Publications

functional characterization of osmotically inducible protein c (mg_427) from mycoplasma genitalium.	mycoplasma genitalium is the smallest self-replicating bacterium and an important human pathogen responsible for a range of urogenital infections and pathologies. due to its limited genome size, many genes conserved in other bacteria are missing in m. genitalium. genes encoding catalase and superoxide dismutase are absent, and how this pathogen overcomes oxidative stress remains poorly understood. in this study, we characterized mg_427, a homolog of the conserved osmc, which encodes hydroperoxid ...	2014	24363346
trna anticodon shifts in eukaryotic genomes.	embedded in the sequence of each transfer rna are elements that promote specific interactions with its cognate aminoacyl trna-synthetase. although many such "identity elements" are known, their detection is difficult since they rely on unique structural signatures and the combinatorial action of multiple elements spread throughout the trna molecule. since the anticodon is often a major identity determinant itself, it is possible to switch between certain trna functional types by means of anticod ...	2014	24442610
structure and mechanism of soybean atp sulfurylase and the committed step in plant sulfur assimilation.	enzymes of the sulfur assimilation pathway are potential targets for improving nutrient content and environmental stress responses in plants. the committed step in this pathway is catalyzed by atp sulfurylase, which synthesizes adenosine 5'-phosphosulfate (aps) from sulfate and atp. to better understand the molecular basis of this energetically unfavorable reaction, the x-ray crystal structure of atp sulfurylase isoform 1 from soybean (glycine max atp sulfurylase) in complex with aps was determi ...	2014	24584934
halorhabdus tiamatea: proteogenomics and glycosidase activity measurements identify the first cultivated euryarchaeon from a deep-sea anoxic brine lake as potential polysaccharide degrader.	euryarchaea from the genus halorhabdus have been found in hypersaline habitats worldwide, yet are represented by only two isolates: halorhabdus utahensis ax-2(t) from the shallow great salt lake of utah, and halorhabdus tiamatea sarl4b(t) from the shaban deep-sea hypersaline anoxic lake (dhal) in the red sea. we sequenced the h. tiamatea genome to elucidate its niche adaptations. among sequenced archaea, h. tiamatea features the highest number of glycoside hydrolases, the majority of which were ...	2014	24428220
transcription elongation. heterogeneous tracking of rna polymerase and its biological implications.	regulation of transcription elongation via pausing of rna polymerase has multiple physiological roles. the pausing mechanism depends on the sequence heterogeneity of the dna being transcribed, as well as on certain interactions of polymerase with specific dna sequences. in order to describe the mechanism of regulation, we introduce the concept of heterogeneity into the previously proposed alternative models of elongation, power stroke and brownian ratchet. we also discuss molecular origins and p ...	2014	25764114
insights into the glycosylase search for damage from single-molecule fluorescence microscopy.	the first step of base excision repair utilizes glycosylase enzymes to find damage within a genome. a persistent question in the field of dna repair is how glycosylases interact with dna to specifically find and excise target damaged bases with high efficiency and specificity. ensemble studies have indicated that glycosylase enzymes rely upon both sliding and distributive modes of search, but ensemble methods are limited in their ability to directly observe these modes. here we review insights i ...	2014	24560296
high-affinity gold nanoparticle pin to label and localize histidine-tagged protein in macromolecular assemblies.	there is significant demand for experimental approaches to aid protein localization in electron microscopy micrographs and ultimately in three-dimensional reconstructions of macromolecular assemblies. we report preparation and use of a reagent consisting of tris-nitrilotriacetic acid (tris-nta) conjugated with a monofunctional gold nanoparticle ((aunp)tris-nta) for site-specific, non-covalent labeling of protein termini fused to a histidine-tag (his-tag). multivalent binding of tris-nta to a his ...	2014	24560806
mechanism of trans-translation revealed by in vitro studies.	tmrna is a bacterial small rna having a structure resembling the upper half of trna and its 3' end accepts alanine followed by binding to ef-tu like trna. instead of lacking a lower half of the cloverleaf structure including the anticodon, tmrna has a short coding sequence for tag-peptide that serves as a target of cellular proteases. an elaborate coordination of two functions as trna and mrna facilitates an irregular translation termed trans-translation: a single polypeptide is synthesized from ...	2014	24600445
tetartohedral twinning in idi-2 from thermus thermophilus: crystallization under anaerobic conditions.	type-2 isopentenyl diphosphate isomerase (idi-2) is a key flavoprotein involved in the biosynthesis of isoprenoids. since fully reduced flavin mononucleotide (fmnh2) is needed for activity, it was decided to crystallize the enzyme under anaerobic conditions in order to understand how this reduced cofactor binds within the active site and interacts with the substrate isopentenyl diphosphate (ipp). in this study, the protein was expressed and purified under aerobic conditions and then reduced and ...	2014	24598924
paclitaxel induces apoptosis in breast cancer cells through different calcium--regulating mechanisms depending on external calcium conditions.	previously, we reported that endoplasmic reticulum calcium stores were a direct target for paclitaxel initiation of apoptosis. furthermore, the actions of paclitaxel attenuated bcl-2 resistance to apoptosis through endoplasmic reticulum-mediated calcium release. to better understand the calcium-regulated mechanisms of paclitaxel-induced apoptosis in breast cancer cells, we investigated the role of extracellular calcium, specifically; whether influx of extracellular calcium contributed to and/or ...	2014	24549172
dna-guided dna interference by a prokaryotic argonaute.	rna interference is widely distributed in eukaryotes and has a variety of functions, including antiviral defence and gene regulation. all rna interference pathways use small single-stranded rna (ssrna) molecules that guide proteins of the argonaute (ago) family to complementary ssrna targets: rna-guided rna interference. the role of prokaryotic ago variants has remained elusive, although bioinformatics analysis has suggested their involvement in host defence. here we demonstrate that ago of the ...	2014	24531762
