Publications

thermotoga maritima nusg: domain interaction mediates autoinhibition and thermostability.	nusg, the only universally conserved transcription factor, comprises an n- and a c-terminal domain (ntd, ctd) that are flexibly connected and move independently in escherichia coli and other organisms. in nusg from the hyperthermophilic bacterium thermotoga maritima (tmnusg), however, ntd and ctd interact tightly. this closed state stabilizes the ctd, but masks the binding sites for the interaction partners rho, nuse and rna polymerase (rnap), suggesting that tmnusg is autoinhibited. furthermore ...	2016	27899597
thermotoga maritima nusg: domain interaction mediates autoinhibition and thermostability.	nusg, the only universally conserved transcription factor, comprises an n- and a c-terminal domain (ntd, ctd) that are flexibly connected and move independently in escherichia coli and other organisms. in nusg from the hyperthermophilic bacterium thermotoga maritima (tmnusg), however, ntd and ctd interact tightly. this closed state stabilizes the ctd, but masks the binding sites for the interaction partners rho, nuse and rna polymerase (rnap), suggesting that tmnusg is autoinhibited. furthermore ...	2016	27899597
redox cofactors insertion in prokaryotic molybdoenzymes occurs via a conserved folding mechanism.	a major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. this holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. this large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (mo/w-bispgd) and fe/s clusters. here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational cha ...	2016	27886223
computing and applying atomic regulons to understand gene expression and regulation.	understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. an important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. these gene sets, atomic regulons (ars), represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes an ...	2016	27933038
a thermostable bilirubin-oxidizing enzyme from activated sludge isolated by a metagenomic approach.	a gene coding for a multicopper oxidase (bopa) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. the recombinant bopa protein produced in escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (abts) in the presence of copper, suggesting that bopa is laccase. a bioinformatic analysis of the bopa gene sequence indicated that it has a phylogenetically bacterial origin, possibly der ...	2016	27885197
beyond antibodies: development of a novel protein scaffold based on human chaperonin 10.	human chaperonin 10 (hcpn10) was utilised as a novel scaffold for presenting peptides of therapeutic and diagnostic significance. molecular dynamic simulations and protein sizing analyses identified a peptide linker (p1) optimal for the formation of the quarternary hcpn10 heptamer structure. hcpn10 scaffold displaying peptides targeting factor viia (ce76-p1) and cd44 (cp7) were expressed in e. coli. functional studies of ce76-p1 indicated nanomolar affinity for factor viia (3 nm) similar to the ...	2016	27874025
first resistance mechanisms characterization in glyphosate-resistant leptochloa virgata.	leptochloa virgata (l.) p. beauv. is an annual weed common in citrus groves in the states of puebla and veracruz, mexico limiting their production. since 2010, several l. virgata populations were identified as being resistant to glyphosate, but studies of their resistance mechanisms developed by this species have been conducted. in this work, three glyphosate-resistant populations (r8, r14, and r15) collected in citrus orchards from mexico, were used to study their resistance mechanisms comparin ...	2016	27917189
a natural light-driven inward proton pump.	light-driven outward h(+) pumps are widely distributed in nature, converting sunlight energy into proton motive force. here we report the characterization of an oppositely directed h(+) pump with a similar architecture to outward pumps. a deep-ocean marine bacterium, parvularcula oceani, contains three rhodopsins, one of which functions as a light-driven inward h(+) pump when expressed in escherichia coli and mouse neural cells. detailed mechanistic analyses of the purified proteins reveal that ...	2016	27853152
boosting functionality of synthetic dna circuits with tailored deactivation.	molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. the function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. here we introduce a mechanism to tune the nonlinearities associated with individual no ...	2016	27845324
two proofreading steps amplify the accuracy of genetic code translation.	aminoacyl-trnas (aa-trnas) are selected by the messenger rna programmed ribosome in ternary complex with elongation factor tu (ef-tu) and gtp and then, again, in a proofreading step after gtp hydrolysis on ef-tu. we use trna mutants with different affinities for ef-tu to demonstrate that proofreading of aa-trnas occurs in two consecutive steps. first, aa-trnas in ternary complex with ef-tu·gdp are selected in a step where the accuracy increases linearly with increasing aa-trna affinity to ef-tu. ...	2016	27837019
identification of ybey-protein interactions involved in 16s rrna maturation and stress regulation in escherichia coli.	ybey is part of a core set of rnases in escherichia coli and other bacteria. this highly conserved endoribonuclease has been implicated in several important processes such as 16s rrna 3' end maturation, 70s ribosome quality control, and regulation of mrnas and small noncoding rnas, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. thus, ybey likely interacts with numerous protein or rna partners that are involved in various aspects of cell ...	2016	27834201
cryo-em study of start codon selection during archaeal translation initiation.	eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aif1, e/aif1a, the ternary complex (tc, e/aif2-gtp-met-trnai(met)) and mrna bound to the small ribosomal subunit. e/aif2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. here, we present cryo-em structures of the full archaeal 30s initiation complex showing two conformational states of the tc. in the first state, the tc is bound to the riboso ...	2016	27819266
identification of essential genes in the salmonella phage spn3us reveals novel insights into giant phage head structure and assembly.	giant tailed bacterial viruses, or phages, such as pseudomonas aeruginosa phage ϕkz, have long genomes packaged into large, atypical virions. many aspects of ϕkz and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. we hypothesized that the salmonella enterica phage spn3us could be a useful model phage to address this gap in knowledge. the 240-kb spn3us genome shares a core set of 91 genes with ϕkz and related ph ...	2016	27605673
the hemq coprohaem decarboxylase generates reactive oxygen species: implications for the evolution of classical haem biosynthesis.	bacteria require a haem biosynthetic pathway for the assembly of a variety of protein complexes, including cytochromes, peroxidases, globins, and catalase. haem is synthesised via a series of tetrapyrrole intermediates, including non-metallated porphyrins, such as protoporphyrin ix, which is well known to generate reactive oxygen species in the presence of light and oxygen. staphylococcus aureus has an ancient haem biosynthetic pathway that proceeds via the formation of coproporphyrin iii, a les ...	2016	27597779
