a small basic protein, yaej, from escherichia coli, which is similar in sequence and structure to the catalytic domain 3 of polypeptide chain release factor (rf). in vitro translation experiments us ...	2010	21051357
characterization of cytochrome p450 monooxygenase cyp154h1 from the thermophilic soil bacterium thermobifida fusca.	cytochrome p450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. we have cloned the gene for a new cytochrome p450 monooxygenase, named cyp154h1, from the moderately thermophilic soil bacterium thermobifida fusca. the enzyme was overexpressed in escherichia coli at up to 14% of total soluble protein and purified to homogeneity in three steps. cyp154h1 activity was reconstituted using putidaredoxin reductase and putidare ...	2010	21057946
characterization of cytochrome p450 monooxygenase cyp154h1 from the thermophilic soil bacterium thermobifida fusca.	cytochrome p450 monooxygenases are valuable biocatalysts due to their ability to hydroxylate unactivated carbon atoms using molecular oxygen. we have cloned the gene for a new cytochrome p450 monooxygenase, named cyp154h1, from the moderately thermophilic soil bacterium thermobifida fusca. the enzyme was overexpressed in escherichia coli at up to 14% of total soluble protein and purified to homogeneity in three steps. cyp154h1 activity was reconstituted using putidaredoxin reductase and putidare ...	2010	21057946
packaging hiv virion components through dynamic equilibria of a human trna synthetase.	aminoacyl trna synthetases, components of the translation apparatus, have alternative functions outside of translation. the structural and mechanistic basis of these alternative functions is of great interest. as an example, reverse transcription of the hiv genome is primed by a human lysine-specific trna (trna(lys3)) that is packaged (into the virion) by the hiv gag protein with lysyl-trna synthetase (lysrs). not understood is the structural basis for simultaneous packaging of trna(lys3), lysrs ...	2010	21058683
the c-terminal domain of the mutl homolog from neisseria gonorrhoeae forms an inverted homodimer.	the mismatch repair (mmr) pathway serves to maintain the integrity of the genome by removing mispaired bases from the newly synthesized strand. in e. coli, muts, mutl and muth coordinate to discriminate the daughter strand through a mechanism involving lack of methylation on the new strand. this facilitates the creation of a nick by muth in the daughter strand to initiate mismatch repair. many bacteria and eukaryotes, including humans, do not possess a homolog of muth. although the exact strateg ...	2010	21060849
the mycobacterium tuberculosis drugome and its polypharmacological implications.	we report a computational approach that integrates structural bioinformatics, molecular modelling and systems biology to construct a drug-target network on a structural proteome-wide scale. the approach has been applied to the genome of mycobacterium tuberculosis (m.tb), the causative agent of one of today's most widely spread infectious diseases. the resulting drug-target interaction network for all structurally characterized approved drugs bound to putative m.tb receptors, we refer to as the ' ...	2010	21079673
effects of site-directed mutagenesis of mgla on motility and swarming of myxococcus xanthus.	the mgla gene from the bacterium myxococcus xanthus encodes a 22kda protein related to the ras superfamily of monomeric gtpases. mgla is required for the normal function of a-motility (adventurous), s-motility (social), fruiting body morphogenesis, and sporulation. mgla and its homologs differ from all eukaryotic and other prokaryotic gtpases because they have a threonine (thr78) in place of the highly conserved aspartate residue of the consensus pm3 (phosphate-magnesium binding) region. to iden ...	2010	21083931
product-assisted catalysis as the basis of the reaction specificity of threonine synthase.	threonine synthase (ts), which is a pyridoxal 5'-phosphate (plp)-dependent enzyme, catalyzes the elimination of the γ-phosphate group from o-phospho-l-homoserine (ophs) and the subsequent addition of water at cβ to form l-threonine. the catalytic course of ts is the most complex among the plp enzymes, and it is an intriguing problem how the elementary steps are controlled in ts to carry out selective reactions. when l-vinylglycine was added to thermus thermophilus hb8 ts in the presence of phosp ...	2010	21084312
the role of oligomerization and cooperative regulation in protein function: the case of tryptophan synthase.	the oligomerization/co-localization of protein complexes and their cooperative regulation in protein function is a key feature in many biological systems. the synergistic regulation in different subunits often enhances the functional properties of the multi-enzyme complex. the present study used molecular dynamics and brownian dynamics simulations to study the effects of allostery, oligomerization and intermediate channeling on enhancing the protein function of tryptophan synthase (trps). trps u ...	2010	21085641