ion mobility-mass spectrometry of a rotary atpase reveals atp-induced reduction in conformational flexibility.	rotary atpases play fundamental roles in energy conversion as their catalytic rotation is associated with interdomain fluctuations and heterogeneity of conformational states. using ion mobility mass spectrometry we compared the conformational dynamics of the intact atpase from thermus thermophilus with those of its membrane and soluble subcomplexes. our results define regions with enhanced flexibility assigned to distinct subunits within the overall assembly. to provide a structural context for ...	2014	24557135
the k-junction motif in rna structure.	the k-junction is a structural motif in rna comprising a three-way helical junction based upon kink turn (k-turn) architecture. a computer program written to examine relative helical orientation identified the three-way junction of the arabidopsis tpp riboswitch as an elaborated k-turn. the escherichia coli tpp riboswitch contains a related k-junction, and analysis of >11 000 sequences shows that the structure is common to these riboswitches. the k-junction exhibits all the key features of an n1 ...	2014	24531930
chlorite dismutases - a heme enzyme family for use in bioremediation and generation of molecular oxygen.	chlorite is a serious environmental concern, as rising concentrations of this harmful anthropogenic compound have been detected in groundwater, drinking water, and soil. chlorite dismutases (clds) are therefore important molecules in bioremediation as clds catalyze the degradation of chlorite to chloride and molecular oxygen. clds are heme b-containing oxidoreductases present in numerous bacterial and archaeal phyla. this review presents the phylogeny of functional clds and cld-like proteins, an ...	2014	24519858
using ¹⁵n-ammonium to characterise and map potassium binding sites in proteins by nmr spectroscopy.	a variety of enzymes are activated by the binding of potassium ions. the potassium binding sites of these enzymes are very specific, but ammonium ions can often replace potassium ions in vitro because of their similar ionic radii. in these cases, ammonium can be used as a proxy for potassium to characterise potassium binding sites in enzymes: the (1) h,(15) n spin-pair of enzyme-bound (15) nh4 (+) can be probed by (15) n-edited heteronuclear nmr experiments. here, we demonstrate the use of nmr s ...	2014	24520048
the putative trna 2-thiouridine synthetase ncs6 is an essential sulfur carrier in methanococcus maripaludis.	thiolation of carbon-2 of uridine located in the first position of the anticodons of trnauug(gln), trnauuc(glu), and trnauuu(lys) is a conserved rna modification event requiring the 2-thiouridine synthetase ncs6/ctu1 in archaea and eukaryotes. ncs6/ctu1 activates uridine by adenylation, but its role in sulfur transfer is unclear. here we show that mmp1356, the ncs6/ctu1 homolog in the archaeon methanococcus maripaludis, forms a persulfide enzyme adduct with an active site cysteine; this suggests ...	2014	24530533
structural basis and target-specific modulation of adp sensing by the synechococcus elongatus pii signaling protein.	pii signaling proteins comprise one of the most versatile signaling devices in nature and have a highly conserved structure. in cyanobacteria, pipx and n-acetyl-l-glutamate kinase are receptors of pii signaling, and these interactions are modulated by adp, atp, and 2-oxoglutarate. these effector molecules bind interdependently to three anti-cooperative binding sites on the trimeric pii protein and thereby affect its structure. here we used the pii protein from synechococcus elongatus pcc 7942 to ...	2014	24519945
a new system for naming ribosomal proteins.	a system for naming ribosomal proteins is described that the authors intend to use in the future. they urge others to adopt it. the objective is to eliminate the confusion caused by the assignment of identical names to ribosomal proteins from different species that are unrelated in structure and function. in the system proposed here, homologous ribosomal proteins are assigned the same name, regardless of species. it is designed so that new names are similar enough to old names to be easily recog ...	2014	24524803
inhibition of the 4fe-4s proteins ispg and isph: an epr, endor and hyscore investigation.	ispg and isph are proteins that are involved in isoprenoid biosynthesis in most bacteria as well as in malaria parasites and are important drug targets. they contain cubane-type 4fe-4s clusters that are involved in unusual 2h(+)/2e(-) reductions. here, we report the results of electron paramagnetic resonance spectroscopic investigations of the binding of amino- and thiolo-hmbpp (hmbpp=e-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate) isph substrate-analog inhibitors to both proteins, as well as the ...	2014	24999381
fast proton-coupled electron transfer observed for a high-fidelity structural and functional [2fe-2s] rieske model.	rieske cofactors have a [2fe-2s] cluster with unique {his2cys2} ligation and distinct fe subsites. the histidine ligands are functionally relevant, since they allow for coupling of electron and proton transfer (pcet) during quinol oxidation in respiratory and photosynthetic et chains. here we present the highest fidelity synthetic analogue for the rieske [2fe-2s] cluster reported so far. this synthetic analogue 5(x-) emulates the heteroleptic {his2cys2} ligation of the [2fe-2s] core, and it also ...	2014	24506804
structural studies of yeast δ(1)-pyrroline-5-carboxylate dehydrogenase (aldh4a1): active site flexibility and oligomeric state.	the proline catabolic enzyme δ(1)-pyrroline-5-carboxylate dehydrogenase (aldh4a1) catalyzes the nad(+)-dependent oxidation of γ-glutamate semialdehyde to l-glutamate. in saccharomyces cerevisiae, aldh4a1 is encoded by the put2 gene and known as put2p. here we report the steady-state kinetic parameters of the purified recombinant enzyme, two crystal structures of put2p, and the determination of the oligomeric state and quaternary structure from small-angle x-ray scattering and sedimentation veloc ...	2014	24502590
in vitro assembly and activity of an archaeal crispr-cas type i-a cascade interference complex.	clustered regularly interspaced short palindromic repeats (crispr)-crispr-associated (cas) systems of type i use a cas ribonucleoprotein complex for antiviral defense (cascade) to mediate the targeting and degradation of foreign dna. to address molecular features of the archaeal type i-a cascade interference mechanism, we established the in vitro assembly of the thermoproteus tenax cascade from six recombinant cas proteins, synthetic crispr rnas (crrnas) and target dna fragments. rna-seq analyse ...	2014	24500198
coexistence of bacterial leucyl-trna synthetases with archaeal trna binding domains that distinguish trna(leu) in the archaeal mode.	leucyl-trna (transfer rna) synthetase (leurs) is a multi-domain enzyme, which is divided into bacterial and archaeal/eukaryotic types. in general, one specific leurs, the domains of which are of the same type, exists in a single cell compartment. however, some species, such as the haloalkaliphile natrialba magadii, encode two cytoplasmic leurss, nmleurs1 and nmleurs2, which are the first examples of naturally occurring chimeric enzymes with different domains of bacterial and archaeal types. furt ...	2014	24500203
