Publications

cmr4 is the slicer in the rna-targeting cmr crispr complex.	clustered regularly interspaced short palindromic repeat (crispr) loci and crispr-associated (cas) proteins form an adaptive immune system that protects prokaryotes against plasmids and viruses. the cmr complex, a type iii-b effector complex, uses the crispr rna (crrna) as a guide to target rna. here, we show that the cmr complex of pyrococcus furiosus cleaves rna at multiple sites that are 6 nt apart and are positioned relative to the 5'-end of the crrna. we identified cmr4 as the slicer and de ...	2014	25541196
ttomp85, a β-barrel assembly protein, functions by barrel augmentation.	outer membrane proteins are vital for gram-negative bacteria and organisms that inherited organelles from them. proteins from the omp85/bama family conduct the insertion of membrane proteins into the outer membrane. we show that an eight-stranded outer membrane β-barrel protein, ttoa, is inserted and folded into liposomes by an omp85 homologue. furthermore, we recorded the channel conductance of this omp85 protein in black lipid membranes, alone and in the presence of peptides comprising the seq ...	2014	25537637
ttomp85, a β-barrel assembly protein, functions by barrel augmentation.	outer membrane proteins are vital for gram-negative bacteria and organisms that inherited organelles from them. proteins from the omp85/bama family conduct the insertion of membrane proteins into the outer membrane. we show that an eight-stranded outer membrane β-barrel protein, ttoa, is inserted and folded into liposomes by an omp85 homologue. furthermore, we recorded the channel conductance of this omp85 protein in black lipid membranes, alone and in the presence of peptides comprising the seq ...	2014	25537637
molecular analysis of codon 548 in the rpob gene involved in mycobacterium tuberculosis resistance to rifampin.	most mycobacterium tuberculosis rifampin-resistant strains have been associated with mutations in an 81-bp rifampin resistance-determining region (rrdr) in the gene rpob. however, if this region alone were targeted, rifampin-resistant strains with mutations outside the rrdr would not be detected. in this study, among 51 rifampin-resistant clinical isolates analyzed by sequencing 1,681-bp-long dna fragments containing the rrdr, 47 isolates contained mutations within the rrdr, three isolates conta ...	2015	25534743
enhancing allosteric inhibition in thermus thermophilus phosphofructokinase.	the coupling between the binding of the substrate fru-6-p and the inhibitor phospho(enol)pyruvate (pep) in phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus is much weaker than that seen in a pfk from bacillus stearothermophilus. from the crystal structures of bacillus stearothermophilus pfk (bspfk) the residues at positions 59, 158, and 215 in bspfk are located on the path leading from the allosteric site to the nearest active site and are part of the intricate hydroge ...	2014	25531642
enhancing allosteric inhibition in thermus thermophilus phosphofructokinase.	the coupling between the binding of the substrate fru-6-p and the inhibitor phospho(enol)pyruvate (pep) in phosphofructokinase (pfk) from the extreme thermophile thermus thermophilus is much weaker than that seen in a pfk from bacillus stearothermophilus. from the crystal structures of bacillus stearothermophilus pfk (bspfk) the residues at positions 59, 158, and 215 in bspfk are located on the path leading from the allosteric site to the nearest active site and are part of the intricate hydroge ...	2014	25531642
the bacterial flagellar protein export apparatus processively transports flagellar proteins even with extremely infrequent atp hydrolysis.	for self-assembly of the bacterial flagellum, a specific protein export apparatus utilizes atp and proton motive force (pmf) as the energy source to transport component proteins to the distal growing end. the export apparatus consists of a transmembrane pmf-driven export gate and a cytoplasmic atpase complex composed of flih, flii and flij. the flii(6)flij complex is structurally similar to the α(3)β(3)γ complex of f(o)f(1)-atpase. flij allows the gate to efficiently utilize pmf to drive flagell ...	2014	25531309
evolution of oligomeric state through allosteric pathways that mimic ligand binding.	evolution and design of protein complexes are almost always viewed through the lens of amino acid mutations at protein interfaces. we showed previously that residues not involved in the physical interaction between proteins make important contributions to oligomerization by acting indirectly or allosterically. in this work, we sought to investigate the mechanism by which allosteric mutations act, using the example of the pyrr family of pyrimidine operon attenuators. in this family, a perfectly s ...	2014	25525255
protein acetylation affects acetate metabolism, motility and acid stress response in escherichia coli.	although protein acetylation is widely observed, it has been associated with few specific regulatory functions making it poorly understood. to interrogate its functionality, we analyzed the acetylome in escherichia coli knockout mutants of cobb, the only known sirtuin-like deacetylase, and patz, the best-known protein acetyltransferase. for four growth conditions, more than 2,000 unique acetylated peptides, belonging to 809 proteins, were identified and differentially quantified. nearly 65% of t ...	2014	25518064
metatranscriptomics of n2-fixing cyanobacteria in the amazon river plume.	biological n2 fixation is an important nitrogen source for surface ocean microbial communities. however, nearly all information on the diversity and gene expression of organisms responsible for oceanic n2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from ...	2014	25514535
metatranscriptomics of n2-fixing cyanobacteria in the amazon river plume.	biological n2 fixation is an important nitrogen source for surface ocean microbial communities. however, nearly all information on the diversity and gene expression of organisms responsible for oceanic n2 fixation in the environment has come from targeted approaches that assay only a small number of genes and organisms. using genomes of diazotrophic cyanobacteria to extract reads from extensive meta-genomic and -transcriptomic libraries, we examined diazotroph diversity and gene expression from ...	2014	25514535