crystal structures of the atp-binding and adp-release dwells of the v1 rotary motor.	v1-atpases are highly conserved atp-driven rotary molecular motors found in various membrane systems. we recently reported the crystal structures for the enterococcus hirae a3b3df (v1) complex, corresponding to the catalytic dwell state waiting for atp hydrolysis. here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free v1 crystals in adp. in the presence of 20 μm adp, two adp molecules bind to two of three binding sites and cooperatively induce confo ...	2016	27807367
avilamycin and evernimicin induce structural changes in rproteins ul16 and ctc that enhance the inhibition of a-site trna binding.	two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against enterococci, staphylococci, and streptococci, and other gram-positive bacteria. here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. their extended binding sites span the a-trna entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the a-trna elbow, a mechanis ...	2016	27791159
structure of the 70s ribosome from human pathogen staphylococcus aureus.	comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance ...	2016	27906650
structures and stabilization of kinetoplastid-specific split rrnas revealed by comparing leishmanial and human ribosomes.	the recent success in ribosome structure determination by cryoem has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. here, by direct electron-counting cryoem, we have determined the structures of the leishmania donovani and human ribosomes at 2.9 å and 3.6 å, respectively. our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rrna (as ...	2016	27752045
characterization of a highly thermostable and organic solvent-tolerant copper-containing polyphenol oxidase with dye-decolorizing ability from kurthia huakuii lam0618t.	laccases are green biocatalysts that possess attractive advantages for the treatment of resistant environmental pollutants and dye effluents. a putative laccase-like gene, laclk, encoding a protein of 29.3 kda and belonging to the cu-oxidase_4 superfamily, was cloned and overexpressed in escherichia coli. the purified recombinant protein laclk (laclk) was able to oxidize typical laccase substrates such as 2,6-dimethoxyphenol and l-dopamine. the characteristic adsorption maximums of typical lacca ...	2016	27741324
microcystin-bound protein patterns in different cultures of microcystis aeruginosa and field samples.	micocystin (mc) exists in microcystis cells in two different forms, free and protein-bound. we examined the dynamic change in extracellular free mcs, intracellular free mcs and protein-bound mcs in both batch cultures and semi-continuous cultures, using high performance liquid chromatography and western blot. the results showed that the free mc per cell remained constant, while the quantity of protein-bound mcs increased with the growth of microcystis cells in both kinds of culture. significant ...	2016	27754336
functional characterization of a csor-cuea divergon in bradyrhizobium liaoningense ccnwsx0360, involved in copper, zinc and cadmium cotolerance.	random mutagenesis in a symbiotic nitrogen-fixing bradyrhizobium liaoningense ccnwsx0360 (bln0360) using tn5 identified five copper (cu) resistance-related genes. they were functionally sorted into three groups: transmembrane transport (cuea and tolc); oxidation (copa); and protection of the membrane barrier (lpte and ctpa). the gene cuea, together with the upstream csor (cu-sensitive operon repressor), constituted a csor-cuea divergon which plays a crucial role in cu homeostasis. deletion of cu ...	2016	27725778
structural characterization of antibiotic self-immunity trna synthetase in plant tumour biocontrol agent.	antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. the biocontrol agrobacterium radiobacter k84 secretes the trojan horse antibiotic agrocin 84 that is selectively transported into the plant pathogen a. tumefaciens and processed into the toxin tm84. we previously showed that tm84 employs a unique trna-dependent mechanism to inhibit leucyl-trna synthetase (leurs), while the tm84-producer prevents self-poisoning by expressing a resistant leurs agnb2. we now identify ...	2016	27713402
in vitro engineering of novel bioactivity in the natural enzymes.	enzymes catalyze various biochemical functions with high efficiency and specificity. in vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. enzyme engineering technology involves directed evolution, rational designing, semi-rational designing, and structure-based designing using chemical modifications. similarly, combined computat ...	2016	27774447
mechanism of ph-dependent activation of the sodium-proton antiporter nhaa.	escherichia coli nhaa is a prototype sodium-proton antiporter, which has been extensively characterized by x-ray crystallography, biochemical and biophysical experiments. however, the identities of proton carriers and details of ph-regulated mechanism remain controversial. here we report constant ph molecular dynamics data, which reveal that nhaa activation involves a net charge switch of a ph sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the fu ...	2016	27708266
nusg inhibits rna polymerase backtracking by stabilizing the minimal transcription bubble.	universally conserved factors from nusg family bind at the upstream fork junction of transcription elongation complexes and modulate rna synthesis in response to translation, processing, and folding of the nascent rna. escherichia coli nusg enhances transcription elongation in vitro by a poorly understood mechanism. here we report that e. coli nusg slows gre factor-stimulated cleavage of the nascent rna, but does not measurably change the rates of single nucleotide addition and translocation by ...	2016	27697152
target and non-target site mechanisms developed by glyphosate-resistant hairy beggarticks (bidens pilosa l.) populations from mexico.	in 2014 hairy beggarticks (bidens pilosa l.) has been identified as being glyphosate-resistant in citrus orchards from mexico. the target and non-target site mechanisms involved in the response to glyphosate of two resistant populations (r1 and r2) and one susceptible (s) were studied. experiments of dose-response, shikimic acid accumulation, uptake-translocation, enzyme activity and 5-enolpyruvyl shikimate-3-phosphate synthase (epsps) gene sequencing were carried out in each population. the r1 ...	2016	27752259
a cascade of thermophilic enzymes as an approach to the synthesis of modified nucleotides.	we propose a new approach for the synthesis of biologically important nucleotides which includes a multi-enzymatic cascade conversion of d-pentoses into purine nucleotides. the approach exploits nucleic acid exchange enzymes from thermophilic microorganisms: ribokinase, phosphoribosylpyrophosphate synthetase, and adenine phosphoribosyltransferase. we cloned the ribokinase gene from thermus sp. 2.9, as well as two different genes of phosphoribosylpyrophosphate synthetase (prpp-synthetase) and the ...	2016	28050269
