Publications

choosing a suitable method for the identification of replication origins in microbial genomes.	as the replication of genomic dna is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. making sense of dna replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. thus, clearly comprehending the positions and sequences of replicat ...	2015	26483774
evaluation and directed evolution for thermostability improvement of a gh 13 thermostable α-glucosidase from thermus thermophilus tc11.	thermal stable α-glucosidases with transglycosylation activity could be applied to the industrial production of oligosaccharides as well as conjugation of sugars to biologically useful materials. therefore, α-glucosidases isolated from thermophiles have gained attention over the past decade. in this study, the characterization of a highly thermostable α-glucosidase and its thermostability improved mutant from newly isolated strain thermus thermophilus tc11 were investigated.	2015	26490269
a non-canonical multisubunit rna polymerase encoded by a giant bacteriophage.	the infection of pseudomonas aeruginosa by the giant bacteriophage phikz is resistant to host rna polymerase (rnap) inhibitor rifampicin. phikz encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit rnaps. polypeptides of one set are encoded by middle phage genes and are found in the phikz virions. polypeptides of the second set are encoded by early phage genes and are absent from virions. here, we report isolation of a five- ...	2015	26490960
thermodynamics of protein denaturation at temperatures over 100 °c: cuta1 mutant proteins substituted with hydrophobic and charged residues.	although the thermodynamics of protein denaturation at temperatures over 100 °c is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. we designed certain hydrophobic mutant proteins of cuta1 from escherichia coli, which have denaturation temperatures (td) ranging from 101 to 113 °c and show a reversible heat denaturation. using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mut ...	2015	26497062
structural dissection of the maltodextrin disproportionation cycle of the arabidopsis plastidial disproportionating enzyme 1 (dpe1).	the degradation of transitory starch in the chloroplast to provide fuel for the plant during the night requires a suite of enzymes that generate a series of short chain linear glucans. however, glucans of less than four glucose units are no longer substrates for these enzymes, whereas export from the plastid is only possible in the form of either maltose or glucose. in order to make use of maltotriose, which would otherwise accumulate, disproportionating enzyme 1 (dpe1; a 4-α-glucanotransferase) ...	2015	26504082
defining the mrna recognition signature of a bacterial toxin protein.	bacteria contain multiple type ii toxins that selectively degrade mrnas bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (a) site, but how these endonucleases achieve substrate specificity remains poorly understood. here, we identify the critical features for how the host inhibition of growth b (higb) toxin recognizes each of the three a-sit ...	2015	26508639
from structure-function analyses to protein engineering for practical applications of dna ligase.	dna ligases are indispensable in all living cells and ubiquitous in all organs. dna ligases are broadly utilized in molecular biology research fields, such as genetic engineering and dna sequencing technologies. here we review the utilization of dna ligases in a variety of in vitro gene manipulations, developed over the past several decades. during this period, fewer protein engineering attempts for dna ligases have been made, as compared to those for dna polymerases. we summarize the recent pro ...	2015	26508902
structure and two-metal mechanism of a eukaryal nick-sealing rna ligase.	atp-dependent rna ligases are agents of rna repair that join 3'-oh and 5'-po4 rna ends. naegleria gruberi rna ligase (ngrrnl) exemplifies a family of rna nick-sealing enzymes found in bacteria, viruses, and eukarya. crystal structures of ngrrnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-nζ)-amp•mn(2+) intermediate; ligase•atp•(mn(2+))2 michaelis complex; and ligase•mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound " ...	2015	26512110
structure and function of mitochondrial membrane protein complexes.	biological energy conversion in mitochondria is carried out by the membrane protein complexes of the respiratory chain and the mitochondrial atp synthase in the inner membrane cristae. recent advances in electron cryomicroscopy have made possible new insights into the structural and functional arrangement of these complexes in the membrane, and how they change with age. this review places these advances in the context of what is already known, and discusses the fundamental questions that remain ...	2015	26515107
the kink turn, a key architectural element in rna structure.	kink turns (k-turns) are widespread structural elements that introduce an axial bend into duplex rna with an included angle of 50°. these mediate key tertiary interactions and bind specific proteins including members of the l7ae family. the standard k-turn comprises a three-nucleotide bulge followed by g·a and a·g pairs. the rna kinks by an association of the two minor grooves, stabilized by the formation of a number of key cross-strand hydrogen bonds mostly involving the adenine bases of the g· ...	2016	26522935