structural basis for the interaction of protein s1 with the escherichia coli ribosome.	in gram-negative bacteria, the multi-domain protein s1 is essential for translation initiation, as it recruits the mrna and facilitates its localization in the decoding centre. in sharp contrast to its functional importance, s1 is still lacking from the high-resolution structures available for escherichia coli and thermus thermophilus ribosomes and thus the molecular mechanism governing the s1-ribosome interaction has still remained elusive. here, we present the structure of the n-terminal s1 do ...	2014	25510494
structural basis for the interaction of protein s1 with the escherichia coli ribosome.	in gram-negative bacteria, the multi-domain protein s1 is essential for translation initiation, as it recruits the mrna and facilitates its localization in the decoding centre. in sharp contrast to its functional importance, s1 is still lacking from the high-resolution structures available for escherichia coli and thermus thermophilus ribosomes and thus the molecular mechanism governing the s1-ribosome interaction has still remained elusive. here, we present the structure of the n-terminal s1 do ...	2014	25510494
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
crystal structure of subunits d and f in complex gives insight into energy transmission of the eukaryotic v-atpase from saccharomyces cerevisiae.	eukaryotic v1vo-atpases hydrolyze atp in the v1 domain coupled to ion pumping in vo. a unique mode of regulation of v-atpases is the reversible disassembly of v1 and vo, which reduces atpase activity and causes silencing of ion conduction. the subunits d and f are proposed to be key in these enzymatic processes. here, we describe the structures of two conformations of the subunit df assembly of saccharomyces cerevisiae (scdf) v-atpase at 3.1 å resolution. subunit d (scd) consists of a long pair ...	2014	25505269
crystal structure of subunits d and f in complex gives insight into energy transmission of the eukaryotic v-atpase from saccharomyces cerevisiae.	eukaryotic v1vo-atpases hydrolyze atp in the v1 domain coupled to ion pumping in vo. a unique mode of regulation of v-atpases is the reversible disassembly of v1 and vo, which reduces atpase activity and causes silencing of ion conduction. the subunits d and f are proposed to be key in these enzymatic processes. here, we describe the structures of two conformations of the subunit df assembly of saccharomyces cerevisiae (scdf) v-atpase at 3.1 å resolution. subunit d (scd) consists of a long pair ...	2014	25505269
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
the bypass of zipa by overexpression of ftsn requires a previously unknown conserved ftsn motif essential for ftsa-ftsn interaction supporting a model in which ftsa monomers recruit late cell division proteins to the z ring.	assembly of the divisome in escherichia coli occurs in two temporally distinct steps. first, ftsz filaments attached to the membrane through interaction with ftsa and zipa coalesce into a z ring at midcell. then, additional proteins are recruited to the z ring in a hierarchical manner to form a complete divisome, activated by the arrival of ftsn. recently, we proposed that the interaction of ftsa with itself competes with its ability to recruit downstream division proteins (both require the ic d ...	2015	25496259
a mechanistic model of cor15 protein function in plant freezing tolerance: integration of structural and functional characteristics.	plants as sessile organisms are strongly challenged by environmental stresses. many plants species are able to cold-acclimate, acquiring higher freezing tolerance upon exposure to low but non-freezing temperatures. among a plethora of adaptational processes, this involves the accumulation of cold regulated (cor) proteins that are assumed to stabilize and protect cellular structures during freezing. however, their molecular functions are largely unknown. we recently reported a comprehensive study ...	2014	25496049
first evidence for substrate channeling between proline catabolic enzymes: a validation of domain fusion analysis for predicting protein-protein interactions.	proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase (p5cdh) catalyze the four-electron oxidation of proline to glutamate via the intermediates p5c and l-glutamate-γ-semialdehyde (gsa). in gram-negative bacteria, prodh and p5cdh are fused together in the bifunctional enzyme proline utilization a (puta) whereas in other organisms prodh and p5cdh are expressed as separate monofunctional enzymes. substrate channeling has previously been shown for bifunctional putas, bu ...	2014	25492892
first evidence for substrate channeling between proline catabolic enzymes: a validation of domain fusion analysis for predicting protein-protein interactions.	proline dehydrogenase (prodh) and δ(1)-pyrroline-5-carboxylate (p5c) dehydrogenase (p5cdh) catalyze the four-electron oxidation of proline to glutamate via the intermediates p5c and l-glutamate-γ-semialdehyde (gsa). in gram-negative bacteria, prodh and p5cdh are fused together in the bifunctional enzyme proline utilization a (puta) whereas in other organisms prodh and p5cdh are expressed as separate monofunctional enzymes. substrate channeling has previously been shown for bifunctional putas, bu ...	2014	25492892
crispr rna binding and dna target recognition by purified cascade complexes from escherichia coli.	clustered regularly interspaced short palindromic repeats (crisprs) and their associated cas proteins comprise a prokaryotic rna-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. the type i-e crispr interference complex cascade from escherichia coli is composed of five different cas proteins and a 61-nt-long guide rna (crrna). crrnas contain a unique 32-nt spacer flanked by a repeat-derived 5' handle (8 nt) and a 3' handle (21 nt). the space ...	2014	25488810
crispr rna binding and dna target recognition by purified cascade complexes from escherichia coli.	clustered regularly interspaced short palindromic repeats (crisprs) and their associated cas proteins comprise a prokaryotic rna-guided adaptive immune system that interferes with mobile genetic elements, such as plasmids and phages. the type i-e crispr interference complex cascade from escherichia coli is composed of five different cas proteins and a 61-nt-long guide rna (crrna). crrnas contain a unique 32-nt spacer flanked by a repeat-derived 5' handle (8 nt) and a 3' handle (21 nt). the space ...	2014	25488810