ns-μs time-resolved step-scan ftir of ba₃ oxidoreductase from thermus thermophilus: protonic connectivity of w941-w946-w927.	time-resolved step-scan ftir spectroscopy has been employed to probe the dynamics of the ba₃ oxidoreductase from thermus thermophilus in the ns-μs time range and in the ph/pd 6-9 range. the data revealed a ph/pd sensitivity of the d372 residue and of the ring-a propionate of heme a₃. based on the observed transient changes a model in which the protonic connectivity of w941-w946-927 to the d372 and the ring-a propionate of heme a₃ is described.	2016	27690021
birth of archaeal cells: molecular phylogenetic analyses of g1p dehydrogenase, g3p dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having g1p polar lipids.	bacteria and eukarya have cell membranes with sn-glycerol-3-phosphate (g3p), whereas archaeal membranes contain sn-glycerol-1-phosphate (g1p). determining the time at which cells with either g3p-lipid membranes or g1p-lipid membranes appeared is important for understanding the early evolution of terrestrial life. to clarify this issue, we reconstructed molecular phylogenetic trees of g1pdh (g1p dehydrogenase; egsa/aram) which is responsible for g1p synthesis and g3pdhs (g3p dehydrogenase; gpsa a ...	2016	27774041
unexpected functional implication of a stable succinimide in the structural stability of methanocaldococcus jannaschii glutaminase.	protein ageing is often mediated by the formation of succinimide intermediates. these short-lived intermediates derive from asparaginyl deamidation and aspartyl dehydration and are rapidly converted into β-aspartyl or d-aspartyl residues. here we report the presence of a highly stable succinimide intermediate in the glutaminase subunit of gmp synthetase from the hyperthermophile methanocaldoccocus jannaschii. by comparing the biophysical properties of the wild-type protein and of several mutants ...	2016	27677693
analysis of the core genome and pan-genome of autotrophic acetogenic bacteria.	acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (co2) to multicarbon compounds coupled to the oxidation of inorganic substrates, such as hydrogen (h2) or carbon monoxide (co), via the wood-ljungdahl pathway. owing to the metabolic capability of co2 fixation, much attention has been focused on understanding the unique pathways associated with acetogens, particularly their metabolic coupling of co2 fixation to energy conservation. most known acetogens are phylogenetica ...	2016	27733845
uniformity of peptide release is maintained by methylation of release factors.	termination of protein synthesis on the ribosome is catalyzed by release factors (rfs), which share a conserved glycine-glycine-glutamine (ggq) motif. the glutamine residue is methylated in vivo, but a mechanistic understanding of its contribution to hydrolysis is lacking. here, we show that the modification, apart from increasing the overall rate of termination on all dipeptides, substantially increases the rate of peptide release on a subset of amino acids. in the presence of unmethylated rfs, ...	2016	27681416
quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods.	cultivation-independent investigation of microbial ecology is biased by the dna extraction methods used. we aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different dna extraction methods with different cell lysis principles. our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic dna from the food matrices compared to the widely used ...	2016	27669673
metagenomics of thermophiles with a focus on discovery of novel thermozymes.	microbial populations living in environments with temperatures above 50°c (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. the integrated study of the whole-community dna from an environment, known as metagenomics ...	2016	27729905
cryptosporidium and toxoplasma parasites are inhibited by a benzoxaborole targeting leucyl-trna synthetase.	the apicomplexan parasites cryptosporidium and toxoplasma are serious threats to human health. cryptosporidiosis is a severe diarrheal disease in malnourished children and immunocompromised individuals, with the only fda-approved drug treatment currently being nitazoxanide. the existing therapies for toxoplasmosis, an important pathology in immunocompromised individuals and pregnant women, also have serious limitations. with the aim of developing alternative therapeutic options to address these ...	2016	27431220
molecular insights into substrate recognition and catalytic mechanism of the chaperone and fkbp peptidyl-prolyl isomerase slyd.	peptidyl-prolyl isomerases (ppiases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. slyd is a two-domain enzyme containing both a ppiase fk506-binding protein (fkbp) domain and an insert-in-flap (if) chaperone domain. to date, the interactions of these domains with unfolded proteins have remained rather obscure, with structural information on binding to the fkbp domain being limited to complexes involving various inhibitor compounds o ...	2016	27664121
large-scale movements of if3 and trna during bacterial translation initiation.	in bacterial translational initiation, three initiation factors (ifs 1-3) enable the selection of initiator trna and the start codon in the p site of the 30s ribosomal subunit. here, we report 11 single-particle cryo-electron microscopy (cryoem) reconstructions of the complex of bacterial 30s subunit with initiator trna, mrna, and ifs 1-3, representing different steps along the initiation pathway. if1 provides key anchoring points for if2 and if3, thereby enhancing their activities. if2 position ...	2016	27662086
avoidance of stochastic rna interactions can be harnessed to control protein expression levels in bacteria and archaea.	a critical assumption of gene expression analysis is that mrna abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. some of the discrepancy can be accounted for by two important mrna features: codon usage and mrna secondary structure. we present a new global factor, called mrna:ncrna avoidance, and provide evidence that avoidance increases translational efficiency. we also demonstrate a strong selection for the avoidance of stochastic mrna:ncrna in ...	2016	27642845
molecular basis of cobalamin-dependent rna modification.	queuosine (q) was discovered in the wobble position of a transfer rna (trna) 47 years ago, yet the final biosynthetic enzyme responsible for q-maturation, epoxyqueuosine (oq) reductase (queg), was only recently identified. queg is a cobalamin (cbl)-dependent, [4fe-4s] cluster-containing protein that produces the hypermodified nucleoside q in situ on four trnas. to understand how queg is able to perform epoxide reduction, an unprecedented reaction for a cbl-dependent enzyme, we have determined a ...	2016	27638883
specific internalisation of gold nanoparticles into engineered porous protein cages via affinity binding.	porous protein cages are supramolecular protein self-assemblies presenting pores that allow the access of surrounding molecules and ions into their core in order to store and transport them in biological environments. protein cages' pores are attractive channels for the internalisation of inorganic nanoparticles and an alternative for the preparation of hybrid bioinspired nanoparticles. however, strategies based on nanoparticle transport through the pores are largely unexplored, due to the diffi ...	2016	27622533