secondary structures of rrnas from all three domains of life.	accurate secondary structures are important for understanding ribosomes, which are extremely large and highly complex. using 3d structures of ribosomes as input, we have revised and corrected traditional secondary (2°) structures of rrnas. we identify helices by specific geometric and molecular interaction criteria, not by co-variation. the structural approach allows us to incorporate non-canonical base pairs on parity with watson-crick base pairs. the resulting rrna 2° structures are up-to-date ...	2014	24505437
a cylindrical specimen holder for electron cryo-tomography.	the use of slab-like flat specimens for electron cryo-tomography restricts the range of viewing angles that can be used. this leads to the "missing wedge" problem, which causes artefacts and anisotropic resolution in reconstructed tomograms. cylindrical specimens provide a way to eliminate the problem, since they allow imaging from a full range of viewing angles around the tilt axis. such specimens have been used before for tomography of radiation-insensitive samples at room temperature, but nev ...	2014	24275523
an unusual mechanism for ef-tu activation during tmrna-mediated ribosome rescue.	in bacteria, ribosomes stalled on truncated mrnas are rescued by transfer-messenger rna (tmrna) and its protein partner smpb. acting like trna, the aminoacyl-tmrna/smpb complex is delivered to the ribosomal a site by ef-tu and accepts the transfer of the nascent polypeptide. although smpb binding within the decoding center is clearly critical for licensing tmrna entry into the ribosome, it is not known how activation of ef-tu occurs in the absence of a codon-anticodon interaction. a recent cryst ...	2014	24345396
bioorganometallic chemistry with ispg and isph: structure, function, and inhibition of the [fe(4)s(4)] proteins involved in isoprenoid biosynthesis.	enzymes of the methylerythritol phosphate pathway of isoprenoid biosynthesis are attractive anti-infective drug targets. the last two enzymes of this pathway, ispg and isph, are [fe4 s4 ] proteins that are not produced by humans and catalyze 2 h(+) / 2 e(-) reductions with novel mechanisms. in this review, we summarize recent advances in structural, mechanistic, and inhibitory studies of these two enzymes. in particular, mechanistic proposals involving bioorganometallic intermediates are present ...	2014	24481599
elements in nucleotide sensing and hydrolysis of the aaa+ disaggregation machine clpb: a structure-based mechanistic dissection of a molecular motor.	atpases of the aaa+ superfamily are large oligomeric molecular machines that remodel their substrates by converting the energy from atp hydrolysis into mechanical force. this study focuses on the molecular chaperone clpb, the bacterial homologue of hsp104, which reactivates aggregated proteins under cellular stress conditions. based on high-resolution crystal structures in different nucleotide states, mutational analysis and nucleotide-binding kinetics experiments, the atpase cycle of the c-term ...	2014	24531492
crystal structure of e. coli arginyl-trna synthetase and ligand binding studies revealed key residues in arginine recognition.	the arginyl-trna synthetase (argrs) catalyzes the esterification reaction between l-arginine and its cognate trna(arg). previously reported structures of argrs shed considerable light on the trna recognition mechanism, while the aspect of amino acid binding in argrs remains largely unexplored. here we report the first crystal structure of e. coli argrs (eargrs) complexed with l-arginine, and a series of mutational studies using isothermal titration calorimetry (itc). combined with previously rep ...	2014	24474195
global patterns of protein domain gain and loss in superkingdoms.	domains are modules within proteins that can fold and function independently and are evolutionarily conserved. here we compared the usage and distribution of protein domain families in the free-living proteomes of archaea, bacteria and eukarya and reconstructed species phylogenies while tracing the history of domain emergence and loss in proteomes. we show that both gains and losses of domains occurred frequently during proteome evolution. the rate of domain discovery increased approximately lin ...	2014	24499935
discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community.	the development of advanced biofuels from lignocellulosic biomass will require the use of both efficient pretreatment methods and new biomass-deconstructing enzyme cocktails to generate sugars from lignocellulosic substrates. certain ionic liquids (ils) have emerged as a promising class of compounds for biomass pretreatment and have been demonstrated to reduce the recalcitrance of biomass for enzymatic hydrolysis. however, current commercial cellulase cocktails are strongly inhibited by most of ...	2014	24479406
binding of copper and silver to single-site variants of peptidylglycine monooxygenase reveals the structure and chemistry of the individual metal centers.	peptidylglycine monooxygenase (phm) catalyzes the final step in the biosynthesis of amidated peptides that serve as important signaling molecules in numerous endocrine pathways. the catalytic mechanism has attracted much attention because of a number of unique attributes, including the presence of a pair of uncoupled copper centers separated by 11 å (termed cuh and cum), an unusual cu(i)smet interaction at the oxygen binding m-site, and the postulated cu(ii)-superoxo intermediate. understanding ...	2014	24471980
the omega subunit of the rna polymerase core directs transcription efficiency in cyanobacteria.	the eubacterial rna polymerase core, a transcription machinery performing dna-dependent rna polymerization, consists of two α subunits and β, β' and ω subunits. an additional σ subunit is recruited for promoter recognition and transcription initiation. cyanobacteria, a group of eubacteria characterized by oxygenic photosynthesis, have a unique composition of the rna polymerase (rnap) core due to splitting of the β' subunit to n-terminal γ and c-terminal β' subunits. the physiological roles of th ...	2014	24476911
a bacteriophage transcription regulator inhibits bacterial transcription initiation by σ-factor displacement.	bacteriophages (phages) appropriate essential processes of bacterial hosts to benefit their own development. the multisubunit bacterial rna polymerase (rnap) enzyme, which catalyses dna transcription, is targeted by phage-encoded transcription regulators that selectively modulate its activity. here, we describe the structural and mechanistic basis for the inhibition of bacterial rnap by the transcription regulator p7 encoded by xanthomonas oryzae phage xp10. we reveal that p7 uses a two-step mec ...	2014	24482445