the σ enigma: bacterial σ factors, archaeal tfb and eukaryotic tfiib are homologs.	structural comparisons of initiating rna polymerase complexes and structure-based amino acid sequence alignments of general transcription initiation factors (eukaryotic tfiib, archaeal tfb and bacterial σ factors) show that these proteins are homologs. tfiib and tfb each have two-five-helix cyclin-like repeats (clrs) that include a c-terminal helix-turn-helix (hth) motif (clr/hth domains). four homologous hth motifs are present in bacterial σ factors that are relics of clr/hth domains. sequence ...	2014	25483602
essential structural and functional roles of the cmr4 subunit in rna cleavage by the cmr crispr-cas complex.	the cmr complex is the multisubunit effector complex of the type iii-b clustered regularly interspaced short palindromic repeats (crispr)-cas immune system. the cmr complex recognizes a target rna through base pairing with the integral crispr rna (crrna) and cleaves the target at multiple regularly spaced locations within the complementary region. to understand the molecular basis of the function of this complex, we have assembled information from electron microscopic and x-ray crystallographic ...	2014	25482566
fada5 a thiolase from mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis.	with the exception of hiv, tuberculosis (tb) is the leading cause of mortality among infectious diseases. the urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant mycobacterium tuberculosis (mtb) strains. proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against tb. fada5, a thiolase from mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation ...	2014	25482540
fada5 a thiolase from mycobacterium tuberculosis: a steroid-binding pocket reveals the potential for drug development against tuberculosis.	with the exception of hiv, tuberculosis (tb) is the leading cause of mortality among infectious diseases. the urgent need to develop new antitubercular drugs is apparent due to the increasing number of drug-resistant mycobacterium tuberculosis (mtb) strains. proteins involved in cholesterol import and metabolism have recently been discovered as potent targets against tb. fada5, a thiolase from mtb, is catalyzing the last step of the β-oxidation reaction of the cholesterol side-chain degradation ...	2014	25482540
transcription regulation mechanisms of bacteriophages: recent advances and future prospects.	phage diversity significantly contributes to ecology and evolution of new bacterial species through horizontal gene transfer. therefore, it is essential to understand the mechanisms underlying phage-host interactions. after initial infection, the phage utilizes the transcriptional machinery of the host to direct the expression of its own genes. this review presents a view on the transcriptional regulation mechanisms of bacteriophages, and its contribution to phage diversity and classification. t ...	2014	25482231
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 biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical s-adenosylmethionine enzymes.	sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. the biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links ...	2014	25477512
the biosynthesis of thiol- and thioether-containing cofactors and secondary metabolites catalyzed by radical s-adenosylmethionine enzymes.	sulfur atoms are present as thiol and thioether functional groups in amino acids, coenzymes, cofactors, and various products of secondary metabolic pathways. the biosynthetic pathways for several sulfur-containing biomolecules require the substitution of sulfur for hydrogen at unreactive aliphatic or electron-rich aromatic carbon atoms. examples discussed in this review include biotin, lipoic acid, methylthioether modifications found in some nucleic acids and proteins, and thioether cross-links ...	2014	25477512
movement of elongation factor g between compact and extended conformations.	previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor g (ef-g). here, we follow the movement of domain iv of ef-g relative to domain ii of ef-g using ensemble and single-molecule förster resonance energy transfer. our results indicate that ribosome-free ef-g predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain iv moves away f ...	2014	25463439
movement of elongation factor g between compact and extended conformations.	previous structural studies suggested that ribosomal translocation is accompanied by large interdomain rearrangements of elongation factor g (ef-g). here, we follow the movement of domain iv of ef-g relative to domain ii of ef-g using ensemble and single-molecule förster resonance energy transfer. our results indicate that ribosome-free ef-g predominantly adopts a compact conformation that can also, albeit infrequently, transition into a more extended conformation in which domain iv moves away f ...	2014	25463439
rna targeting by the type iii-a crispr-cas csm complex of thermus thermophilus.	crispr-cas is a prokaryotic adaptive immune system that provides sequence-specific defense against foreign nucleic acids. here we report the structure and function of the effector complex of the type iii-a crispr-cas system of thermus thermophilus: the csm complex (ttcsm). ttcsm is composed of five different protein subunits (csm1-csm5) with an uneven stoichiometry and a single crrna of variable size (35-53 nt). the ttcsm crrna content is similar to the type iii-b cmr complex, indicating that cr ...	2014	25457165
interplay between e. coli dnak, clpb and grpe during protein disaggregation.	the dnak/hsp70 chaperone system and clpb/hsp104 collaboratively disaggregate protein aggregates and reactivate inactive proteins. the teamwork is specific: escherichia coli dnak interacts with e. coli clpb and yeast hsp70, ssa1, interacts with yeast hsp104. this interaction is between the middle domains of hexameric clpb/hsp104 and the dnak/hsp70 nucleotide-binding domain (nbd). to identify the site on e. coli dnak that interacts with clpb, we substituted amino acid residues throughout the dnak ...	2014	25451597