role of recj-like protein with 5'-3' exonuclease activity in oligo(deoxy)nucleotide degradation.	recj-like proteins belonging to the dhh family have been proposed to function as oligoribonucleases and 3'-phosphoadenosine 5'-phosphate (pap) phosphatases in bacteria and archaea, which do not have orn (oligoribonuclease) and cysq (pap phosphatase) homologs. in this study, we analyzed the biochemical and physiological characterization of the recj-like protein ttha0118 from thermus thermophilus hb8. ttha0118 had high enzymatic activity as an oligodeoxyribonucleotide- and oligoribonucleotide-spec ...	2010	21087930
carbon flux rerouting during mycobacterium tuberculosis growth arrest.	a hallmark of the mycobacterium tuberculosis life cycle is the pathogen's ability to switch between replicative and non-replicative states in response to host immunity. transcriptional profiling by qpcr of ∼ 50 m. tuberculosis genes involved in central and lipid metabolism revealed a re-routing of carbon flow associated with bacterial growth arrest during mouse lung infection. carbon rerouting was marked by a switch from metabolic pathways generating energy and biosynthetic precursors in growing ...	2010	21091505
assembling networks of microbial genomes using linear programming.	microbial genomes exhibit complex sets of genetic affinities due to lateral genetic transfer. assessing the relative contributions of parent-to-offspring inheritance and gene sharing is a vital step in understanding the evolutionary origins and modern-day function of an organism, but recovering and showing these relationships is a challenging problem.	2010	21092133
identification and characterization of a novel fumarase gene by metagenome expression cloning from marine microorganisms.	fumarase catalyzes the reversible hydration of fumarate to l-malate and is a key enzyme in the tricarboxylic acid (tca) cycle and in amino acid metabolism. fumarase is also used for the industrial production of l-malate from the substrate fumarate. thermostable and high-activity fumarases from organisms that inhabit extreme environments may have great potential in industry, biotechnology, and basic research. the marine environment is highly complex and considered one of the main reservoirs of mi ...	2010	21092234
pseudouridine at position 55 in trna controls the contents of other modified nucleotides for low-temperature adaptation in the extreme-thermophilic eubacterium thermus thermophilus.	pseudouridine at position 55 (ψ55) in eubacterial trna is produced by trub. to clarify the role of the ψ55 modification, we constructed a trub gene disruptant (δtrub) strain of thermus thermophilus which is an extreme-thermophilic eubacterium. unexpectedly, the δtrub strain exhibited severe growth retardation at 50 °c. we assumed that these phenomena might be caused by lack of rna chaperone activity of trub, which was previously hypothetically proposed by others. to confirm this idea, we replace ...	2010	21097467
thermus thermophilus glycoside hydrolase family 57 branching enzyme: crystal structure, mechanism of action, and products formed.	branching enzyme (ec 2.4.1.18; glycogen branching enzyme; gbe) catalyzes the formation of α1,6-branching points in glycogen. until recently it was believed that all gbes belong to glycoside hydrolase family 13 (gh13). here we describe the cloning and expression of the thermus thermophilus family gh57-type gbe and report its biochemical properties and crystal structure at 1.35-å resolution. the enzyme has a central (β/α)(7)-fold catalytic domain a with an inserted domain b between β2 and α5 and a ...	2010	21097495
co impedes superfast o2 binding in ba3 cytochrome oxidase from thermus thermophilus.	kinetic studies of heme-copper terminal oxidases using the co flow-flash method are potentially compromised by the fate of the photodissociated co. in this time-resolved optical absorption study, we compared the kinetics of dioxygen reduction by ba(3) cytochrome c oxidase from thermus thermophilus in the absence and presence of co using a photolabile o(2)-carrier. a novel double-laser excitation is introduced in which dioxygen is generated by photolyzing the o(2)-carrier with a 355 nm laser puls ...	2010	21097703
diversity of the early step of the futalosine pathway.	we recently demonstrated that the futalosine pathway was operating in some bacteria for the biosynthesis of menaquinone and that futalosine was converted into dehypoxanthinyl futalosine (dhfl) by an mqnb of thermus thermophilus. in this study, we found that aminodeoxyfutalosine, which has adenine instead of hypoxanthine in futalosine, was directly converted into dhfl by an mqnb of helicobacter pylori. therefore, this step is potentially an attractive target for the development of specific anti-h ...	2010	21098241