4'-o-substitutions determine selectivity of aminoglycoside antibiotics.	clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. here we present a series of 4',6'-o-acetal and 4'-o-ether modifications on glucopyranosyl ring i of aminoglycosides. chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact ...	2014	24473108
a complex of cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in haloferax volcanii.	the clustered regularly interspaced short palindromic repeats/crispr-associated (crispr-cas) system is a prokaryotic defense mechanism against foreign genetic elements. a plethora of crispr-cas versions exist, with more than 40 different cas protein families and several different molecular approaches to fight the invading dna. one of the key players in the system is the crispr-derived rna (crrna), which directs the invader-degrading cas protein complex to the invader. the crispr-cas types i and ...	2014	24459147
characterization of cleavage intermediate and star sites of rm.tth111ii.	tth111ii is a thermostable type iigs restriction enzyme that recognizes dna sites caarca (r = a or g) and cleaves downstream at n11/n9. here, the tth111iirm gene was cloned and expressed in e. coli, and tth111ii was purified. the purified enzyme contains internally-bound s-adenosylmethionine (sam). when the internal sam was removed, the endonuclease activity was stimulated by adding sam or its analog sinefungin. the cleavage intermediate is mostly top-strand nicked dna on a single-site plasmid. ...	2014	24452415
subunit positioning and stator filament stiffness in regulation and power transmission in the v1 motor of the manduca sexta v-atpase.	the vacuolar h(+)-atpase (v-atpase) is an atp-driven proton pump essential to the function of eukaryotic cells. its cytoplasmic v1 domain is an atpase, normally coupled to membrane-bound proton pump vo via a rotary mechanism. how these asymmetric motors are coupled remains poorly understood. low energy status can trigger release of v1 from the membrane and curtail atp hydrolysis. to investigate the molecular basis for these processes, we have carried out cryo-electron microscopy three-dimensiona ...	2014	24075871
folding a stable rna pseudoknot through rearrangement of two hairpin structures.	folding messenger rna into specific structures is a common regulatory mechanism involved in translation. in escherichia coli, the operator of the rpso gene transcript folds into a pseudoknot or double-hairpin conformation. s15, the gene product, binds only to the pseudoknot, thereby repressing its own synthesis when it is present in excess in the cell. the two rna conformations have been proposed to exist in equilibrium. however, it remained unclear how structural changes can be achieved between ...	2014	24459133
dynamic protein ligand interactions--insights from ms.	proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine-tuned for different cellular actions. the study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. during the last two decades ms, and its associated techniques, has become accepted as a method for the study of protein-ligand interactions, not only for covalent complexes, where the use of ms is well est ...	2014	24393119
distinct functions of the rna polymerase σ subunit region 3.2 in rna priming and promoter escape.	the σ subunit of bacterial rna polymerase (rnap) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of rna synthesis, abortive initiation and promoter escape. the post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 that directly contacts promoter dna immediately upstream of the rnap active centre and occupies the rna exit path. analysis of the transcription effects of substitutions and deletions ...	2014	24452800
a highly divergent archaeo-eukaryotic primase from the thermococcus nautilus plasmid, ptn2.	we report the characterization of a dna primase/polymerase protein (polptn2) encoded by the ptn2 plasmid from thermococcus nautilus. sequence analysis revealed that this protein corresponds to a fusion between an n-terminal domain homologous to the small catalytic subunit pris of heterodimeric archaeal and eukaryotic primases (aep) and a c-terminal domain related to their large regulatory subunit pril. this unique domain configuration is not found in other virus- and plasmid-encoded primases in ...	2014	24445805
structural and functional analyses of a sterol carrier protein in spodoptera litura.	in insects, cholesterol is one of the membrane components in cells and a precursor of ecdysteroid biosynthesis. because insects lack two key enzymes, squalene synthase and lanosterol synthase, in the cholesterol biosynthesis pathway, they cannot autonomously synthesize cholesterol de novo from simple compounds and therefore have to obtain sterols from their diet. sterol carrier protein (scp) is a cholesterol-binding protein responsible for cholesterol absorption and transport.	2014	24454688
context of action of proline dehydrogenase (prodh) in the hypersensitive response of arabidopsis.	proline (pro) dehydrogenase (prodh) potentiates the oxidative burst and cell death of the plant hypersensitive response (hr) by mechanisms not yet elucidated. prodh converts pro into ∆1 pyrroline-5-carboxylate (p5c) and can act together with p5c dehydrogenase (p5cdh) to produce glu, or with p5c reductase (p5cr) to regenerate pro and thus stimulate the pro/p5c cycle. to better understand the effects of prodh in hr, we studied the enzyme at three stages of the defense response differing in their r ...	2014	24410747
the isolated carboxy-terminal domain of human mitochondrial leucyl-trna synthetase rescues the pathological phenotype of mitochondrial trna mutations in human cells.	mitochondrial (mt) diseases are multisystem disorders due to mutations in nuclear or mtdna genes. among the latter, more than 50% are located in transfer rna (trna) genes and are responsible for a wide range of syndromes, for which no effective treatment is available at present. we show that three human mt aminoacyl-trna syntethases, namely leucyl-, valyl-, and isoleucyl-trna synthetase are able to improve both viability and bioenergetic proficiency of human transmitochondrial cybrid cells carry ...	2014	24413190
crystal structures of ispf from plasmodium falciparum and burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment.	2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase (ispf) catalyzes the conversion of 4-diphosphocytidyl-2c-methyl-d-erythritol-2-phosphate to 2c-methyl-d-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. ispf is found in the protozoan plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many gram-negative bacteria such as burkholderia cenocepacia. ispf represents a ...	2014	24410837
mlh1-mlh3, a meiotic crossover and dna mismatch repair factor, is a msh2-msh3-stimulated endonuclease.	crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. in saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. these invasion intermediates are converted into double holliday junctions and then resolved into crossovers that facilitate homolog s ...	2014	24403070
charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms.	ribosomes are large and highly charged macromolecular complexes consisting of rna and proteins. here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. we examined 50 s ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. we found th ...	2014	24398678
comea is essential for the transfer of external dna into the periplasm in naturally transformable vibrio cholerae cells.	the dna uptake of naturally competent bacteria has been attributed to the action of dna uptake machineries resembling type iv pilus complexes. however, the protein(s) for pulling the dna across the outer membrane of gram-negative bacteria remain speculative. here we show that the competence protein comea binds incoming dna in the periplasm of naturally competent vibrio cholerae cells thereby promoting dna uptake, possibly through ratcheting and entropic forces associated with comea binding. usin ...	2014	24391524
clostridium difficile glutamate dehydrogenase is a secreted enzyme that confers resistance to h2o2.	clostridium difficile produces an nad-specific glutamate dehydrogenase (gdh), which converts l-glutamate into α-ketoglutarate through an irreversible reaction. the enzyme gdh is detected in the stool samples of patients with c. difficile-associated disease and serves as one of the diagnostic tools to detect c. difficile infection (cdi). we demonstrate here that supernatant fluids of c. difficile cultures contain gdh. to understand the role of gdh in the physiology of c. difficile, an isogenic in ...	2014	24145018
ultradeep pyrosequencing and molecular modeling identify key structural features of hepatitis b virus rnase h, a putative target for antiviral intervention.	last-generation nucleoside/nucleotide analogues are potent against hepatitis b virus (hbv) and have a high barrier to resistance. however, delayed responses have been observed in patients previously exposed to other drugs of the same class, long-term resistance is possible, and cure of infection cannot be achieved with these therapies, emphasizing the need for alternative therapeutic approaches. the hbv rnase h represents an interesting target because its enzyme activity is essential to the hbv ...	2014	24173223
iodotyrosine deiodinase: a unique flavoprotein present in organisms of diverse phyla.	iodide is required for thyroid hormone synthesis in mammals and other vertebrates. the role of both iodide and iodinated tyrosine derivatives is currently unknown in lower organisms, yet the presence of a key enzyme in iodide conservation, iodotyrosine deiodinase (iyd), is suggested by genomic data from a wide range of multicellular organisms as well as some bacteria. a representative set of these genes has now been expressed, and the resulting enzymes all catalyze reductive deiodination of diio ...	2014	24153409
the core of allosteric motion in thermus caldophilus l-lactate dehydrogenase.	for thermus caldophilus l-lactate dehydrogenase (tcldh), fructose 1,6-bisphosphate (fbp) reduced the pyruvate s(0.5) value 10(3)-fold and increased the v(max) value 4-fold at 30 °c and ph 7.0, indicating that tcldh has a much more t state-sided allosteric equilibrium than thermus thermophilus l-lactate dehydrogenase, which has only two amino acid replacements, a154g and h179y. the inactive (t) and active (r) state structures of tcldh were determined at 1.8 and 2.0 å resolution, respectively. the ...	2014	25258319
five checkpoints maintaining the fidelity of transcription by rna polymerases in structural and energetic details.	transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in rna, is essential for life. results from molecular dynamics (md) simulations of eukaryotic rna polymerase (rnap) ii and bacterial rnap with experimental data suggest that fidelity may involve as many as five checkpoints. using md simulations, the effects of different active site ntps in both open and closed trigger loop (tl) structures of rnaps are compared. unfavorable initial binding of mism ...	2014	25550432
five checkpoints maintaining the fidelity of transcription by rna polymerases in structural and energetic details.	transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in rna, is essential for life. results from molecular dynamics (md) simulations of eukaryotic rna polymerase (rnap) ii and bacterial rnap with experimental data suggest that fidelity may involve as many as five checkpoints. using md simulations, the effects of different active site ntps in both open and closed trigger loop (tl) structures of rnaps are compared. unfavorable initial binding of mism ...	2014	25550432
the tfe-induced transient native-like structure of the intrinsically disordered σ₄⁷⁰ domain of escherichia coli rna polymerase.	the transient folding of domain 4 of an e. coli rna polymerase σ⁷⁰ subunit (recσ₄⁷⁰) induced by an increasing concentration of 2,2,2-trifluoroethanol (tfe) in an aqueous solution was monitored by means of cd and heteronuclear nmr spectroscopy. nmr data, collected at a 30% tfe, allowed the estimation of the population of a locally folded recσ₄⁷⁰ structure (csi descriptors) and of local backbone dynamics ((15)n relaxation). the spontaneous organization of the helical regions of the initially unfol ...	2014	25261014
dna polymerases as useful reagents for biotechnology - the history of developmental research in the field.	dna polymerase is a ubiquitous enzyme that synthesizes complementary dna strands according to the template dna in living cells. multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. in addition to their fundamental role in maintaining genome integrity during replication and repair, dna polymerases are widely used for dna manipulation in vitro, including dna cloning, sequencing, labeling, mutagenesis, and other purposes. the fu ...	2014	25221550
replication slippage of the thermophilic dna polymerases b and d from the euryarchaeota pyrococcus abyssi.	replication slippage or slipped-strand mispairing involves the misalignment of dna strands during the replication of repeated dna sequences, and can lead to genetic rearrangements such as microsatellite instability. here, we show that polb and pold replicative dna polymerases from the archaeal model pyrococcus abyssi (pab) slip in vitro during replication of a single-stranded dna template carrying a hairpin structure and short direct repeats. we find that this occurs in both their wild-type (exo ...	2014	25177316
from metagenomics to pure culture: isolation and characterization of the moderately halophilic bacterium spiribacter salinus gen. nov., sp. nov.	recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera alkalilimnicola and arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. here we used several strategies and culture media in order to isolate this organism in pure culture. we report the isolatio ...	2014	24747894