interplay between e. coli dnak, clpb and grpe during protein disaggregation.	the dnak/hsp70 chaperone system and clpb/hsp104 collaboratively disaggregate protein aggregates and reactivate inactive proteins. the teamwork is specific: escherichia coli dnak interacts with e. coli clpb and yeast hsp70, ssa1, interacts with yeast hsp104. this interaction is between the middle domains of hexameric clpb/hsp104 and the dnak/hsp70 nucleotide-binding domain (nbd). to identify the site on e. coli dnak that interacts with clpb, we substituted amino acid residues throughout the dnak ...	2014	25451597
tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by nmr, saxs, chemical crosslinking, and functional studies.	proteins containing iron-sulfur (fe-s) clusters arose early in evolution and are essential to life. organisms have evolved machinery consisting of specialized proteins that operate together to assemble fe-s clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. to date, the best studied system is the iron-sulfur cluster (isc) operon of escherichia coli, and the eight isc proteins it encodes. our investigations over the past five years have id ...	2014	25450980
tangled web of interactions among proteins involved in iron-sulfur cluster assembly as unraveled by nmr, saxs, chemical crosslinking, and functional studies.	proteins containing iron-sulfur (fe-s) clusters arose early in evolution and are essential to life. organisms have evolved machinery consisting of specialized proteins that operate together to assemble fe-s clusters efficiently so as to minimize cellular exposure to their toxic constituents: iron and sulfide ions. to date, the best studied system is the iron-sulfur cluster (isc) operon of escherichia coli, and the eight isc proteins it encodes. our investigations over the past five years have id ...	2014	25450980
a novel mechanism of protein thermostability: a unique n-terminal domain confers heat resistance to fe/mn-sods.	superoxide dismutases (sods), especially thermostable sods, are widely applied in medical treatments, cosmetics, food, agriculture, and other industries given their excellent antioxidant properties. a novel thermostable cambialistic sod from geobacillus thermodenitrificans ng80-2 exhibits maximum activity at 70 °c and high thermostability over a broad range of temperatures (20-80 °c). unlike other reported sods, this enzyme contains an extra repeat-containing n-terminal domain (ntd) of 244 resid ...	2014	25445927
interface matters: the stiffness route to stability of a thermophilic tetrameric malate dehydrogenase.	in this work we investigate by computational means the behavior of two orthologous bacterial proteins, a mesophilic and a thermophilic tetrameric malate dehydrogenase (maldh), at different temperatures. namely, we quantify how protein mechanical rigidity at different length- and time-scales correlates to protein thermophilicity as commonly believed. in particular by using a clustering analysis strategy to explore the conformational space of the folded proteins, we show that at ambient conditions ...	2014	25437494
structural principles of crispr rna processing.	the cas6 superfamily, the cas5d subclass, and the host rnase iii endoribonucleases are responsible for producing small rnas (crrna) that function in the crispr-cas immunity. the three enzymes may also interact with the crrna-associated nucleic acid interference complexes. recent development in structural biology of cas6 and cas5d and their complexes with rna substrates has lent new insights on principles of crrna processing and the structural basis for linking crrna processing to interference. b ...	2014	25435327
structural principles of crispr rna processing.	the cas6 superfamily, the cas5d subclass, and the host rnase iii endoribonucleases are responsible for producing small rnas (crrna) that function in the crispr-cas immunity. the three enzymes may also interact with the crrna-associated nucleic acid interference complexes. recent development in structural biology of cas6 and cas5d and their complexes with rna substrates has lent new insights on principles of crrna processing and the structural basis for linking crrna processing to interference. b ...	2014	25435327
double-sieving-defective aminoacyl-trna synthetase causes protein mistranslation and affects cellular physiology and development.	aminoacyl-trna synthetases (aarss) constitute a family of ubiquitously expressed essential enzymes that ligate amino acids to their cognate trnas for protein synthesis. recently, aars mutations have been linked to various human diseases; however, how these mutations lead to diseases has remained unclear. in order to address the importance of aminoacylation fidelity in multicellular organisms, we generated an amino-acid double-sieving model in drosophila melanogaster using phenylalanyl-trna synth ...	2014	25427601
structure and transport mechanism of the sodium/proton antiporter mjnhap1.	sodium/proton antiporters are essential for sodium and ph homeostasis and play a major role in human health and disease. we determined the structures of the archaeal sodium/proton antiporter mjnhap1 in two complementary states. the inward-open state was obtained by x-ray crystallography in the presence of sodium at ph 8, where the transporter is highly active. the outward-open state was obtained by electron crystallography without sodium at ph 4, where mjnhap1 is inactive. comparison of both str ...	2014	25426803
structure and substrate ion binding in the sodium/proton antiporter panhap.	sodium/proton antiporters maintain intracellular ph and sodium levels. detailed structures of antiporters with bound substrate ions are essential for understanding how they work. we have resolved the substrate ion in the dimeric, electroneutral sodium/proton antiporter panhap from pyrococcus abyssi at 3.2 å, and have determined its structure in two different conformations at ph 8 and ph 4. the ion is coordinated by three acidic sidechains, a water molecule, a serine and a main-chain carbonyl in ...	2014	25426802
structure of putrescine aminotransferase from escherichia coli provides insights into the substrate specificity among class iii aminotransferases.	ygjg is a putrescine aminotransferase enzyme that transfers amino groups from compounds with terminal primary amines to compounds with an aldehyde group using pyridoxal-5'-phosphate (plp) as a cofactor. previous biochemical data show that the enzyme prefers primary diamines, such as putrescine, over ornithine as a substrate. to better understand the enzyme's substrate specificity, crystal structures of ygjg from escherichia coli were determined at 2.3 and 2.1 å resolutions for the free and putre ...	2014	25423189