rsga releases rbfa from 30s ribosome during a late stage of ribosome biosynthesis.	rsga is a 30s ribosomal subunit-binding gtpase with an unknown function, shortage of which impairs maturation of the 30s subunit. we identified multiple gain-of-function mutants of escherichia coli rbfa, the gene for a ribosome-binding factor, that suppress defects in growth and maturation of the 30s subunit of an rsga-null strain. these mutations promote spontaneous release of rbfa from the 30s subunit, indicating that cellular disorders upon depletion of rsga are due to prolonged retention of ...	2010	21102555
rsga releases rbfa from 30s ribosome during a late stage of ribosome biosynthesis.	rsga is a 30s ribosomal subunit-binding gtpase with an unknown function, shortage of which impairs maturation of the 30s subunit. we identified multiple gain-of-function mutants of escherichia coli rbfa, the gene for a ribosome-binding factor, that suppress defects in growth and maturation of the 30s subunit of an rsga-null strain. these mutations promote spontaneous release of rbfa from the 30s subunit, indicating that cellular disorders upon depletion of rsga are due to prolonged retention of ...	2010	21102555
structural basis of molecular recognition of the leishmania small hydrophilic endoplasmic reticulum-associated protein (sherp) at membrane surfaces.	the 57-residue small hydrophilic endoplasmic reticulum-associated protein (sherp) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, leishmania major, the causative agent of human cutaneous leishmaniasis. previous studies have demonstrated that sherp localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests ...	2010	21106528
structural basis of molecular recognition of the leishmania small hydrophilic endoplasmic reticulum-associated protein (sherp) at membrane surfaces.	the 57-residue small hydrophilic endoplasmic reticulum-associated protein (sherp) shows highly specific, stage-regulated expression in the non-replicative vector-transmitted stages of the kinetoplastid parasite, leishmania major, the causative agent of human cutaneous leishmaniasis. previous studies have demonstrated that sherp localizes as a peripheral membrane protein on the cytosolic face of the endoplasmic reticulum and on outer mitochondrial membranes, whereas its high copy number suggests ...	2010	21106528
an assessment of mechanisms underlying peripheral axonal degeneration caused by aminoacyl-trna synthetase mutations.	mutations in glycyl-, tyrosyl-, and alanyl-trna synthetases (gars, yars and aars respectively) cause autosomal dominant charcot-marie-tooth disease, and mutations in gars cause a similar peripheral neuropathy in mice. aminoacyl-trna synthetases (arss) charge amino acids onto their cognate trnas during translation; however, the pathological mechanism(s) of ars mutations remains unclear. to address this, we tested possible mechanisms using mouse models. first, amino acid mischarging was discounted ...	2010	21115117
an assessment of mechanisms underlying peripheral axonal degeneration caused by aminoacyl-trna synthetase mutations.	mutations in glycyl-, tyrosyl-, and alanyl-trna synthetases (gars, yars and aars respectively) cause autosomal dominant charcot-marie-tooth disease, and mutations in gars cause a similar peripheral neuropathy in mice. aminoacyl-trna synthetases (arss) charge amino acids onto their cognate trnas during translation; however, the pathological mechanism(s) of ars mutations remains unclear. to address this, we tested possible mechanisms using mouse models. first, amino acid mischarging was discounted ...	2010	21115117
evolution of respiratory complex i: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.	modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. respiratory complex i from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. mitochondrial complex i contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. however, the full protein composition of ...	2010	21115482
evolution of respiratory complex i: "supernumerary" subunits are present in the alpha-proteobacterial enzyme.	modern α-proteobacteria are thought to be closely related to the ancient symbiont of eukaryotes, an ancestor of mitochondria. respiratory complex i from α-proteobacteria and mitochondria is well conserved at the level of the 14 "core" subunits, consistent with that notion. mitochondrial complex i contains the core subunits, present in all species, and up to 31 "supernumerary" subunits, generally thought to have originated only within eukaryotic lineages. however, the full protein composition of ...	2010	21115482