complete kinetic mechanism for recycling of the bacterial ribosome.	how ef-g and rrf act together to split a post-termination ribosomal complex into its subunits has remained obscure. here, using stopped-flow experiments with rayleigh light scattering detection and quench-flow experiments with radio-detection of gtp hydrolysis, we have clarified the kinetic mechanism of ribosome recycling and obtained precise estimates of its kinetic parameters. ribosome splitting requires that ef-g binds to an already rrf-containing ribosome. ef-g binding to rrf-free ribosomes ...	2016	26527791
computational analysis of candidate prion-like proteins in bacteria and their role.	prion proteins were initially associated with diseases such as creutzfeldt jakob and transmissible spongiform encephalopathies. however, deeper research revealed them as versatile tools, exploited by the cells to execute fascinating functions, acting as epigenetic elements or building membrane free compartments in eukaryotes. one of the most intriguing properties of prion proteins is their ability to propagate a conformational assembly, even across species. in this context, it has been observed ...	2015	26528269
adaptation of the autotrophic acetogen sporomusa ovata to methanol accelerates the conversion of co2 to organic products.	acetogens are efficient microbial catalysts for bioprocesses converting c1 compounds into organic products. here, an adaptive laboratory evolution approach was implemented to adapt sporomusa ovata for faster autotrophic metabolism and co2 conversion to organic chemicals. s. ovata was first adapted to grow quicker autotrophically with methanol, a toxic c1 compound, as the sole substrate. better growth on different concentrations of methanol and with h2-co2 indicated the adapted strain had a more ...	2015	26530351
structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism.	paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ...	2015	26538563
structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism.	paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ...	2015	26538563
cold and hot extremozymes: industrial relevance and current trends.	the development of enzymes for industrial applications relies heavily on the use of microorganisms. the intrinsic properties of microbial enzymes, e.g., consistency, reproducibility, and high yields along with many others, have pushed their introduction into a wide range of products and industrial processes. extremophilic microorganisms represent an underutilized and innovative source of novel enzymes. these microorganisms have developed unique mechanisms and molecular means to cope with extreme ...	2015	26539430
watson-crick-like pairs in ccug repeats: evidence for tautomeric shifts or protonation.	rna transcripts that include expanded ccug repeats are associated with myotonic dystrophy type 2. crystal structures of two ccug-containing oligomers show that the rna strands associate into slipped duplexes that contain noncanonical c-u pairs that have apparently undergone tautomeric transition or protonation resulting in an unusual watson-crick-like pairing. the overhanging ends of the duplexes interact forming u-u pairs, which also show tautomerism. duplexes consisting of ccug repeats are the ...	2016	26543073
thermus parvatiensis rl(t) sp. nov., isolated from a hot water spring, located atop the himalayan ranges at manikaran, india.	a gram negative, yellow pigmented, rod shaped bacterium designated as rl(t) was isolated from a hot water spring (90-98 °c) located at manikaran in northern india. the isolate grows at 60-80 °c (optimum, 70 °c) and at ph 7.0-9.0 (optimum ph 7.2). phylogenetic analysis of 16s rrna gene sequences and levels of dna-dna relatedness together indicate that the new isolate represents a novel species of the genus thermus with closest affinity to thermus thermophilus hb8(t) (99.5 %) followed by thermus a ...	2015	26543260
spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha.	we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ...	2015	26553877
spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha.	we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ...	2015	26553877
natural guided genome engineering reveals transcriptional regulators controlling quorum-sensing signal degradation.	quorum-quenching (qq) are natural or engineered processes disrupting the quorum-sensing (qs) signalling which controls virulence and persistence (e.g. biofilm) in numerous bacteria. qq involves different enzymes including lactonases, amidases, oxidases and reductases which degrade the qs molecules such as n-acylhomoserine lactones (nahl). rhodococcus erythropolis known to efficiently degrade nahl is proposed as a biocontrol agent and a reservoir of qq-enzymes for biotechnology. in r. erythropoli ...	2015	26554837