n-acetylgalatosamine-mediated regulation of the aga operon by agar in streptococcus pneumoniae.	here, we analyze the transcriptomic response of streptococcus pneumoniae d39 to n-acetylgalactosamine (naga). transcriptome comparison of s. pneumoniae d39 grown in nagam17 (0.5% naga + m17) to that grown in gm17 (0.5% glucose + m17) revealed the elevated expression of various carbon metabolic genes/operons, including a pts operon (denoted here as the aga operon), which is putatively involved in naga transport and utilization, in the presence of naga. we further studied the role of a gntr-family ...	2016	27672623
inhibition of bacterial rnase p rna by phenothiazine derivatives.	there is a need to identify novel scaffolds and targets to develop new antibiotics. methylene blue is a phenothiazine derivative, and it has been shown to possess anti-malarial and anti-trypanosomal activities. here, we show that different phenothiazine derivatives and pyronine g inhibited the activities of three structurally different bacterial rnase p rnas (rprs), including that from mycobacterium tuberculosis, with ki values in the lower μm range. interestingly, three antipsychotic phenothiaz ...	2016	27618117
purification, characterization, cytotoxicity and anticancer activities of l-asparaginase, anti-colon cancer protein, from the newly isolated alkaliphilic streptomyces fradiae neae-82.	l-asparaginase is an important enzyme as therapeutic agents used in combination with other drugs in the treatment of acute lymphoblastic leukemia. a newly isolated actinomycetes strain, streptomyces sp. neae-82, was potentially producing extracellular l-asparaginase, it was identified as streptomyces fradiae neae-82, sequencing product was deposited in the genbank database under accession number kj467538. l-asparaginase was purified from the crude enzyme using ammonium sulfate precipitation, dia ...	2016	27605431
chemistry and molecular dynamics simulations of heme b-hemq and coproheme-hemq.	recently, a novel pathway for heme b biosynthesis in gram-positive bacteria has been proposed. the final poorly understood step is catalyzed by an enzyme called hemq and includes two decarboxylation reactions leading from coproheme to heme b. coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. in the study presented here, we focus on hemqs from listeria monocytogenes (lmhemq) and staphylococcus aureus (sahemq) recombinantly produced as apoproteins in ...	2016	27599156
atomic structure of an archaeal gan suggests its dual roles as an exonuclease in dna repair and a cmg component in dna replication.	in eukaryotic dna replication initiation, hexameric mcm (mini-chromosome maintenance) unwinds the template double-stranded dna to form the replication fork. mcm is activated by two proteins, cdc45 and gins, which constitute the 'cmg' unwindosome complex together with the mcm core. the archaeal dna replication system is quite similar to that of eukaryotes, but only limited knowledge about the dna unwinding mechanism is available, from a structural point of view. here, we describe the crystal stru ...	2016	27599844
crystal structure of the two-subunit trna m(1)a58 methyltransferase trm6-trm61 from saccharomyces cerevisiae.	the n(1) methylation of adenine at position 58 (m(1)a58) of trna is an important post-transcriptional modification, which is vital for maintaining the stability of the initiator methionine trnai(met). in eukaryotes, this modification is performed by the trm6-trm61 holoenzyme. to understand the molecular mechanism that underlies the cooperation of trm6 and trm61 in the methyl transfer reaction, we determined the crystal structure of trm6-trm61 holoenzyme from saccharomyces cerevisiae in the prese ...	2016	27582183
rna regulators responding to ribosomal protein s15 are frequent in sequence space.	there are several natural examples of distinct rna structures that interact with the same ligand to regulate the expression of homologous genes in different organisms. one essential question regarding this phenomenon is whether such rna regulators are the result of convergent or divergent evolution. are the rnas derived from some common ancestor and diverged to the point where we cannot identify the similarity, or have multiple solutions to the same biological problem arisen independently? a key ...	2016	27580716
eiger detector: application in macromolecular crystallography.	the development of single-photon-counting detectors, such as the pilatus, has been a major recent breakthrough in macromolecular crystallography, enabling noise-free detection and novel data-acquisition modes. the new eiger detector features a pixel size of 75 × 75 µm, frame rates of up to 3000 hz and a dead time as low as 3.8 µs. an eiger 1m and eiger 16m were tested on swiss light source beamlines x10sa and x06sa for their application in macromolecular crystallography. the combination of fast ...	2016	27599736
crystal structures of two isozymes of citrate synthase from sulfolobus tokodaii strain 7.	thermoacidophilic archaeon sulfolobus tokodaii strain 7 has two citrate synthase genes (st1805-cs and st0587-cs) in the genome with 45% sequence identity. because they exhibit similar optimal temperatures of catalytic activity and thermal inactivation profiles, we performed structural comparisons between these isozymes to elucidate adaptation mechanisms to high temperatures in thermophilic css. the crystal structures of st1805-cs and st0587-cs were determined at 2.0 å and 2.7 å resolutions, resp ...	2016	27656296
parb partition proteins: complex formation and spreading at bacterial and plasmid centromeres.	in bacteria, active partition systems contribute to the faithful segregation of both chromosomes and low-copy-number plasmids. each system depends on a site-specific dna binding protein to recognize and assemble a partition complex at a centromere-like site, commonly called pars. many plasmid, and all chromosomal centromere-binding proteins are dimeric helix-turn-helix dna binding proteins, which are commonly named parb. although the overall sequence conservation among parbs is not high, the pro ...	2016	27622187
reconstitution of protein translation of mycobacterium reveals functional conservation and divergence with the gram-negative bacterium escherichia coli.	protein translation is essential for all bacteria pathogens. it has also been a major focus of structural and functional studies and an important target of antibiotics. here we report our attempts to biochemically reconstitute mycobacterial protein translation in vitro from purified components. this mycobacterial translation system consists of individually purified recombinant translation factors from mycobacterium tuberculosis (m. tuberculosis), purified trnas and ribosomes from mycobacterium s ...	2016	27564552
classification of the treble clef zinc finger: noteworthy lessons for structure and function evolution.	treble clef (tc) zinc fingers constitute a large fold-group of structural zinc-binding protein domains that mediate numerous cellular functions. we have analysed the sequence, structure, and function relationships among all tcs in the protein data bank. this led to the identification of novel tcs, such as lsr2, yggx and tfiiic τ 60 kda subunit, and prediction of a nuclease-like function for the duf1364 family. the structural malleability of tcs is evident from the many examples with variations t ...	2016	27562564