identification of an rnase j ortholog in sulfolobus solfataricus: implications for 5'-to-3' directional decay and 5'-end protection of mrna in crenarchaeota.	in both bacteria and eukaryotes, degradation is known to start at the 5' and at the 3' extremities of mrnas. until the recent discovery of 5'-to-3' exoribonucleases in hyperthermophilic euryarchaeota, the exosome was assumed to be the key enzyme in mrna degradation in archaea. by means of zymogram assays and bioinformatics, we have identified a 5'-to-3' exoribonuclease activity in the crenarchaeum sulfolobus solfataricus (sso), which is affected by the phosphorylation state of the 5'-end of the ...	2010	21115637
characterization of a mannose-6-phosphate isomerase from thermus thermophilus and increased l-ribose production by its r142n mutant.	an uncharacterized gene from thermus thermophilus, thought to encode a mannose-6-phosphate isomerase, was cloned and expressed in escherichia coli. the maximal activity of the recombinant enzyme for l-ribulose isomerization was observed at ph 7.0 and 75°c in the presence of 0.5 mm cu(2+). among all of the pentoses and hexoses evaluated, the enzyme exhibited the highest activity for the conversion of l-ribulose to l-ribose, a potential starting material for many l-nucleoside-based pharmaceutical ...	2010	21115698
n-acetyl-d-glucosaminylphosphatidylinositol de-n-acetylase from entamoeba histolytica: metal alters catalytic rates but not substrate affinity.	pig-l/gpi12 proteins are endoplasmic reticulum-resident membrane proteins involved in the second step of glycosylphosphatidylinositol anchor biosynthesis in eukaryotes. we show that the entamoeba histolytica pig-l protein is optimally active in the acidic ph range. the enzyme has an intrinsic low level of de-n-acetylase activity in the absence of metal and is significantly stimulated by divalent cations. metal binding induces a large conformational change in the protein that appears to improve c ...	2010	21118807
n-acetyl-d-glucosaminylphosphatidylinositol de-n-acetylase from entamoeba histolytica: metal alters catalytic rates but not substrate affinity.	pig-l/gpi12 proteins are endoplasmic reticulum-resident membrane proteins involved in the second step of glycosylphosphatidylinositol anchor biosynthesis in eukaryotes. we show that the entamoeba histolytica pig-l protein is optimally active in the acidic ph range. the enzyme has an intrinsic low level of de-n-acetylase activity in the absence of metal and is significantly stimulated by divalent cations. metal binding induces a large conformational change in the protein that appears to improve c ...	2010	21118807
mutation in subdomain g' of mitochondrial elongation factor g1 is associated with combined oxphos deficiency in fibroblasts but not in muscle.	the mitochondrial translation system is responsible for the synthesis of 13 proteins required for oxidative phosphorylation (oxphos), the major energy-generating process of our cells. mitochondrial translation is controlled by various nuclear encoded proteins. in 27 patients with combined oxphos deficiencies, in whom complex ii (the only complex that is entirely encoded by the nuclear dna) showed normal activities, and mutations in the mitochondrial genome as well as polymerase gamma were exclud ...	2010	21119709
mutation in subdomain g' of mitochondrial elongation factor g1 is associated with combined oxphos deficiency in fibroblasts but not in muscle.	the mitochondrial translation system is responsible for the synthesis of 13 proteins required for oxidative phosphorylation (oxphos), the major energy-generating process of our cells. mitochondrial translation is controlled by various nuclear encoded proteins. in 27 patients with combined oxphos deficiencies, in whom complex ii (the only complex that is entirely encoded by the nuclear dna) showed normal activities, and mutations in the mitochondrial genome as well as polymerase gamma were exclud ...	2010	21119709
breps: a flexible and automatic protocol to compute enzyme-specific sequence profiles for functional annotation.	models for the simulation of metabolic networks require the accurate prediction of enzyme function. based on a genomic sequence, enzymatic functions of gene products are today mainly predicted by sequence database searching and operon analysis. other methods can support these techniques: we have developed an automatic method "breps" that creates highly specific sequence patterns for the functional annotation of enzymes.	2010	21122127