crystal structure of thermobifida fusca cse1 reveals target dna binding site.	the clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) defense system is the only adaptive and inheritable immunity found in prokaryotes. the immunity is achieved through a multistep process of adaptation, expression, and interference. in the type i-e system, interference is mediated by the crispr-associated complex for antiviral defense (cascade), which recognizes invading double-stranded dna (dsdna) through the protospacer adjacent motif (pam) by one of ...	2014	25420472
crystal structure of thermobifida fusca cse1 reveals target dna binding site.	the clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) defense system is the only adaptive and inheritable immunity found in prokaryotes. the immunity is achieved through a multistep process of adaptation, expression, and interference. in the type i-e system, interference is mediated by the crispr-associated complex for antiviral defense (cascade), which recognizes invading double-stranded dna (dsdna) through the protospacer adjacent motif (pam) by one of ...	2014	25420472
proton transfer in the k-channel analog of b-type cytochrome c oxidase from thermus thermophilus.	a key enzyme in aerobic metabolism is cytochrome c oxidase (cco), which catalyzes the reduction of molecular oxygen to water in the mitochondrial and bacterial membranes. substrate electrons and protons are taken up from different sides of the membrane and protons are pumped across the membrane, thereby generating an electrochemical gradient. the well-studied a-type cco uses two different entry channels for protons: the d-channel for all pumped and two consumed protons, and the k-channel for the ...	2014	25418102
diversity and regulation of atp sulfurylase in photosynthetic organisms.	atp sulfurylase (atps) catalyzes the first committed step in the sulfate assimilation pathway, the activation of sulfate prior to its reduction. atps has been studied in only a few model organisms and even in these cases to a much smaller extent than the sulfate reduction and cysteine synthesis enzymes. this is possibly because the latter were considered of greater regulatory importance for sulfate assimilation. recent evidences (reported in this paper) challenge this view and suggest that atps ...	2014	25414712
recq helicase and recj nuclease provide complementary functions to resect dna for homologous recombination.	recombinational dna repair by the recf pathway of escherichia coli requires the coordinated activities of reca, recfor, recq, recj, and single-strand dna binding (ssb) proteins. these proteins facilitate formation of homologously paired joint molecules between linear double-stranded (dsdna) and supercoiled dna. repair starts with resection of the broken dsdna by recq, a 3'→5' helicase, recj, a 5'→3' exonuclease, and ssb protein. the ends of a dsdna break can be blunt-ended, or they may possess e ...	2014	25411316
argonaute piwi domain and microrna duplex structure regulate small rna sorting in arabidopsis.	small rnas (srnas) are loaded into argonaute (ago) proteins to induce gene silencing. in plants, the 5'-terminal nucleotide is important for srna sorting into different agos. here we show that microrna (mirna) duplex structure also contributes to mirna sorting. base pairing at the 15th nucleotide of a mirna duplex is important for mirna sorting in both arabidopsis ago1 and ago2. ago2 favours mirna duplexes with no middle mismatches, whereas ago1 tolerates, or prefers, duplexes with central misma ...	2014	25406978
structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis.	catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ...	2014	25406313
structural and functional characterization of a ketosteroid transcriptional regulator of mycobacterium tuberculosis.	catabolism of host cholesterol is critical to the virulence of mycobacterium tuberculosis and is a potential target for novel therapeutics. kstr2, a tetr family repressor (tfr), regulates the expression of 15 genes encoding enzymes that catabolize the last half of the cholesterol molecule, represented by 3aα-h-4α(3'-propanoate)-7aβ-methylhexahydro-1,5-indane-dione (hip). binding of kstr2 to its operator sequences is relieved upon binding of hip-coa. a 1.6-å resolution crystal structure of the ks ...	2014	25406313
16s rrna gene mutations associated with decreased susceptibility to tetracycline in mycoplasma bovis.	mycoplasma bovis isolates with decreased susceptibilities to tetracyclines are increasingly reported worldwide. the acquired molecular mechanisms associated with this phenomenon were investigated in 70 clinical isolates of m. bovis. sequence analysis of the two 16s rrna-encoding genes (rrs3 and rrs4 alleles) containing the primary binding pocket for tetracycline (tet-1 site) was performed on isolates with tetracycline hydrochloride mics of 0.125 to 16 μg/ml. mutations at positions a965t, a967t/c ...	2015	25403668
viruses of haloarchaea.	in hypersaline environments, haloarchaea (halophilic members of the archaea) are the dominant organisms, and the viruses that infect them, haloarchaeoviruses are at least ten times more abundant. since their discovery in 1974, described haloarchaeoviruses include head-tailed, pleomorphic, spherical and spindle-shaped morphologies, representing myoviridae, siphoviridae, podoviridae, pleolipoviridae, sphaerolipoviridae and fuselloviridae families. this review overviews current knowledge of haloarc ...	2014	25402735
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
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
phylogenetically driven sequencing of extremely halophilic archaea reveals strategies for static and dynamic osmo-response.	organisms across the tree of life use a variety of mechanisms to respond to stress-inducing fluctuations in osmotic conditions. cellular response mechanisms and phenotypes associated with osmoadaptation also play important roles in bacterial virulence, human health, agricultural production and many other biological systems. to improve understanding of osmoadaptive strategies, we have generated 59 high-quality draft genomes for the haloarchaea (a euryarchaeal clade whose members thrive in hypersa ...	2014	25393412
cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics.	the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ...	2014	25392417