mitochondrial-nuclear interactions mediate sex-specific transcriptional profiles in drosophila.	the assembly and function of mitochondria require coordinated expression from two distinct genomes, the mitochondrial dna (mtdna) and nuclear dna (ndna). mutations in either genome can be a source of phenotypic variation, yet their coexpression has been largely overlooked as a source of variation, particularly in the emerging paradigm of mitochondrial replacement therapy. here we tested how the transcriptome responds to mtdna and ndna variation, along with mitonuclear interactions (mtdna × ndna) ...	2016	27558138
a mutagenic study identifying critical residues for the structure and function of rice manganese transporter osmtp8.1.	rice (oryza sativa) mtp8.1 (osmtp8.1) is a tonoplast-localized manganese transporter of the cation diffusion facilitator family. here we present a structure-function analysis of osmtp8.1 based on the site-directed and random mutagenesis and complementation assays in manganese hypersensitive yeast, in combination with three-dimensional (3d) structure modeling based on the crystal structure of the escherichia coli cdf family member, ecyiip. two metal-binding sites are conserved in osmtp8.1 with ec ...	2016	27555514
efficient crispr-mediated post-transcriptional gene silencing in a hyperthermophilic archaeon using multiplexed crrna expression.	crispr (clustered regularly interspaced short palindromic repeats)-mediated rna degradation is catalyzed by a type iii system in the hyperthermophilic archaeon sulfolobus solfataricus earlier work demonstrated that the system can be engineered to target specifically mrna of an endogenous host reporter gene, namely the β-galactosidase in s. solfataricus here, we investigated the effect of single and multiple spacers targeting the mrna of a second reporter gene, α-amylase, at the same, and at diff ...	2016	27507792
three-dimensional model of human nicotinamide nucleotide transhydrogenase (nnt) and sequence-structure analysis of its disease-causing variations.	defective mitochondrial proteins are emerging as major contributors to human disease. nicotinamide nucleotide transhydrogenase (nnt), a widely expressed mitochondrial protein, has a crucial role in the defence against oxidative stress. nnt variations have recently been reported in patients with familial glucocorticoid deficiency (fgd) and in patients with heart failure. moreover, knockout animal models suggest that nnt has a major role in diabetes mellitus and obesity. in this study, we used exp ...	2016	27459240
cloning, expression, and characterization of a novel thermophilic monofunctional catalase from geobacillus sp. chb1.	catalases are widely used in many scientific areas. a catalase gene (kat) from geobacillus sp. chb1 encoding a monofunctional catalase was cloned and recombinant expressed in escherichia coli (e. coli), which was the first time to clone and express this type of catalase of genus geobacillus strains as far as we know. this kat gene was 1,467 bp in length and encoded a catalase with 488 amino acid residuals, which is only 81% similar to the previously studied bacillus sp. catalase in terms of amin ...	2016	27579320
cleavage of model substrates by arabidopsis thaliana prorp1 reveals new insights into its substrate requirements.	two broad classes of rnase p trim the 5' leader of precursor trnas (pre-trnas): ribonucleoprotein (rnp)- and proteinaceous (prorp)-variants. these two rnase p types, which use different scaffolds for catalysis, reflect independent evolutionary paths. while the catalytic rna-based rnp form is present in all three domains of life, the prorp family is restricted to eukaryotes. to obtain insights on substrate recognition by prorps, we examined the 5' processing ability of recombinant arabidopsis tha ...	2016	27494328
structures of torsina and its disease-mutant complexed with an activator reveal the molecular basis for primary dystonia.	the most common cause of early onset primary dystonia, a neuromuscular disease, is a glutamate deletion (δe) at position 302/303 of torsina, a aaa+ atpase that resides in the endoplasmic reticulum. while the function of torsina remains elusive, the δe mutation is known to diminish binding of two torsina atpase activators: lamina-associated protein 1 (lap1) and its paralog, luminal domain like lap1 (lull1). using a nanobody as a crystallization chaperone, we obtained a 1.4 å crystal structure of ...	2016	27490483
origins of tmrna: the missing link in the birth of protein synthesis?	the rna world hypothesis refers to the early period on earth in which rna was central in assuring both genetic continuity and catalysis. the end of this era coincided with the development of the genetic code and protein synthesis, symbolized by the apparition of the first non-random messenger rna (mrna). modern transfer-messenger rna (tmrna) is a unique hybrid molecule which has the properties of both mrna and transfer rna (trna). it acts as a key molecule during trans-translation, a major quali ...	2016	27484476
redox signaling through dna.	biological electron transfer reactions between metal cofactors are critical to many essential processes within the cell. duplex dna is, moreover, capable of mediating the transport of charge through its π-stacked nitrogenous bases. increasingly, [4fe4s] clusters, generally redox-active cofactors, have been found to be associated with enzymes involved in dna processing. dna-binding enzymes containing [4fe4s] clusters can thus utilize dna charge transport (dna ct) for redox signaling to coordinate ...	2016	28090121
protein phosphorylation and its role in archaeal signal transduction.	reversible protein phosphorylation is the main mechanism of signal transduction that enables cells to rapidly respond to environmental changes by controlling the functional properties of proteins in response to external stimuli. however, whereas signal transduction is well studied in eukaryotes and bacteria, the knowledge in archaea is still rather scarce. archaea are special with regard to protein phosphorylation, due to the fact that the two best studied phyla, the euryarchaeota and crenarchae ...	2016	27476079
duf3380 domain from a salmonella phage endolysin shows potent n-acetylmuramidase activity.	bacteriophage-encoded endolysins are highly diverse enzymes that cleave the bacterial peptidoglycan layer. current research focuses on their potential applications in medicine, in food conservation, and as biotechnological tools. despite the wealth of applications relying on the use of endolysin, little is known about the enzymatic properties of these enzymes, especially in the case of endolysins of bacteriophages infecting gram-negative species. automated genome annotations therefore remain to ...	2016	27287318
data for molecular dynamics simulations of b-type cytochrome c oxidase with the amber force field.	cytochrome c oxidase (cco) is a vital enzyme that catalyzes the reduction of molecular oxygen to water and pumps protons across mitochondrial and bacterial membranes. this article presents parameters for the cofactors of ba3-type cco that are compatible with the all-atom amber ff12sb and ff14sb force fields. specifically, parameters were developed for the cua pair, heme b, and the dinuclear center that consists of heme a3 and cub bridged by a hydroperoxo group. the data includes geometries in xy ...	2016	27547799