head swivel on the ribosome facilitates translocation by means of intra-subunit trna hybrid sites.	the elongation cycle of protein synthesis involves the delivery of aminoacyl-transfer rnas to the aminoacyl-trna-binding site (a site) of the ribosome, followed by peptide-bond formation and translocation of the trnas through the ribosome to reopen the a site. the translocation reaction is catalysed by elongation factor g (ef-g) in a gtp-dependent manner. despite the availability of structures of various ef-g-ribosome complexes, the precise mechanism by which trnas move through the ribosome stil ...	2010	21124459
construction and analyses of tetrameric forms of yeast nad(+)-specific isocitrate dehydrogenase.	yeast nad(+)-specific isocitrate dehydrogenase (idh) is an octameric enzyme composed of four heterodimers of regulatory idh1 and catalytic idh2 subunits. the crystal structure suggested that the interactions between tetramers in the octamer are restricted to defined regions in idh1 subunits from each tetramer. using truncation and mutagenesis, we constructed three tetrameric forms of idh. truncation of five residues from the amino terminus of idh1 did not alter the octameric form of the enzyme, ...	2010	21133413
construction and analyses of tetrameric forms of yeast nad(+)-specific isocitrate dehydrogenase.	yeast nad(+)-specific isocitrate dehydrogenase (idh) is an octameric enzyme composed of four heterodimers of regulatory idh1 and catalytic idh2 subunits. the crystal structure suggested that the interactions between tetramers in the octamer are restricted to defined regions in idh1 subunits from each tetramer. using truncation and mutagenesis, we constructed three tetrameric forms of idh. truncation of five residues from the amino terminus of idh1 did not alter the octameric form of the enzyme, ...	2010	21133413
mutations in the intersubunit bridge regions of 16s rrna affect decoding and subunit-subunit interactions on the 70s ribosome.	the small and large subunits of the ribosome are held together by a series of bridges, involving rna-rna, rna-protein and protein-protein interactions. some 12 bridges have been described for the escherichia coli 70s ribosome. in this work, we have targeted for mutagenesis, some of the 16s rrna residues involved in the formation of intersubunit bridges b3, b5, b6, b7b and b8. in addition to effects on subunit association, the mutant ribosomes also affect the fidelity of translation; bridges b5, ...	2010	21138965
mutations in the intersubunit bridge regions of 16s rrna affect decoding and subunit-subunit interactions on the 70s ribosome.	the small and large subunits of the ribosome are held together by a series of bridges, involving rna-rna, rna-protein and protein-protein interactions. some 12 bridges have been described for the escherichia coli 70s ribosome. in this work, we have targeted for mutagenesis, some of the 16s rrna residues involved in the formation of intersubunit bridges b3, b5, b6, b7b and b8. in addition to effects on subunit association, the mutant ribosomes also affect the fidelity of translation; bridges b5, ...	2010	21138965
structure of a crispr-associated protein cas2 from desulfovibrio vulgaris.	crisprs (clustered regularly interspaced short palindromic repeats) provide bacteria and archaea with rna-guided acquired immunity to invasive dnas. crispr-associated (cas) proteins carry out the immune effector functions. cas2 is a universal component of the crispr system. here, a 1.35 å resolution crystal structure of cas2 from the bacterium desulfovibrio vulgaris (dvucas2) is reported. dvucas2 is a homodimer, with each protomer consisting of an n-terminal βαββαβ ferredoxin fold (amino acids 1 ...	2010	21139194
cloning, purification, crystallization and preliminary x-ray crystallographic analysis of the n-terminal domain of dead-box rna helicase from staphylococcus aureus strain mu50.	dead-box helicases are enzymes with an atp-dependent rna-unwinding function that are involved in a variety of cellular processes including rna splicing, ribosome biogenesis and rna degradation. in this study, the n-terminal domain of dead-box rna helicase from staphylococcus aureus strain mu50 was overexpressed in escherichia coli, purified and crystallized. diffraction data were collected to 2.60 å resolution using a synchrotron-radiation source. the crystal belonged to space group p1, with uni ...	2010	21139222
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.	leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...	2010	21144880
structure of leishmania major methionyl-trna synthetase in complex with intermediate products methionyladenylate and pyrophosphate.	leishmania parasites cause two million new cases of leishmaniasis each year with several hundreds of millions of people at risk. due to the paucity and shortcomings of available drugs, we have undertaken the crystal structure determination of a key enzyme from leishmania major in hopes of creating a platform for the rational design of new therapeutics. crystals of the catalytic core of methionyl-trna synthetase from l. major (lmmetrs) were obtained with the substrates mgatp and methionine presen ...	2010	21144880