cecafdb: a curated database for the documentation, visualization and comparative analysis of central carbon metabolic flux distributions explored by 13c-fluxomics.	the central carbon metabolic flux database (cecafdb, available at http://www.cecafdb.org) is a manually curated, multipurpose and open-access database for the documentation, visualization and comparative analysis of the quantitative flux results of central carbon metabolism among microbes and animal cells. it encompasses records for more than 500 flux distributions among 36 organisms and includes information regarding the genotype, culture medium, growth conditions and other specific information ...	2014	25392417
structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the lysz·lysw complex from thermus thermophilus.	in the biosynthesis of lysine by thermus thermophilus, the metabolite α-ketoglutarate is converted to the intermediate α-aminoadipate (aaa), which is protected by the 54-amino acid acidic protein lysw. in this study, we determined the crystal structure of lysz from t. thermophilus (ttlysz), an amino acid kinase that catalyzes the second step in the aaa to lysine conversion, which was in a complex with lysw at a resolution of 1.85 å. a crystal analysis coupled with isothermal titration calorimetr ...	2014	25392000
structural insight into amino group-carrier protein-mediated lysine biosynthesis: crystal structure of the lysz·lysw complex from thermus thermophilus.	in the biosynthesis of lysine by thermus thermophilus, the metabolite α-ketoglutarate is converted to the intermediate α-aminoadipate (aaa), which is protected by the 54-amino acid acidic protein lysw. in this study, we determined the crystal structure of lysz from t. thermophilus (ttlysz), an amino acid kinase that catalyzes the second step in the aaa to lysine conversion, which was in a complex with lysw at a resolution of 1.85 å. a crystal analysis coupled with isothermal titration calorimetr ...	2014	25392000
molecular details of a starch utilization pathway in the human gut symbiont eubacterium rectale.	eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. starch is one of the most abundant glycans in the human diet, and e. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. here we present the results of a quantitative proteomics study in which we identify two glycoside hydr ...	2014	25388295
molecular details of a starch utilization pathway in the human gut symbiont eubacterium rectale.	eubacterium rectale is a prominent human gut symbiont yet little is known about the molecular strategies this bacterium has developed to acquire nutrients within the competitive gut ecosystem. starch is one of the most abundant glycans in the human diet, and e. rectale increases in vivo when the host consumes a diet rich in resistant starch, although it is not a primary degrader of this glycan. here we present the results of a quantitative proteomics study in which we identify two glycoside hydr ...	2014	25388295
thermodynamic system drift in protein evolution.	proteins from thermophiles are generally more thermostable than their mesophilic homologs, but little is known about the evolutionary process driving these differences. here we attempt to understand how the diverse thermostabilities of bacterial ribonuclease h1 (rnh) proteins evolved. rnh proteins from thermus thermophilus (ttrnh) and escherichia coli (ecrnh) share similar structures but differ in melting temperature (t(m)) by 20 °c. ttrnh's greater stability is caused in part by the presence of ...	2014	25386647
interacting cytoplasmic loops of subunits a and c of escherichia coli f1f0 atp synthase gate h+ transport to the cytoplasm.	h(+)-transporting f1f0 atp synthase catalyzes the synthesis of atp via coupled rotary motors within f0 and f1. h(+) transport at the subunit a-c interface in transmembranous f0 drives rotation of a cylindrical c10 oligomer within the membrane, which is coupled to rotation of subunit γ within the α3β3 sector of f1 to mechanically drive atp synthesis. f1f0 functions in a reversible manner, with atp hydrolysis driving h(+) transport. atp-driven h(+) transport in a select group of cysteine mutants i ...	2014	25385585
first principles studies of electron tunneling in proteins.	a first principles study of electronic tunneling along the chain of seven fe/s clusters in respiratory complex i, a key enzyme in the respiratory electron transport chain, is described. the broken-symmetry states of the fe/s metal clusters calculated at both dft and semi-empirical zindo levels were utilized to examine both the extremely weak electronic couplings between fe/s clusters and the tunneling pathways, which provide a detailed atomistic-level description of the charge transfer process i ...	2011	25383312
electron tunneling pathways in respiratory complex i. the role of the internal water between the enzyme subunits.	recently, the atomistic details of the electronic wiring of seven fe/s clusters (n3, n1b, n4, n5, n6a, n6b, n2) of respiratory complex i, along which electrons are injected into the electron transport chain, have been revealed; the tunneling pathways between the clusters and the contributing key residues were identified [1]. in this study, the sensitivity of the electron tunneling pathways to the internal water at the protein subunit boundaries is investigated by simulating tunneling pathways of ...	2011	25383069
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
phenotyping the quality of complex medium components by simple online-monitored shake flask experiments.	media containing yeast extracts and other complex raw materials are widely used for the cultivation of microorganisms. however, variations in the specific nutrient composition can occur, due to differences in the complex raw material ingredients and in the production of these components. these lot-to-lot variations can affect growth rate, product yield and product quality in laboratory investigations and biopharmaceutical production processes. in the fda's process analytical technology (pat) ini ...	2014	25376163
silencing by h-ns potentiated the evolution of salmonella.	the bacterial h-ns protein silences expression from sequences with higher at-content than the host genome and is believed to buffer the fitness consequences associated with foreign gene acquisition. loss of h-ns results in severe growth defects in salmonella, but the underlying reasons were unclear. an experimental evolution approach was employed to determine which secondary mutations could compensate for the loss of h-ns in salmonella. six independently derived s. typhimurium hns mutant strains ...	2014	25375226