inteins as indicators of gene flow in the halobacteria.	this research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the halobacteria. we surveyed 118 genomes representing 26 genera of halobacteria for intein sequences. we then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. we identified 24 proteins in the halobacteria that hav ...	2014	25018750
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant mycobacterium tuberculosis.	rifamycin b, a product of amycolatopsis mediterranei s699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and aids-related mycobacterial infections. however, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of mycobacterium tuberculosis. as part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of ...	2014	24923585
molecular basis of rna polymerase promoter specificity switch revealed through studies of thermus bacteriophage transcription regulator.	transcription initiation is the central point of gene expression regulation. understanding of molecular mechanism of transcription regulation requires, ultimately, the structural understanding of consequences of transcription factors binding to dna-dependent rna polymerase (rnap), the enzyme of transcription. we recently determined a structure of a complex between transcription factor gp39 encoded by a thermus bacteriophage and thermus rnap holoenzyme. in this addendum to the original publicatio ...	2014	25105059
pcr performance of a thermostable heterodimeric archaeal dna polymerase.	dna polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (pcr), cdna cloning, genome sequencing, and nucleic acid based diagnostics. taking into account the multiple dna amplification techniques in use, different dna polymerases must be optimized for each type of application. one of the current tendencies is to reengineer or to discover new dna polymerases with increased performance and broadened substrate ...	2014	24847315
mycobacterial rna polymerase requires a u-tract at intrinsic terminators and is aided by nusg at suboptimal terminators.	intrinsic terminators, which encode gc-rich rna hairpins followed immediately by a 7-to-9-nucleotide (nt) u-rich "u-tract," play principal roles of punctuating and regulating transcription in most bacteria. however, canonical intrinsic terminators with strong u-tracts are underrepresented in some bacterial lineages, notably mycobacteria, leading to proposals that their rna polymerases stop at noncanonical intrinsic terminators encoding various rna structures lacking u-tracts. we generated recomb ...	2014	24713321
the impact of drug resistance on mycobacterium tuberculosis physiology: what can we learn from rifampicin?	the emergence of drug-resistant pathogens poses a major threat to public health. although influenced by multiple factors, high-level resistance is often associated with mutations in target-encoding or related genes. the fitness cost of these mutations is, in turn, a key determinant of the spread of drug-resistant strains. rifampicin (rif) is a frontline anti-tuberculosis agent that targets the rpob-encoded β subunit of the dna-dependent rna polymerase (rnap). in mycobacterium tuberculosis (mtb), ...	2014	26038512
antibiotic streptolydigin requires noncatalytic mg2+ for binding to rna polymerase.	multisubunit rna polymerase, an enzyme that accomplishes transcription in all living organisms, is a potent target for antibiotics. the antibiotic streptolydigin inhibits rna polymerase by sequestering the active center in a catalytically inactive conformation. here, we show that binding of streptolydigin to rna polymerase strictly depends on a noncatalytic magnesium ion which is likely chelated by the aspartate of the bridge helix of the active center. substitutions of this aspartate may explai ...	2014	24342645
structural basis for promoter specificity switching of rna polymerase by a phage factor.	transcription of dna to rna by dna-dependent rna polymerase (rnap) is the first step of gene expression and a major regulation point. bacteriophages hijack their host's transcription machinery and direct it to serve their needs. the gp39 protein encoded by thermus thermophilus phage p23-45 binds the host's rnap and inhibits transcription initiation from its major "-10/-35" class promoters. phage promoters belonging to the minor "extended -10" class are minimally inhibited. we report the crystal ...	2014	24589779
novel highly thermostable endolysin from thermus scotoductus mat2119 bacteriophage ph2119 with amino acid sequence similarity to eukaryotic peptidoglycan recognition proteins.	in this study, we present the discovery and characterization of a highly thermostable endolysin from bacteriophage ph2119 infecting thermus strain mat2119 isolated from geothermal areas in iceland. nucleotide sequence analysis of the 16s rrna gene affiliated the strain with the species thermus scotoductus. bioinformatics analysis has allowed identification in the genome of phage 2119 of an open reading frame (468 bp in length) coding for a 155-amino-acid basic protein with an mr of 17,555. ph211 ...	2014	24271162
structure of the carboxy-terminal domain of mycobacterium tuberculosis card protein: an essential rrna transcriptional regulator.	the card protein is highly expressed in mycobacterial strains under basal conditions and is transcriptionally induced during multiple types of genotoxic stress and starvation. the card protein binds the β subunit of rna polymerase and influences gene expression. the disruption of interactions between card and the β subunit of rna polymerase has a significant effect on mycobacterial survival, resistance to stress and pathogenesis. to understand the structure of card and its interaction with the β ...	2014	24637748
bacterial genome instability.	bacterial genomes are remarkably stable from one generation to the next but are plastic on an evolutionary time scale, substantially shaped by horizontal gene transfer, genome rearrangement, and the activities of mobile dna elements. this implies the existence of a delicate balance between the maintenance of genome stability and the tolerance of genome instability. in this review, we describe the specialized genetic elements and the endogenous processes that contribute to genome instability. we ...	2014	24600039
s-layers: principles and applications.	monomolecular arrays of protein or glycoprotein subunits forming surface layers (s-layers) are one of the most commonly observed prokaryotic cell envelope components. s-layers are generally the most abundantly expressed proteins, have been observed in species of nearly every taxonomical group of walled bacteria, and represent an almost universal feature of archaeal envelopes. the isoporous lattices completely covering the cell surface provide organisms with various selection advantages including ...	2014	24483139
nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells.	legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ...	2014	25547789