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.	ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...	2010	21147776
electron cryomicroscopy structure of a membrane-anchored mitochondrial aaa protease.	ftsh-related aaa proteases are conserved membrane-anchored, atp-dependent molecular machines, which mediate the processing and turnover of soluble and membrane-embedded proteins in eubacteria, mitochondria, and chloroplasts. homo- and hetero-oligomeric proteolytic complexes exist, which are composed of homologous subunits harboring an atpase domain of the aaa family and an h41 metallopeptidase domain. mutations in subunits of mitochondrial m-aaa proteases have been associated with different neur ...	2010	21147776
phenotypic characterization of transgenic mice overexpressing neuregulin-1.	neuregulin-1 (nrg1) is one of the susceptibility genes for schizophrenia and implicated in the neurotrophic regulation of gabaergic and dopaminergic neurons, myelination, and nmda receptor function. postmortem studies often indicate a pathologic association of increased nrg1 expression or signaling with this illness. however, the psychobehavioral implication of nrg1 signaling has mainly been investigated using hypomorphic mutant mice for individual nrg1 splice variants.	2010	21151609
molecular dynamics of ribosomal elongation factors g and tu.	translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...	2010	21152913
molecular dynamics of ribosomal elongation factors g and tu.	translation on the ribosome is controlled by external factors. during polypeptide lengthening, elongation factors ef-tu and ef-g consecutively interact with the bacterial ribosome. ef-tu binds and delivers an aminoacyl-trna to the ribosomal a site and ef-g helps translocate the trnas between their binding sites after the peptide bond is formed. these processes occur at the expense of gtp. ef-tu:trna and ef-g are of similar shape, share a common binding site, and undergo large conformational chan ...	2010	21152913
functional role of ribosomal signatures.	although structure and sequence signatures in ribosomal rna and proteins are defining characteristics of the three domains of life and instrumental in constructing the modern phylogeny, little is known about their functional roles in the ribosome. in this work, the largest coevolving rna/protein signatures in the bacterial 30s ribosome are investigated both experimentally and computationally through all-atom molecular-dynamics simulations. the complex includes the n-terminal fragment of the ribo ...	2010	21156135
intrinsic resistance to aminoglycosides in enterococcus faecium is conferred by the 16s rrna m5c1404-specific methyltransferase efmm.	aminoglycosides are ribosome-targeting antibiotics and a major drug group of choice in the treatment of serious enterococcal infections. here we show that aminoglycoside resistance in enterococcus faecium strain cip 54-32 is conferred by the chromosomal gene efmm, encoding the e. faecium methyltransferase, as well as by the previously characterized aac(6')-ii that encodes a 6'-n-aminoglycoside acetyltransferase. inactivation of efmm in e. faecium increases susceptibility to the aminoglycosides k ...	2010	21159796
biochemistry. catalyzing no to n2o in the nitrogen cycle.		2010	21164002
methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.	the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ...	2010	21166890
methylthioadenosine/s-adenosylhomocysteine nucleosidase, a critical enzyme for bacterial metabolism.	the importance of methylthioadenosine/s-adenosylhomocysteine (mta/sah) nucleosidase in bacteria has started to be appreciated only in the past decade. a comprehensive analysis of its various roles here demonstrates that it is an integral component of the activated methyl cycle, which recycles adenine and methionine through s-adenosylmethionine (sam)-mediated methylation reactions, and also produces the universal quorum-sensing signal, autoinducer-2 (ai-2). sam is also essential for synthesis of ...	2010	21166890
a mechanism for single-stranded dna-binding protein (ssb) displacement from single-stranded dna upon ssb-reco interaction.	displacement of single-stranded dna (ssdna)-binding protein (ssb) from ssdna is necessary for filament formation of reca on ssdna to initiate homologous recombination. the interaction between reco and ssb is considered to be important for ssb displacement; however, the interaction has not been characterized at the atomic level. in this study, to clarify the mechanism underlying ssb displacement from ssdna upon reco binding, we examined the interaction between thermus thermophilus reco and cognat ...	2010	21169364