structure of type ii dehydroquinase from pseudomonas aeruginosa.	pseudomonas aeruginosa causes opportunistic infections and is resistant to most antibiotics. ongoing efforts to generate much-needed new antibiotics include targeting enzymes that are vital for p. aeruginosa but are absent in mammals. one such enzyme, type ii dehydroquinase (dhqase), catalyzes the interconversion of 3-dehydroquinate and 3-dehydroshikimate, a necessary step in the shikimate pathway. this step is vital for the proper synthesis of phenylalanine, tryptophan, tyrosine and other aroma ...	2014	25372814
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
temperature-dependent radiation sensitivity and order of 70s ribosome crystals.	all evidence to date indicates that at t = 100 k all protein crystals exhibit comparable sensitivity to x-ray damage when quantified using global metrics such as change in scaling b factor or integrated intensity versus dose. this is consistent with observations in cryo-electron microscopy, and results because nearly all diffusive motions of protein and solvent, including motions induced by radiation damage, are frozen out. but how do the sensitivities of different proteins compare at room tempe ...	2014	25372680
multilayered polyelectrolyte microcapsules: interaction with the enzyme cytochrome c oxidase.	cell-sized polyelectrolyte capsules functionalized with a redox-driven proton pump protein were assembled for the first time. the interaction of polyelectrolyte microcapsules, fabricated by electrostatic layer-by-layer assembly, with cytochrome c oxidase molecules was investigated. we found that the cytochrome c oxidase retained its functionality, that the functionalized microcapsules interacting with cytochrome c oxidase were permeable and that the permeability characteristics of the microcapsu ...	2014	25372607
a novel cytosolic nadh:quinone oxidoreductase from methanothermobacter marburgensis.	methanothermobacter marburgensis is a strictly anaerobic, thermophilic methanogenic archaeon that uses methanogenesis to convert h2 and co2 to energy. m. marburgensis is one of the best-studied methanogens, and all genes required for methanogenic metabolism have been identified. nonetheless, the present study describes a gene (gene id 9704440) coding for a putative	2014	25372605
molecular mechanisms of survival strategies in extreme conditions.	today, one of the major challenges in biophysics is to disclose the molecular mechanisms underlying biological processes. in such a frame, the understanding of the survival strategies in extreme conditions received a lot of attention both from the scientific and applicative points of view. since nature provides precious suggestions to be applied for improving the quality of life, extremophiles are considered as useful model-systems. the main goal of this review is to present an overview of some ...	2012	25371270
molecular insights into dna interference by crispr-associated nuclease-helicase cas3.	mobile genetic elements in bacteria are neutralized by a system based on clustered regularly interspaced short palindromic repeats (crisprs) and crispr-associated (cas) proteins. type i crispr-cas systems use a "cascade" ribonucleoprotein complex to guide rna specifically to complementary sequence in invader double-stranded dna (dsdna), a process called "interference." after target recognition by cascade, formation of an r-loop triggers recruitment of a cas3 nuclease-helicase, completing the int ...	2014	25368186
structural basis for ion selectivity revealed by high-resolution crystal structure of mg2+ channel mgte.	magnesium is the most abundant divalent cation in living cells and is crucial to several biological processes. mgte is a mg(2+) channel distributed in all domains of life that contributes to the maintenance of cellular mg(2+) homeostasis. here we report the high-resolution crystal structures of the transmembrane domain of mgte, bound to mg(2+), mn(2+) and ca(2+). the high-resolution mg(2+)-bound crystal structure clearly visualized the hydrated mg(2+) ion within its selectivity filter. based on ...	2014	25367295
target rna capture and cleavage by the cmr type iii-b crispr-cas effector complex.	the effector complex of the cmr/type iii-b crispr (clustered regularly interspaced short palindromic repeat)-cas (crispr-associated) system cleaves rnas recognized by the crispr rna (crrna) of the complex and includes six protein subunits of unknown functions. using reconstituted pyrococcus furiosus cmr complexes, we found that each of the six cmr proteins plays a critical role in either crrna interaction or target rna capture. cmr2, cmr3, cmr4, and cmr5 are all required for formation of a crrna ...	2014	25367038
subnanometre-resolution electron cryomicroscopy structure of a heterodimeric abc exporter.	atp-binding cassette (abc) transporters translocate substrates across cell membranes, using energy harnessed from atp binding and hydrolysis at their nucleotide-binding domains. abc exporters are present both in prokaryotes and eukaryotes, with examples implicated in multidrug resistance of pathogens and cancer cells, as well as in many human diseases. tmrab is a heterodimeric abc exporter from the thermophilic gram-negative eubacterium thermus thermophilus; it is homologous to various multidrug ...	2014	25363761
subnanometre-resolution electron cryomicroscopy structure of a heterodimeric abc exporter.	atp-binding cassette (abc) transporters translocate substrates across cell membranes, using energy harnessed from atp binding and hydrolysis at their nucleotide-binding domains. abc exporters are present both in prokaryotes and eukaryotes, with examples implicated in multidrug resistance of pathogens and cancer cells, as well as in many human diseases. tmrab is a heterodimeric abc exporter from the thermophilic gram-negative eubacterium thermus thermophilus; it is homologous to various multidrug ...	2014	25363761
rna. complete pairing not needed.		2014	25359948