determination of rna polymerase binding surfaces of transcription factors by nmr spectroscopy.	in bacteria, rna polymerase (rnap), the central enzyme of transcription, is regulated by n-utilization substance (nus) transcription factors. several of these factors interact directly, and only transiently, with rnap to modulate its function. as details of these interactions are largely unknown, we probed the rnap binding surfaces of escherichia coli (e. coli) nus factors by nuclear magnetic resonance (nmr) spectroscopy. perdeuterated factors with [(1)h,(13)c]-labeled methyl groups of val, leu, ...	2015	26560741
mglc, a paralog of myxococcus xanthus gtpase-activating protein mglb, plays a divergent role in motility regulation.	in order to optimize interactions with their environment and one another, bacteria regulate their motility. in the case of the rod-shaped cells of myxococcus xanthus, regulated motility is essential for social behaviors. m. xanthus moves over surfaces using type iv pilus-dependent motility and gliding motility. these two motility systems are coordinated by a protein module that controls cell polarity and consists of three polarly localized proteins, the small g protein mgla, the cognate mgla gtp ...	2016	26574508
fold and flexibility: what can proteins' mechanical properties tell us about their folding nucleus?	the determination of a protein's folding nucleus, i.e. a set of native contacts playing an important role during its folding process, remains an elusive yet essential problem in biochemistry. in this work, we investigate the mechanical properties of 70 protein structures belonging to 14 protein families presenting various folds using coarse-grain brownian dynamics simulations. the resulting rigidity profiles combined with multiple sequence alignments show that a limited set of rigid residues, wh ...	2015	26577596
current and future resources for functional metagenomics.	functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted dna of mixed microbial populations. a functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain dna cloned from environmental metagenomes. the information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. in this perspective, we b ...	2015	26579102
antibiotic drugs targeting bacterial rnas.	rnas have diverse structures that include bulges and internal loops able to form tertiary contacts or serve as ligand binding sites. the recent increase in structural and functional information related to rnas has put them in the limelight as a drug target for small molecule therapy. in addition, the recognition of the marked difference between prokaryotic and eukaryotic rrna has led to the development of antibiotics that specifically target bacterial rrna, reduce protein translation and thereby ...	2014	26579393
colombos v3.0: leveraging gene expression compendia for cross-species analyses.	colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ...	2015	26586805
colombos v3.0: leveraging gene expression compendia for cross-species analyses.	colombos is a database that integrates publicly available transcriptomics data for several prokaryotic model organisms. compared to the previous version it has more than doubled in size, both in terms of species and data available. the manually curated condition annotation has been overhauled as well, giving more complete information about samples' experimental conditions and their differences. functionality-wise cross-species analyses now enable users to analyse expression data for all species ...	2015	26586805
identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna.	the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ...	2015	26590840
identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna.	the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ...	2015	26590840
active site coupling in plasmodium falciparum gmp synthetase is triggered by domain rotation.	gmp synthetase (gmps), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. crystal structures of plasmodium falciparum gmps in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the gatase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. we suggest that conformational ...	2015	26592566
discovery and functional characterization of diverse class 2 crispr-cas systems.	microbial crispr-cas systems are divided into class 1, with multisubunit effector complexes, and class 2, with single protein effectors. currently, only two class 2 effectors, cas9 and cpf1, are known. we describe here three distinct class 2 crispr-cas systems. the effectors of two of the identified systems, c2c1 and c2c3, contain ruvc-like endonuclease domains distantly related to cpf1. the third system, c2c2, contains an effector with two predicted hepn rnase domains. whereas production of mat ...	2015	26593719
extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals.	enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few ...	2015	26594201
aminopeptidase t of m29 family acts as a novel intracellular virulence factor for listeria monocytogenes infection.	the foodborne pathogen listeria monocytogenes employs a number of virulence determinants including metalloproteases to infect hosts. here for the first time, we identified an m29 family aminopeptidase t (encoded by lmo1603) from l. monocytogenes that possesses a typical feature to catalyze the cleavage of amino acids from peptide substrates, with a preference for arginine. the purified recombinant lmo1603 was activated by fe(3+), zn(2+) and mn(2+), but strongly stimulated by co(2+), indicating t ...	2015	26610705