characterization of outer membrane proteome of akkermansia muciniphila reveals sets of novel proteins exposed to the human intestine.	akkermansia muciniphila is a common member of the human gut microbiota and belongs to the planctomycetes-verrucomicrobia-chlamydiae superphylum. decreased levels of a. muciniphila have been associated with many diseases, and thus it is considered to be a beneficial resident of the intestinal mucus layer. surface-exposed molecules produced by this organism likely play important roles in colonization and communication with other microbes and the host, but the protein composition of the outer membr ...	2016	27507967
cryo-em studies of the structure and dynamics of vacuolar-type atpases.	electron cryomicroscopy (cryo-em) has significantly advanced our understanding of molecular structure in biology. recent innovations in both hardware and software have made cryo-em a viable alternative for targets that are not amenable to x-ray crystallography or nuclear magnetic resonance (nmr) spectroscopy. cryo-em has even become the method of choice in some situations where x-ray crystallography and nmr spectroscopy are possible but where cryo-em can determine structures at higher resolution ...	2016	27532044
a mutation in the 16s rrna decoding region attenuates the virulence of mycobacterium tuberculosis.	mycobacterium tuberculosis contains a single rrna operon that encodes targets for antituberculosis agents, including kanamycin. to date, only four mutations in the kanamycin binding sites of 16s rrna have been reported in kanamycin-resistant clinical isolates. we hypothesized that another mutation(s) in the region may dramatically decrease m. tuberculosis viability and virulence. here, we describe an rrna mutation, u1406a, which was generated in vitro and confers resistance to kanamycin while hi ...	2016	27245411
the mechanism of rna 5′ capping with nad+, nadh and desphospho-coa.	the chemical nature of the 5′ end of rna is a key determinant of rna stability, processing, localization and translation efficiency, and has been proposed to provide a layer of ‘epitranscriptomic’ gene regulation. recently it has been shown that some bacterial rna species carry a 5′-end structure reminiscent of the 5′ 7-methylguanylate ‘cap’ in eukaryotic rna. in particular, rna species containing a 5′-end nicotinamide adenine dinucleotide (nad+) or 3′-desphospho-coenzyme a (dpcoa) have been ide ...	2016	27383794
sensitive proton-detected solid-state nmr spectroscopy of large proteins with selective ch3 labelling: application to the 50s ribosome subunit.	solid-state nmr spectroscopy allows the characterization of the structure, interactions and dynamics of insoluble and/or very large proteins. sensitivity and resolution are often major challenges for obtaining atomic-resolution information, in particular for very large protein complexes. here we show that the use of deuterated, specifically ch3-labelled proteins result in significant sensitivity gains compared to previously employed chd2 labelling, while line widths increase only marginally. we ...	2016	27385633
identification of preferred dna-binding sites for the thermus thermophilus transcriptional regulator sbtr by the combinatorial approach repsa.	one of the first steps towards elucidating the biological function of a putative transcriptional regulator is to ascertain its preferred dna-binding sequences. this may be rapidly and effectively achieved through the application of a combinatorial approach, one involving very large numbers of randomized oligonucleotides and reiterative selection and amplification steps to enrich for high-affinity nucleic acid-binding sequences. previously, we had developed the novel combinatorial approach restri ...	2016	27428627
a bayesian inference method for the analysis of transcriptional regulatory networks in metagenomic data.	metagenomics enables the analysis of bacterial population composition and the study of emergent population features, such as shared metabolic pathways. recently, we have shown that metagenomics datasets can be leveraged to characterize population-wide transcriptional regulatory networks, or meta-regulons, providing insights into how bacterial populations respond collectively to specific triggers. here we formalize a bayesian inference framework to analyze the composition of transcriptional regul ...	2016	27398089
a combined cryo-em and molecular dynamics approach reveals the mechanism of ermbl-mediated translation arrest.	nascent polypeptides can induce ribosome stalling, regulating downstream genes. stalling of ermbl peptide translation in the presence of the macrolide antibiotic erythromycin leads to resistance in streptococcus sanguis. to reveal this stalling mechanism we obtained 3.6-å-resolution cryo-em structures of ermbl-stalled ribosomes with erythromycin. the nascent peptide adopts an unusual conformation with the c-terminal asp10 side chain in a previously unseen rotated position. together with molecula ...	2016	27380950
resistance mutations generate divergent antibiotic susceptibility profiles against translation inhibitors.	mutations conferring resistance to translation inhibitors often alter the structure of rrna. reduced susceptibility to distinct structural antibiotic classes may, therefore, emerge when a common ribosomal binding site is perturbed, which significantly reduces the clinical utility of these agents. the translation inhibitors negamycin and tetracycline interfere with trna binding to the aminoacyl-trna site on the small 30s ribosomal subunit. however, two negamycin resistance mutations display unexp ...	2016	27382179
mechanism of endonuclease cleavage by the higb toxin.	bacteria encode multiple type ii toxin-antitoxin modules that cleave ribosome-bound mrnas in response to stress. all ribosome-dependent toxin family members structurally characterized to date adopt similar microbial rnase architectures despite possessing low sequence identities. therefore, determining which residues are catalytically important in this specialized rnase family has been a challenge in the field. structural studies of rele and yoeb toxins bound to the ribosome provided significant ...	2016	27378776
the sam68 nuclear body is composed of two rnase-sensitive substructures joined by the adaptor hnrnpl.	the mammalian cell nucleus contains membraneless suborganelles referred to as nuclear bodies (nbs). some nbs are formed with an architectural rna (arcrna) as the structural core. here, we searched for new nbs that are built on unidentified arcrnas by screening for ribonuclease (rnase)-sensitive nbs using 32,651 fluorescently tagged human cdna clones. we identified 32 tagged proteins that required rna for their localization in distinct nuclear foci. among them, seven rna-binding proteins commonly ...	2016	27377249
structure and mechanism of a molecular rheostat, an rna thermometer that modulates immune evasion by neisseria meningitidis.	neisseria meningitidis causes bacterial meningitis and septicemia. it evades the host complement system by upregulating expression of immune evasion factors in response to changes in temperature. rna thermometers within mrnas control expression of bacterial immune evasion factors, including cssa, in the 5'-untranslated region of the operon for capsule biosynthesis. we dissect the molecular mechanisms of thermoregulation and report the structure of the cssa thermometer. we show that the rna therm ...	2016	27369378