arfa recognizes the lack of mrna in the mrna channel after rf2 binding for ribosome rescue.	although trans-translation mediated by tmrna-smpb has long been known as the sole system to relieve bacterial stalled ribosomes, arfa has recently been identified as an alternative factor for ribosome rescue in escherichia coli. this process requires hydrolysis of nascent peptidyl-trna by rf2, which usually acts as a stop codon-specific peptide release factor. it poses a fascinating question of how arfa and rf2 recognize and rescue the stalled ribosome. here, we mapped the location of arfa in th ...	2014	25355516
structural insights into translational recoding by frameshift suppressor trnasufj.	the three-nucleotide mrna reading frame is tightly regulated during translation to ensure accurate protein expression. translation errors that lead to aberrant protein production can result from the uncoupled movement of the trna in either the 5' or 3' direction on mrna. here, we report the biochemical and structural characterization of +1 frameshift suppressor trna(sufj), a trna known to decode four, instead of three, nucleotides. frameshift suppressor trna(sufj) contains an insertion 5' to its ...	2014	25352689
the mechanism of torsin atpase activation.	torsins are membrane-associated atpases whose activity is dependent on two activating cofactors, lamina-associated polypeptide 1 (lap1) and luminal domain-like lap1 (lull1). the mechanism by which these cofactors regulate torsin activity has so far remained elusive. in this study, we identify a conserved domain in these activators that is predicted to adopt a fold resembling an aaa+ (atpase associated with a variety of cellular activities) domain. within these domains, a strictly conserved arg r ...	2014	25352667
on the validation of crystallographic symmetry and the quality of structures.	in 2008, zwart and colleagues observed that the fraction of the structures deposited in the pdb alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (ncs) was about 6%, and that this percentage was rising annually. a few years later, poon and colleagues found that 2% of all the crystal structures in the pdb belonged to higher symmetry space groups than those assigned to them. here, i report an analysis of the x-ray diffraction data deposited for this class of structures, wh ...	2014	25352397
on the validation of crystallographic symmetry and the quality of structures.	in 2008, zwart and colleagues observed that the fraction of the structures deposited in the pdb alleged to have "pseudosymmetry" or "special noncrystallographic symmetry" (ncs) was about 6%, and that this percentage was rising annually. a few years later, poon and colleagues found that 2% of all the crystal structures in the pdb belonged to higher symmetry space groups than those assigned to them. here, i report an analysis of the x-ray diffraction data deposited for this class of structures, wh ...	2014	25352397
the bioconversion of red ginseng ethanol extract into compound k by saccharomyces cerevisiae hj-014.	a β-glucosidase producing yeast strain was isolated from korean traditional rice wine. based on the sequence of the ycl008c gene and analysis of the fatty acid composition, the isolate was identified as saccharomyces cerevisiae strain hj-014. s. cerevisiae hj-014 produced ginsenoside rd, f2, and compound k from the ethanol extract of red ginseng. the production was increased by shaking culture, where the bioconversion efficiency was increased 2-fold compared to standing culture. the production o ...	2014	25346602
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
trigger-helix folding pathway and si3 mediate catalysis and hairpin-stabilized pausing by escherichia coli rna polymerase.	the conformational dynamics of the polymorphous trigger loop (tl) in rna polymerase (rnap) underlie multiple steps in the nucleotide addition cycle and diverse regulatory mechanisms. these mechanisms include nascent rna hairpin-stabilized pausing, which inhibits tl folding into the trigger helices (th) required for rapid nucleotide addition. the nascent rna pause hairpin forms in the rna exit channel and promotes opening of the rnap clamp domain, which in turn stabilizes a partially folded, paus ...	2014	25336618
noncanonical cell-to-cell dna transfer in thermus spp. is insensitive to argonaute-mediated interference.	horizontal gene transfer drives the rapid evolution of bacterial populations. classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. however, some species have nonconserved transfer mechanisms that are not well known. this is the case for the ancient extreme thermophile thermus thermophilus. in this work, we show that t. thermophilus strains are capable of exchanging large dna fragments by a novel mechanism that requires cell-to-c ...	2014	25331432
noncanonical cell-to-cell dna transfer in thermus spp. is insensitive to argonaute-mediated interference.	horizontal gene transfer drives the rapid evolution of bacterial populations. classical processes that promote the lateral flow of genetic information are conserved throughout the prokaryotic world. however, some species have nonconserved transfer mechanisms that are not well known. this is the case for the ancient extreme thermophile thermus thermophilus. in this work, we show that t. thermophilus strains are capable of exchanging large dna fragments by a novel mechanism that requires cell-to-c ...	2014	25331432
rna-protein distance patterns in ribosomes reveal the mechanism of translational attenuation.	elucidating protein translational regulation is crucial for understanding cellular function and drug development. a key molecule in protein translation is ribosome, which is a super-molecular complex extensively studied for more than a half century. the structure and dynamics of ribosome complexes were resolved recently thanks to the development of x-ray crystallography, cryo-em, and single molecule biophysics. current studies of the ribosome have shown multiple functional states, each with a un ...	2014	25326828
thermoadaptation-directed enzyme evolution in an error-prone thermophile derived from geobacillus kaustophilus hta426.	thermostability is an important property of enzymes utilized for practical applications because it allows long-term storage and use as catalysts. in this study, we constructed an error-prone strain of the thermophile geobacillus kaustophilus hta426 and investigated thermoadaptation-directed enzyme evolution using the strain. a mutation frequency assay using the antibiotics rifampin and streptomycin revealed that g. kaustophilus had substantially higher mutability than escherichia coli and bacill ...	2014	25326311