nuclease activity of legionella pneumophila cas2 promotes intracellular infection of amoebal host cells.	legionella pneumophila, the primary agent of legionnaires' disease, flourishes in both natural and man-made environments by growing in a wide variety of aquatic amoebae. recently, we determined that the cas2 protein of l. pneumophila promotes intracellular infection of acanthamoeba castellanii and hartmannella vermiformis, the two amoebae most commonly linked to cases of disease. the cas2 family of proteins is best known for its role in the bacterial and archeal clustered regularly interspaced s ...	2014	25547789
uracil-dna glycosylases-structural and functional perspectives on an essential family of dna repair enzymes.	uracil-dna glycosylases (udgs) are evolutionarily conserved dna repair enzymes that initiate the base excision repair pathway and remove uracil from dna. the udg superfamily is classified into six families based on their substrate specificity. this review focuses on the family i enzymes since these are the most extensively studied members of the superfamily. the structural basis for substrate specificity and base recognition as well as for dna binding, nucleotide flipping and catalytic mechanism ...	2014	25252105
effect of the l499m mutation of the ascomycetous botrytis aclada laccase on redox potential and catalytic properties.	laccases are members of a large family of multicopper oxidases that catalyze the oxidation of a wide range of organic and inorganic substrates accompanied by the reduction of dioxygen to water. these enzymes contain four cu atoms per molecule organized into three sites: t1, t2 and t3. in all laccases, the t1 copper ion is coordinated by two histidines and one cysteine in the equatorial plane and is covered by the side chains of hydrophobic residues in the axial positions. the redox potential of ...	2014	25372682
structural and biochemical characterization of chlamydia trachomatis hypothetical protein ct263 supports that menaquinone synthesis occurs through the futalosine pathway.	the obligate intracellular human pathogen chlamydia trachomatis is the etiological agent of blinding trachoma and sexually transmitted disease. genomic sequencing of chlamydia indicated this medically important bacterium was not exclusively dependent on the host cell for energy. in order for the electron transport chain to function, electron shuttling between membrane-embedded complexes requires lipid-soluble quinones (e.g. menaquionone or ubiquinone). the sources or biosynthetic pathways requir ...	2014	25253688
cocrystal structures of glycyl-trna synthetase in complex with trna suggest multiple conformational states in glycylation.	aminoacyl-trna synthetases are an ancient enzyme family that specifically charges trna molecules with cognate amino acids for protein synthesis. glycyl-trna synthetase (glyrs) is one of the most intriguing aminoacyl-trna synthetases due to its divergent quaternary structure and abnormal charging properties. in the past decade, mutations of human glyrs (hglyrs) were also found to be associated with charcot-marie-tooth disease. however, the mechanisms of traditional and alternative functions of hg ...	2014	24898252
metalloproteins containing cytochrome, iron-sulfur, or copper redox centers.		2014	24758379
natural competence and the evolution of dna uptake specificity.	many bacteria are naturally competent, able to actively transport environmental dna fragments across their cell envelope and into their cytoplasm. because incoming dna fragments can recombine with and replace homologous segments of the chromosome, competence provides cells with a potent mechanism of horizontal gene transfer as well as access to the nutrients in extracellular dna. this review starts with an introductory overview of competence and continues with a detailed consideration of the dna ...	2014	24488316
chlamydia exploit the mammalian tryptophan-depletion defense strategy as a counter-defensive cue to trigger a survival state of persistence.	we previously proposed that in chlamydiaceae rapid vegetative growth and a quiescent state of survival (persistence) depend upon alternative protein translational profiles dictated by host tryptophan (trp) availability. these alternative profiles correspond, respectively, with a set of chlamydial proteins having higher-than-predicted contents of trp ("up-trp" selection), or with another set exhibiting lower-than-predicted contents of trp ("down-trp" selection). a comparative evaluation of chlamy ...	2014	24616884
crystal structure and putative substrate identification for the entamoeba histolytica low molecular weight tyrosine phosphatase.	entamoeba histolytica is a eukaryotic intestinal parasite of humans, and is endemic in developing countries. we have characterized the e. histolytica putative low molecular weight protein tyrosine phosphatase (lmw-ptp). the structure for this amebic tyrosine phosphatase was solved, showing the ligand-induced conformational changes necessary for binding of substrate. in amebae, it was expressed at low but detectable levels as detected by immunoprecipitation followed by immunoblotting. a mutant lm ...	2014	24548880
origin and evolution of the peptidyl transferase center from proto-trnas.	we tested the hypothesis of tamura (2011) [3] that molecules of trna gave origin to ribosomes, particularly to the peptidyl transferase center (ptc) of the 23s ribosomal rna. we reconstructed the ancestral sequences from all types of trna and compared them in their sequences with the current ptc of 23s ribosomal rna from different organisms. we built an ancestral sequence of proto-trnas that showed a remarkable overall identity of 50.53% with the catalytic site of ptc. we conclude that the pepti ...	2014	24649398
radical s-adenosylmethionine enzymes.		2014	24476342
new mini- zincin structures provide a minimal scaffold for members of this metallopeptidase superfamily.	the acel_2062 protein from acidothermus cellulolyticus is a protein of unknown function. initial sequence analysis predicted that it was a metallopeptidase from the presence of a motif conserved amongst the asp-zincins, which are peptidases that contain a single, catalytic zinc ion ligated by the histidines and aspartic acid within the motif (hexxhxxgxxd). the acel_2062 protein was chosen by the joint center for structural genomics for crystal structure determination to explore novel protein seq ...	2014	24383880
mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card.	escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ...	2014	25510492
mycobacterial rna polymerase forms unstable open promoter complexes that are stabilized by card.	escherichia coli has served as the archetypal organism on which the overwhelming majority of biochemical characterizations of bacterial rna polymerase (rnap) have been focused; the properties of e. coli rnap have been accepted as generally representative for all bacterial rnaps. here, we directly compare the initiation properties of a mycobacterial transcription system with e. coli rnap on two different promoters. the detailed characterizations include abortive transcription assays, rnap/promote ...	2014	25510492