potential dna binding and nuclease functions of comec domains characterized in silico.	bacterial competence, which can be natural or induced, allows the uptake of exogenous double stranded dna (dsdna) into a competent bacterium. this process is known as transformation. a multiprotein assembly binds and processes the dsdna to import one strand and degrade another yet the underlying molecular mechanisms are relatively poorly understood. here distant relationships of domains in competence protein ec (comec) of bacillus subtilis (uniprot: p39695) were characterized. dna-protein intera ...	2016	27318187
a highly thermostable kanamycin resistance marker expands the tool kit for genetic manipulation of caldicellulosiruptor bescii.	caldicellulosiruptor bescii, an anaerobic gram-positive bacterium with an optimal growth temperature of 78°c, is the most thermophilic cellulose degrader known. it is of great biotechnological interest, as it efficiently deconstructs nonpretreated lignocellulosic plant biomass. currently, its genetic manipulation relies on a mutant uracil auxotrophic background strain that contains a random deletion in the pyrf genome region. the pyrf gene serves as a genetic marker to select for uracil prototro ...	2016	27208106
implications of limited thermophilicity of nitrite reduction for control of sulfide production in oil reservoirs.	nitrate reduction to nitrite in oil fields appears to be more thermophilic than the subsequent reduction of nitrite. concentrated microbial consortia from oil fields reduced both nitrate and nitrite at 40 and 45°c but only nitrate at and above 50°c. the abundance of the nirs gene correlated with mesophilic nitrite reduction activity. thauera and pseudomonas were the dominant mesophilic nitrate-reducing bacteria (mnrb), whereas petrobacter and geobacillus were the dominant thermophilic nrb (tnrb) ...	2016	27208132
a bioinformatics analysis reveals a group of mocr bacterial transcriptional regulators linked to a family of genes coding for membrane proteins.	the mocr bacterial transcriptional regulators are characterized by an n-terminal domain, 60 residues long on average, possessing the winged-helix-turn-helix (whth) architecture responsible for dna recognition and binding, linked to a large c-terminal domain (350 residues on average) that is homologous to fold type-i pyridoxal 5'-phosphate (plp) dependent enzymes like aspartate aminotransferase (aat). these regulators are involved in the expression of genes taking part in several metabolic pathwa ...	2016	27446613
hydrogen peroxide-resistant cota and yjqc of bacillus altitudinis spores are a promising biocatalyst for catalyzing reduction of sinapic acid and sinapine in rapeseed meal.	for the more efficient detoxification of phenolic compounds, a promising avenue would be to develop a multi-enzyme biocatalyst comprising peroxidase, laccase and other oxidases. however, the development of this multi-enzyme biocatalyst is limited by the vulnerability of fungal laccases and peroxidases to hydrogen peroxide (h2o2)-induced inactivation. therefore, h2o2-resistant peroxidase and laccase should be exploited. in this study, h2o2-stable cota and yjqc were isolated from the outer coat of ...	2016	27362423
structural insights into a novel class of aspartate aminotransferase from corynebacterium glutamicum.	aspartate aminotransferase from corynebacterium glutamicum (cgaspat) is a plp-dependent enzyme that catalyzes the production of l-aspartate and α-ketoglutarate from l-glutamate and oxaloacetate in l-lysine biosynthesis. in order to understand the molecular mechanism of cgaspat and compare it with those of other aspartate aminotransferases (aspats) from the aminotransferase class i, we determined the crystal structure of cgaspat. cgaspat functions as a dimer, and the cgaspat monomer consists of t ...	2016	27355211
translating the epitranscriptome.	rna modifications are indispensable for the translation machinery to provide accurate and efficient protein synthesis. whereas the importance of transfer rna (trna) and ribosomal rna (rrna) modifications has been well described and is unquestioned for decades, the significance of internal messenger rna (mrna) modifications has only recently been revealed. novel experimental methods have enabled the identification of thousands of modified sites within the untranslated and translated regions of mr ...	2016	27345446
translating the epitranscriptome.	rna modifications are indispensable for the translation machinery to provide accurate and efficient protein synthesis. whereas the importance of transfer rna (trna) and ribosomal rna (rrna) modifications has been well described and is unquestioned for decades, the significance of internal messenger rna (mrna) modifications has only recently been revealed. novel experimental methods have enabled the identification of thousands of modified sites within the untranslated and translated regions of mr ...	2016	27345446
the slicer activity of argonaute1 is required specifically for the phasing, not production, of trans-acting short interfering rnas in arabidopsis.	argonaute1 (ago1) mediates posttranscriptional silencing by micrornas (mirnas) and short interfering rnas (sirnas). ago1-catalyzed rna cleavage (slicing) represses mirna targets, but current models also highlight the roles of slicing in formation of sirnas and sirna-ago1 complexes. mirna-guided slicing is required for biogenesis of phased, trans-acting sirnas (tasirnas), whose cleaved precursor fragments are converted to double-stranded rna by rna-dependent rna polymerase 6 (rdr6). in addition, ...	2016	27354557
transcription regulation in archaea.	the known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary. accurate and responsive mechanisms to ensure that gene expression patterns match the needs of the cell necessitate regulatory strategies that control the activities and output of the archaeal transcription apparatus. archaea are reliant on a single rna polymerase for all transcription, and many of the known regulatory mechanisms employed for archaeal transcripti ...	2016	27137495
mechanistic and structural studies of protein-only rnase p compared to ribonucleoproteins reveal the two faces of the same enzymatic activity.	rnase p, the essential activity that performs the 5' maturation of trna precursors, can be achieved either by ribonucleoproteins containing a ribozyme present in the three domains of life or by protein-only enzymes called protein-only rnase p (prorp) that occur in eukaryote nuclei and organelles. a fast growing list of studies has investigated three-dimensional structures and mode of action of prorp proteins. results suggest that similar to ribozymes, prorp proteins have two main domains. a clea ...	2016	27348014
structural basis for the recognition of guide rna and target dna heteroduplex by argonaute.	argonaute proteins are key players in the gene silencing mechanisms mediated by small nucleic acids in all domains of life from bacteria to eukaryotes. however, little is known about the argonaute protein that recognizes guide rna/target dna. here, we determine the 2 å crystal structure of rhodobacter sphaeroides argonaute (rsago) in a complex with 18-nucleotide guide rna and its complementary target dna. the heteroduplex maintains watson-crick base-pairing even in the 3'-region of the guide rna ...	2016	27325485