enzyme-modified particles for selective biocatalytic hydrogenation by hydrogen-driven nadh recycling.	we describe a new approach to selective h2-driven hydrogenation that exploits a sequence of enzymes immobilised on carbon particles. we used a catalyst system that comprised alcohol dehydrogenase, hydrogenase and an nad(+) reductase on carbon black to demonstrate a greater than 98 % conversion of acetophenone to phenylethanol. oxidation of h2 by the hydrogenase provides electrons through the carbon for nad(+) reduction to recycle the nadh cofactor required by the alcohol dehydrogenase. this bioc ...	2015	26613009
low temperature adaptation is not the opposite process of high temperature adaptation in terms of changes in amino acid composition.	previous studies focused on psychrophilic adaptation generally have demonstrated that multiple mechanisms work together to increase protein flexibility and activity, as well as to decrease the thermostability of proteins. however, the relationship between high and low temperature adaptations remains unclear. to investigate this issue, we collected the available predicted whole proteome sequences of species with different optimal growth temperatures, and analyzed amino acid variations and substit ...	2015	26614525
concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii.	we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ...	2015	26619013
concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii.	we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ...	2015	26619013
dancing through life: molecular dynamics simulations and network-centric modeling of allosteric mechanisms in hsp70 and hsp110 chaperone proteins.	hsp70 and hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. although many aspects of allosteric regulatory mechanisms in hsp70 and hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. in this work, ...	2015	26619280
distribution and dynamics of electron transport complexes in cyanobacterial thylakoid membranes.	the cyanobacterial thylakoid membrane represents a system that can carry out both oxygenic photosynthesis and respiration simultaneously. the organization, interactions and mobility of components of these two electron transport pathways are indispensable to the biosynthesis of thylakoid membrane modules and the optimization of bioenergetic electron flow in response to environmental changes. these are of fundamental importance to the metabolic robustness and plasticity of cyanobacteria. this revi ...	2016	26619924
clinical metagenomic identification of balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing.	primary amoebic meningoencephalitis (pam) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes.	2015	26620704
clpb n-terminal domain plays a regulatory role in protein disaggregation.	clpb/hsp100 is an atp-dependent disaggregase that solubilizes and reactivates protein aggregates in cooperation with the dnak/hsp70 chaperone system. the clpb-substrate interaction is mediated by conserved tyrosine residues located in flexible loops in nucleotide-binding domain-1 that extend into the clpb central pore. in addition to the tyrosines, the clpb n-terminal domain (ntd) was suggested to provide a second substrate-binding site; however, the manner in which the ntd recognizes and binds ...	2015	26621746
engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.	lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ...	2015	26621798
engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis.	lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ...	2015	26621798
mechanism of protective immunity by vaccination with recombinant echinococcus granulosus glutathione s-transferase (chinese strain) in mice.	the aim of this study was to investigate the immunoprotective effects of recombinant echinococcus granulosus glutathione s-transferase (reggst) against the development of protoscolices (pscs), and to determine the mechanisms underlying this protection. icr mice were subcutaneously immunized three times with reggst at weeks 0, 2 and 4, followed by the intraperitoneal administration of e. granulosus pscs at week 10. six mice in each group were sacrificed at 0, 2, 4, 6, 10, 18 and 30 weeks followin ...	2015	26622451
x-ray-induced catalytic active-site reduction of a multicopper oxidase: structural insights into the proton-relay mechanism and o2-reduction states.	during x-ray data collection from a multicopper oxidase (mco) crystal, electrons and protons are mainly released into the system by the radiolysis of water molecules, leading to the x-ray-induced reduction of o2 to 2h2o at the trinuclear copper cluster (tnc) of the enzyme. in this work, 12 crystallographic structures of thermus thermophilus hb27 multicopper oxidase (tth-mco) in holo, apo and hg-bound forms and with different x-ray absorbed doses have been determined. in holo tth-mco structures w ...	2015	26627648