evolution and diversity of the ras superfamily of small gtpases in prokaryotes.	the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ...	2014	25480683
evolution and diversity of the ras superfamily of small gtpases in prokaryotes.	the ras superfamily of small gtpases are single domain nucleotide-dependent molecular switches that act as highly tuned regulators of complex signal transduction pathways. originally identified in eukaryotes for their roles in fundamental cellular processes including proliferation, motility, polarity, nuclear transport, and vesicle transport, recent studies have revealed that single domain gtpases also control complex functions such as cell polarity, motility, predation, development and antibiot ...	2014	25480683
the predatory bacterium bdellovibrio bacteriovorus aspartyl-trna synthetase recognizes trnaasn as a substrate.	the predatory bacterium bdellovibrio bacteriovorus preys on other gram-negative bacteria and was predicted to be an asparagine auxotroph. however, despite encoding asparaginyl-trna synthetase and glutaminyl-trna synthetase, b. bacteriovorus also contains the amidotransferase gatcab. deinococcus radiodurans, and thermus thermophilus also encode both of these aminoacyl-trna synthetases with gatcab. both also code for a second aspartyl-trna synthetase and use the additional aspartyl-trna synthetase ...	2014	25338061
zinc and atp binding of the hexameric aaa-atpase pilf from thermus thermophilus: role in complex stability, piliation, adhesion, twitching motility, and natural transformation.	the traffic aaa-atpase pilf is essential for pilus biogenesis and natural transformation of thermus thermophilus hb27. recently, we showed that pilf forms hexameric complexes containing six zinc atoms coordinated by conserved tetracysteine motifs. here we report that zinc binding is essential for complex stability. however, zinc binding is neither required for pilus biogenesis nor natural transformation. a number of the mutants did not exhibit any pili during growth at 64 °c but still were trans ...	2014	25202014
a review of metabolic and enzymatic engineering strategies for designing and optimizing performance of microbial cell factories.	microbial cell factories (mcfs) are of considerable interest to convert low value renewable substrates to biofuels and high value chemicals. this review highlights the progress of computational models for the rational design of an mcf to produce a target bio-commodity. in particular, the rational design of an mcf involves: (i) product selection, (ii) de novo biosynthetic pathway identification (i.e., rational, heterologous, or artificial), (iii) mcf chassis selection, (iv) enzyme engineering of ...	2014	25379147
molecular phylogeny and intricate evolutionary history of the three isofunctional enzymes involved in the oxidation of protoporphyrinogen ix.	tetrapyrroles such as heme and chlorophyll are essential for biological processes, including oxygenation, respiration, and photosynthesis. in the tetrapyrrole biosynthesis pathway, protoporphyrinogen ix oxidase (protox) catalyzes the formation of protoporphyrin ix, the last common intermediate for the biosynthesis of heme and chlorophyll. three nonhomologous isofunctional enzymes, hemg, hemj, and hemy, for protox have been identified. to reveal the distribution and evolution of the three protox ...	2014	25108393
multiple regulatory mechanisms control the expression of the geobacillus stearothermophilus gene for extracellular xylanase.	geobacillus stearothermophilus t-6 produces a single extracellular xylanase (xyn10a) capable of producing short, decorated xylo-oligosaccharides from the naturally branched polysaccharide, xylan. gel retardation assays indicated that the master negative regulator, xylr, binds specifically to xylr operators in the promoters of xylose and xylan-utilization genes. this binding is efficiently prevented in vitro by xylose, the most likely molecular inducer. expression of the extracellular xylanase is ...	2014	25070894
outside-in assembly pathway of the type iv pilus system in myxococcus xanthus.	type iv pili (t4p) are ubiquitous bacterial cell surface structures that undergo cycles of extension, adhesion, and retraction. t4p function depends on a highly conserved envelope-spanning macromolecular machinery consisting of 10 proteins that localizes polarly in myxococcus xanthus. using this localization, we investigated the entire t4p machinery assembly pathway by systematically profiling the stability of all and the localization of eight of these proteins in the absence of other t4p machin ...	2014	24187092
type iv pilus biogenesis, twitching motility, and dna uptake in thermus thermophilus: discrete roles of antagonistic atpases pilf, pilt1, and pilt2.	natural transformation has a large impact on lateral gene flow and has contributed significantly to the ecological diversification and adaptation of bacterial species. thermus thermophilus hb27 has emerged as the leading model organism for studies of dna transporters in thermophilic bacteria. recently, we identified a zinc-binding polymerization nucleoside triphosphatase (ntpase), pilf, which is essential for the transport of dna through the outer membrane. here, we present genetic evidence that ...	2014	24212586
improved cultivation and metagenomics as new tools for bioprospecting in cold environments.	only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. this resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent dna sequence information can be combined with functional screening. the coupling of these two approaches circumvents the need ...	2014	25399309
improved cultivation and metagenomics as new tools for bioprospecting in cold environments.	only a small minority of microorganisms from an environmental sample can be cultured in the laboratory leaving the enormous bioprospecting potential of the uncultured diversity unexplored. this resource can be accessed by improved cultivation methods in which the natural environment is brought into the laboratory or through metagenomic approaches where culture-independent dna sequence information can be combined with functional screening. the coupling of these two approaches circumvents the need ...	2014	25399309
stability curve prediction of homologous proteins using temperature-dependent statistical potentials.	the unraveling and control of protein stability at different temperatures is a fundamental problem in biophysics that is substantially far from being quantitatively and accurately solved, as it requires a precise knowledge of the temperature dependence of amino acid interactions. in this paper we attempt to gain insight into the thermal stability of proteins by designing a tool to predict the full stability curve as a function of the temperature for a set of 45 proteins belonging to 11 homologou ...	2014	25032839