monitoring tetracycline through a solid-state nanopore sensor.	antibiotics as emerging environmental contaminants, are widely used in both human and veterinary medicines. a solid-state nanopore sensing method is reported in this article to detect tetracycline, which is based on tet-off and tet-on systems. rtta (reverse tetracycline-controlled trans-activator) and tre (tetracycline responsive element) could bind each other under the action of tetracycline to form one complex. when the complex passes through nanopores with 8 ~ 9 nanometers in diameter, we cou ...	2016	27306259
thermus and the pink discoloration defect in cheese.	a dna sequencing-based strategy was applied to study the microbiology of continental-type cheeses with a pink discoloration defect. the basis for this phenomenon has remained elusive, despite decades of research. the bacterial composition of cheese containing the defect was compared to that of control cheese using 16s rrna gene and shotgun metagenomic sequencing as well as quantitative pcr (qpcr). throughout, it was apparent that thermus, a carotenoid-producing genus, was present at higher level ...	2016	27822529
amicoumacin a induces cancer cell death by targeting the eukaryotic ribosome.	amicoumacin a is an antibiotic that was recently shown to target bacterial ribosomes. it affects translocation and provides an additional contact interface between the ribosomal rna and mrna. the binding site of amicoumacin a is formed by universally conserved nucleotides of rrna. in this work, we showed that amicoumacin a inhibits translation in yeast and mammalian systems by affecting translation elongation. we determined the structure of the amicoumacin a complex with yeast ribosomes at a res ...	2016	27296282
structural basis of transcription activation.	class ii transcription activators function by binding to a dna site overlapping a core promoter and stimulating isomerization of an initial rna polymerase (rnap)-promoter closed complex into a catalytically competent rnap-promoter open complex. here, we report a 4.4 angstrom crystal structure of an intact bacterial class ii transcription activation complex. the structure comprises thermus thermophilus transcription activator protein tthb099 (tap) [homolog of escherichia coli catabolite activator ...	2016	27284196
mass spectrometry analysis and transcriptome sequencing reveal glowing squid crystal proteins are in the same superfamily as firefly luciferase.	the japanese firefly squid hotaru-ika (watasenia scintillans) produces intense blue light from photophores at the tips of two arms. these photophores are densely packed with protein microcrystals that catalyse the bioluminescent reaction using atp and the substrate coelenterazine disulfate. the squid is the only organism known to produce light using protein crystals. we extracted microcrystals from arm tip photophores and identified the constituent proteins using mass spectrometry and transcript ...	2016	27279452
molecular mechanisms of substrate specificities of uridinecytidine kinase.	a uridine-cytidine kinase (uck) catalyzes the phosphorylation of uridine (urd) and cytidine (cyd) and plays a significant role in the pyrimidine-nucleotide salvage pathway. unlike ordinary ones, uck from thermus thermophilus hb8 (ttck) loses catalytic activity on urd due to lack of a substrate binding ability and possesses an unusual amino acid, i.e. tyrosine 93 (tyr93) at the binding site, whereas histidine (his) is located in the other ucks. mutagenesis experiments revealed that a replacement ...	2016	27924260
focal targeting of the bacterial envelope by antimicrobial peptides.	antimicrobial peptides (amps) are utilized by both eukaryotic and prokaryotic organisms. amps such as the human beta defensins, human neutrophil peptides, human cathelicidin, and many bacterial bacteriocins are cationic and capable of binding to anionic regions of the bacterial surface. cationic amps (camps) target anionic lipids [e.g., phosphatidylglycerol (pg) and cardiolipins (cl)] in the cell membrane and anionic components [e.g., lipopolysaccharide (lps) and lipoteichoic acid (lta)] of the ...	2016	27376064
unusually situated binding sites for bacterial transcription factors can have hidden functionality.	a commonly accepted paradigm of molecular biology is that transcription factors control gene expression by binding sites at the 5' end of a gene. however, there is growing evidence that transcription factor targets can occur within genes or between convergent genes. in this work, we have investigated one such target for the cyclic amp receptor protein (crp) of enterotoxigenic escherichia coli. we show that crp binds between two convergent genes. when bound, crp regulates transcription of a small ...	2016	27258043
mechanism of b-box 2 domain-mediated higher-order assembly of the retroviral restriction factor trim5α.	restriction factors and pattern recognition receptors are important components of intrinsic cellular defenses against viral infection. mammalian trim5α proteins are restriction factors and receptors that target the capsid cores of retroviruses and activate ubiquitin-dependent antiviral responses upon capsid recognition. here, we report crystallographic and functional studies of the trim5α b-box 2 domain, which mediates higher-order assembly of trim5 proteins. the b-box can form both dimers and t ...	2016	27253059
characterization of the flexibility of the peripheral stalk of prokaryotic rotary a-atpases by atomistic simulations.	rotary atpases are involved in numerous physiological processes, with the three distinct types (f/a/v-atpases) sharing functional properties and structural features. the basic mechanism involves the counter rotation of two motors, a soluble atp hydrolyzing/synthesizing domain and a membrane-embedded ion pump connected through a central rotor axle and a stator complex. within the a/v-atpase family conformational flexibility of the eg stators has been shown to accommodate catalytic cycling and is ...	2016	27177595
the chthonomonas calidirosea genome is highly conserved across geographic locations and distinct chemical and microbial environments in new zealand's taupō volcanic zone.	chthonomonas calidirosea t49(t) is a low-abundance, carbohydrate-scavenging, and thermophilic soil bacterium with a seemingly disorganized genome. we hypothesized that the c. calidirosea genome would be highly responsive to local selection pressure, resulting in the divergence of its genomic content, genome organization, and carbohydrate utilization phenotype across environments. we tested this hypothesis by sequencing the genomes of four c. calidirosea isolates obtained from four separate geoth ...	2016	27060125
a colorimetric microplate assay for dna-binding activity of his-tagged muts protein.	a simple microplate method was designed for rapid testing dna-binding activity of proteins. the principle of the assay involves binding of tested dna by his-tagged protein immobilized on a nickel-coated elisa plate, following colorimetric detection of biotinylated dna with avidin conjugated to horseradish peroxidase. the method was used to compare dna mismatch binding activities of muts proteins from three bacterial species. the assay required relatively low amounts of tested protein (approximat ...	2016	27241123