non-specific blocking of mir-17-5p guide strand in triple negative breast cancer cells by amplifying passenger strand activity.	conventional wisdom holds that only one of the two strands in a micro ribonucleic acid (mirna) precursor duplex is selected as the active mirna guide strand. the complementary mirna passenger strand, however, is thought to be inactive. high levels of the oncogenic mirna (oncomir) guide strand called mir-17-5p is overexpressed in triple negative breast cancer (tnbc) and can inhibit ribosomal translation of tumor suppressor gene mrnas, such as programmed cell death 4 (pdcd4) or phosphatase and ten ...	2015	26629823
consistency analysis of genome-scale models of bacterial metabolism: a metamodel approach.	genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. with the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. the results showed that a large number of reactions (~22%) are blocked in all the models where they are present. to unravel the nature of such inconsistencies a metamodel was construed by joining the 130 mo ...	2015	26629901
characterization of aspartate kinase from corynebacterium pekinense and the critical site of arg169.	aspartate kinase (ak) is the key enzyme in the biosynthesis of aspartate-derived amino acids. recombinant ak was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. homogeneous ak was predicted as a decamer with a molecular weight of ~48 kda and a half-life of 4.5 h. the enzymatic activity was enhanced by ethanol and ni(2+). moreover, steady-state kinetic study confirmed that ak is an allosteric enzyme, and it ...	2015	26633359
metagenomics of an alkaline hot spring in galicia (spain): microbial diversity analysis and screening for novel lipolytic enzymes.	a fosmid library was constructed with the metagenomic dna from the water of the lobios hot spring (76°c, ph = 8.2) located in ourense (spain). metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 mbp. 23,207 orfs (open reading frames) were predicted from the assembly. biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. the six ...	2015	26635759
time-dependent transcriptional changes in axenic giardia duodenalis trophozoites.	giardia duodenalis is the most common gastrointestinal protozoan parasite of humans and a significant contributor to the global burden of both diarrheal disease and post-infectious chronic disorders. although g. duodenalis can be cultured axenically, significant gaps exist in our understanding of the molecular biology and metabolism of this pathogen. the present study employed rna sequencing to characterize the mrna transcriptome of g. duodenalis trophozoites in axenic culture, at log (48 h of g ...	2015	26636323
single-cell-genomics-facilitated read binning of candidate phylum em19 genomes from geothermal spring metagenomes.	the vast majority of microbial life remains uncatalogued due to the inability to cultivate these organisms in the laboratory. this "microbial dark matter" represents a substantial portion of the tree of life and of the populations that contribute to chemical cycling in many ecosystems. in this work, we leveraged an existing single-cell genomic data set representing the candidate bacterial phylum "calescamantes" (em19) to calibrate machine learning algorithms and define metagenomic bins directly ...	2016	26637598
cytoplasmic copz-like protein and periplasmic rusticyanin and acop proteins as possible copper resistance determinants in acidithiobacillus ferrooxidans atcc 23270.	acidophilic organisms, such as acidithiobacillus ferrooxidans, possess high-level resistance to copper and other metals. a. ferrooxidans contains canonical copper resistance determinants present in other bacteria, such as copa atpases and rnd efflux pumps, but these components do not entirely explain its high metal tolerance. the aim of this study was to find other possible copper resistance determinants in this bacterium. transcriptional expression of a. ferrooxidans genes coding for a cytoplas ...	2016	26637599
atp regulation in bioproduction.	adenosine-5'-triphosphate (atp) is consumed as a biological energy source by many intracellular reactions. thus, the intracellular atp supply is required to maintain cellular homeostasis. the dependence on the intracellular atp supply is a critical factor in bioproduction by cell factories. recent studies have shown that changing the atp supply is critical for improving product yields. in this review, we summarize the recent challenges faced by researchers engaged in the development of engineere ...	2015	26655598
nmr structure and function of helicoverpa armigera sterol carrier protein-2, an important insecticidal target from the cotton bollworm.	the cotton bollworm, helicoverpa armigera, has developed strong resistance to many insecticides. sterol carrier protein-2 (scp-2) is an important non-specific lipid transfer protein in insects and appears to be a potential new target. in order to elucidate the structure and function of helicoverpa armigera scp-2 (hascp-2), nmr spectroscopy, docking simulations, mutagenesis and bioassays were performed. hascp-2 composed of five α-helices and four stranded β-sheets. the folds of α-helices and β-sh ...	2015	26655641
structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle.	the bacterial sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. intermediates in the sox pathway are covalently attached to the heterodimeric carrier protein soxyz through conjugation to a cysteine on a protein swinging arm. we have investigated how the carrier protein shuttles intermediates between the enzymes of the sox pathway using the interaction between soxyz and the enzyme soxb as our model. the carrier protein and enzyme interact only w ...	2015	26655737
markerless gene deletion with cytosine deaminase in thermus thermophilus strain hb27.	we developed a counterselectable deletion system for thermus thermophilus hb27 based on cytosine deaminase (encoded by coda) from thermaerobacter marianensis dsm 12885 and the sensitivity of t. thermophilus hb27 to the antimetabolite 5-fluorocytosine (5-fc). the deletion vector comprises the puc18 origin of replication, a thermostable kanamycin resistance marker functional in t. thermophilus hb27, and coda under the control of a constitutive putative trehalose promoter from t. thermophilus hb27. ...	2016	26655764
deciphering the dynamics of non-covalent interactions affecting thermal stability of a protein: molecular dynamics study on point mutant of thermus thermophilus isopropylmalate dehydrogenase.	thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. in this study dynamic changes in the non-covalent interac ...	2015	26657745
synergistic effect of atp for ruva-ruvb-holliday junction dna complex formation.	the escherichia coli ruvb hexameric ring motor proteins, together with ruvas, promote branch migration of holliday junction dna. zero mode waveguides (zmws) constitute of nanosized holes and enable the visualization of a single fluorescent molecule under micromolar order of the molecules, which is applicable to characterize the formation of ruva-ruvb-holliday junction dna complex. in this study, we used zmws and counted the number of ruvbs binding to ruva-holliday junction dna complex. our data ...	2015	26658024
metagenomics: retrospect and prospects in high throughput age.	in recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. in the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. a brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenom ...	2015	26664751
structural similarities and differences between two functionally distinct seca proteins, mycobacterium tuberculosis seca1 and seca2.	while seca is the atpase component of the major bacterial secretory (sec) system, mycobacteria and some gram-positive pathogens have a second paralog, seca2. in bacteria with two seca paralogs, each seca is functionally distinct, and they cannot compensate for one another. compared to seca1, seca2 exports a distinct and smaller set of substrates, some of which have roles in virulence. in the mycobacterial system, some seca2-dependent substrates lack a signal peptide, while others contain a signa ...	2016	26668263
initiation factor 2 stabilizes the ribosome in a semirotated conformation.	intersubunit rotation and movement of the l1 stalk, a mobile domain of the large ribosomal subunit, have been shown to accompany the elongation cycle of translation. the initiation phase of protein synthesis is crucial for translational control of gene expression; however, in contrast to elongation, little is known about the conformational rearrangements of the ribosome during initiation. bacterial initiation factors (ifs) 1, 2, and 3 mediate the binding of initiator trna and mrna to the small r ...	2015	26668356
evolutionary limitation and opportunities for developing trna synthetase inhibitors with 5-binding-mode classification.	aminoacyl-trna synthetases (aarss) are enzymes that catalyze the transfer of amino acids to their cognate trnas as building blocks for translation. each of the aars families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. in addition, aarss in higher species have evolved important non-translational functions. these translational and non-translational functions of aars are attractive for developing antibacterial, antifungal, and antiparasitic agents ...	2015	26670257
mechanisms of ribosome stalling by secm at multiple elongation steps.	regulation of translating ribosomes is a major component of gene expression control network. in escherichia coli, ribosome stalling by the c-terminal arrest sequence of secm regulates the seca-dependent secretion pathway. previous studies reported many residues of secm peptide and ribosome exit tunnel are critical for stalling. however, the underlying molecular mechanism is still not clear at the atomic level. here, we present two cryo-em structures of the secm-stalled ribosomes at 3.3-3.7 å res ...	2015	26670735
structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue.	purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ...	2015	26673726
structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue.	purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ...	2015	26673726
co-evolution of bacterial ribosomal protein s15 with diverse mrna regulatory structures.	rna-protein interactions are critical in many biological processes, yet how such interactions affect the evolution of both partners is still unknown. rna and protein structures are impacted very differently by mechanisms of genomic change. while most protein families are identifiable at the nucleotide level across large phylogenetic distances, rna families display far less nucleotide similarity and are often only shared by closely related bacterial species. ribosomal protein s15 has two rna bind ...	2015	26675164