metagenomic analyses: past and future trends.	metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ...	2010	21169428
metagenomic analyses: past and future trends.	metagenomics has revolutionized microbiology by paving the way for a cultivation-independent assessment and exploitation of microbial communities present in complex ecosystems. metagenomics comprising construction and screening of metagenomic dna libraries has proven to be a powerful tool to isolate new enzymes and drugs of industrial importance. so far, the majority of the metagenomically exploited habitats comprised temperate environments, such as soil and marine environments. recently, metage ...	2010	21169428
lateral transfer of the denitrification pathway genes among thermus thermophilus strains.	nitrate respiration is a common and strain-specific property in thermus thermophilus encoded by the nitrate respiration conjugative element (nce) that can be laterally transferred by conjugation. in contrast, nitrite respiration and further denitrification steps are restricted to a few isolates of this species. these later steps of the denitrification pathway are under the regulatory control of an nce-encoded transcription factor, but nothing is known about their coding sequences or its putative ...	2010	21169443
a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12.	β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ...	2010	21169565
a proteomic and transcriptomic approach reveals new insight into beta-methylthiolation of escherichia coli ribosomal protein s12.	β-methylthiolation is a novel post-translational modification mapping to a universally conserved asp 88 of the bacterial ribosomal protein s12. this s12 specific modification has been identified on orthologs from multiple bacterial species. the origin and functional significance was investigated with both a proteomic strategy to identify candidate s12 interactors and expression microarrays to search for phenotypes that result from targeted gene knockouts of select candidates. utilizing an endoge ...	2010	21169565
crystal structure of stable protein cuta1 from psychrotrophic bacterium shewanella sp. sib1.	cuta1 is widely found in bacteria, plants and animals, including humans. the functions of cuta1, however, have not been well clarified. it is known that cuta1s from pyrococcus horikoshii, thermus thermophilus and oryza sativa unfold at temperatures remarkably higher than the growth temperatures of the host organisms. in this work the crystal structure of cuta1 from the psychrotrophic bacterium shewanella sp. sib1 (sib1-cuta1) in a trimeric form was determined at 2.7 å resolution. this is the fir ...	2010	21169681
the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects.	rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ...	2010	21177858
the structural and biochemical characterization of human rnase h2 complex reveals the molecular basis for substrate recognition and aicardi-goutières syndrome defects.	rnase h2 cleaves rna sequences that are part of rna/dna hybrids or that are incorporated into dna, thus, preventing genomic instability and the accumulation of aberrant nucleic acid, which in humans induces aicardi-goutières syndrome, a severe autoimmune disorder. the 3.1 å crystal structure of human rnase h2 presented here allowed us to map the positions of all 29 mutations found in aicardi-goutières syndrome patients, several of which were not visible in the previously reported mouse rnase h2. ...	2010	21177858
valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder.	the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro.	2010	21184843
valproate uncompetitively inhibits arachidonic acid acylation by rat acyl-coa synthetase 4: relevance to valproate's efficacy against bipolar disorder.	the ability of chronic valproate (vpa) to reduce arachidonic acid (aa) turnover in brain phospholipids of unanesthetized rats has been ascribed to its inhibition of acyl-coa synthetase (acsl)-mediated activation of aa to aa-coa. our aim was to identify a rat acsl isoenzyme that could be inhibited by vpa in vitro.	2010	21184843
structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila.	fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ...	2010	21185305
structural and functional studies of fatty acyl adenylate ligases from e. coli and l. pneumophila.	fatty acyl-amp ligase (faal) is a new member of a family of adenylate-forming enzymes that were recently discovered in mycobacterium tuberculosis. they are similar in sequence to fatty acyl-coenzyme a (coa) ligases (facls). however, while facls perform a two-step catalytic reaction, amp ligation followed by coa ligation using atp and coa as cofactors, faals produce only the acyl adenylate and are unable to perform the second step. we report x-ray crystal structures of full-length faal from esche ...	2010	21185305
rna polymerase and transcription elongation factor spt4/5 complex structure.	spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ...	2010	21187417
rna polymerase and transcription elongation factor spt4/5 complex structure.	spt4/5 in archaea and eukaryote and its bacterial homolog nusg is the only elongation factor conserved in all three domains of life and plays many key roles in cotranscriptional regulation and in recruiting other factors to the elongating rna polymerase. here, we present the crystal structure of spt4/5 as well as the structure of rna polymerase-spt4/5 complex using cryoelectron microscopy reconstruction and single particle analysis. the spt4/5 binds in the middle of rna polymerase claw and enclo ...	2010	21187417
asymmetric atp hydrolysis cycle of the heterodimeric multidrug abc transport complex tmrab from thermus thermophilus.	atp-binding cassette (abc) systems translocate a wide range of solutes across cellular membranes. the thermophilic gram-negative eubacterium thermus thermophilus, a model organism for structural genomics and systems biology, discloses ∼46 abc proteins, which are largely uncharacterized. here, we functionally analyzed the first two and only abc half-transporters of the hyperthermophilic bacterium, tmra and tmrb. the abc system mediates uptake of the drug hoechst 33342 in inside-out oriented vesic ...	2010	21190941
structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains.	argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ...	2010	21193640
structural basis for pirna 2'-o-methylated 3'-end recognition by piwi paz (piwi/argonaute/zwille) domains.	argonaute and piwi proteins are key players in the rna silencing pathway, with the former interacting with micro-rnas (mirnas) and sirnas, whereas the latter targets piwi-interacting rnas (pirnas) that are 2'-o-methylated (2(')-och(3)) at their 3' ends. germline-specific pirnas and piwi proteins play a critical role in genome defense against transposable elements, thereby protecting the genome against transposon-induced defects in gametogenesis and fertility. humans contain four piwi family prot ...	2010	21193640
genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli.	escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ...	2010	21195716
genetic evidence for a novel interaction between transcriptional activator soxs and region 4 of the σ(70) subunit of rna polymerase at class ii soxs-dependent promoters in escherichia coli.	escherichia coli soxs activates transcription of the genes of the soxrs regulon, which provide the cell's defense against oxidative stress. in response to this stress, soxs is synthesized de novo. because the dna binding site of soxs is highly degenerate, soxs efficiently activates transcription by the mechanism of prerecruitment. in prerecruitment, newly synthesized soxs first forms binary complexes with rna polymerase. these complexes then scan the chromosome for class i and ii soxs-dependent ...	2010	21195716
metabolic engineering for improved microbial pentose fermentation.	global concern over the depletion of fossil fuel reserves, and the detrimental impact that combustion of these materials has on the environment, is focusing attention on initiatives to create sustainable approaches for the production and use of biofuels from various biomass substrates. the development of a low-cost, safe and eco-friendly process for the utilization of renewable resources to generate value-added products with biotechnological potential as well as robust microorganisms capable of ...	2010	21468211
complete genome sequence of meiothermus ruber type strain (21).	meiothermus ruber (loginova et al. 1984) nobre et al. 1996 is the type species of the genus meiothermus. this thermophilic genus is of special interest, as its members share relatively low degrees of 16s rrna gene sequence similarity and constitute a separate evolutionary lineage from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. the temperature related split is in accordance with the chemotaxonomic feature of the polar l ...	2010	21304689
complete genome sequence of meiothermus silvanus type strain (vi-r2).	meiothermus silvanus (tenreiro et al. 1995) nobre et al. 1996 belongs to a thermophilic genus whose members share relatively low degrees of 16s rrna gene sequence similarity. meiothermus constitutes an evolutionary lineage separate from members of the genus thermus, from which they can generally be distinguished by their slightly lower temperature optima. m. silvanus is of special interest as it causes colored biofilms in the paper making industry and may thus be of economic importance as a biof ...	2010	21304690