human holliday junction resolvase gen1 uses a chromodomain for efficient dna recognition and cleavage.	holliday junctions (hjs) are key dna intermediates in homologous recombination. they link homologous dna strands and have to be faithfully removed for proper dna segregation and genome integrity. here, we present the crystal structure of human hj resolvase gen1 complexed with dna at 3.0 å resolution. the gen1 core is similar to other rad2/xpg nucleases. however, unlike other members of the superfamily, gen1 contains a chromodomain as an additional dna interaction site. chromodomains are known fo ...	2015	26682650
resveratrol directly binds to mitochondrial complex i and increases oxidative stress in brain mitochondria of aged mice.	resveratrol is often described as a promising therapeutic molecule for numerous diseases, especially in metabolic and neurodegenerative disorders. while the mechanism of action is still debated, an increasing literature reports that resveratrol regulates the mitochondrial respiratory chain function. in a recent study we have identified mitochondrial complex i as a direct target of this molecule. nevertheless, the mechanisms and consequences of such an interaction still require further investigat ...	2015	26684010
saxs fingerprints of aldehyde dehydrogenase oligomers.	enzymes of the aldehyde dehydrogenase (aldh) superfamily catalyze the nicotinamide adenine dinucleotide-dependent oxidation of aldehydes to carboxylic acids. aldhs are important in detoxification of aldehydes, amino acid metabolism, embryogenesis and development, neurotransmission, oxidative stress, and cancer. mutations in genes encoding aldhs cause metabolic disorders, including alcohol flush reaction (aldh2), sjögren-larsson syndrome (aldh3a2), hyperprolinemia type ii (aldh4a1), γ-hydroxybuty ...	2015	26693506
structural insights into a key carotenogenesis related enzyme phytoene synthase of p. falciparum: a novel drug target for malaria.	carotenoids represent a diverse group of pigments derived from the common isoprenoid precursors and fulfill a variety of critical functions in plants and animals. phytoene synthase (psy), a transferase enzyme that catalyzes the first specific step in carotenoid biosynthesis plays a central role in the regulation of a number of essential functions mediated via carotenoids. psys have been deeply investigated in plants, bacteria and algae however in apicomplexans it is poorly studied. in an effort ...	2015	26702306
curing the megaplasmid ptt27 from thermus thermophilus hb27 and maintaining exogenous plasmids in the plasmid-free strain.	stepwise deletions in the only plasmid in thermus thermophilus hb27, megaplasmid ptt27, showed that two distantly located loci were important for maintenance of the plasmid. one is a minimum replicon including one gene, rept, coding a replication initiator, and the other encodes subunits of class i ribonucleotide reductase (rnr) for deoxynucleoside triphosphate (dntp) synthesis. since the initiator protein, rept, bound to direct repeats downstream from its own gene, it was speculated that a more ...	2016	26712540
aerobic and anaerobic thiosulfate oxidation by a cold-adapted, subglacial chemoautotroph.	geochemical data indicate that protons released during pyrite (fes2) oxidation are important drivers of mineral weathering in oxic and anoxic zones of many aquatic environments, including those beneath glaciers. oxidation of fes2 under oxic, circumneutral conditions proceeds through the metastable intermediate thiosulfate (s2o3 (2-)), which represents an electron donor capable of supporting microbial metabolism. subglacial meltwaters sampled from robertson glacier (rg), canada, over a seasonal m ...	2016	26712544
novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2.	the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ...	2015	26712743
novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2.	the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ...	2015	26712743
isc, a novel group of bacterial and archaeal dna transposons that encode cas9 homologs.	bacterial genomes encode numerous homologs of cas9, the effector protein of the type ii crispr-cas systems. the homology region includes the arginine-rich helix and the hnh nuclease domain that is inserted into the ruvc-like nuclease domain. these genes, however, are not linked to cas genes or crispr. here, we show that cas9 homologs represent a distinct group of nonautonomous transposons, which we denote isc (insertion sequences cas9-like). we identify many diverse families of full-length isc t ...	2016	26712934
structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome.	during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ...	2015	26715760
structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome.	during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ...	2015	26715760
cooperation between two periplasmic copper chaperones is required for full activity of the cbb3 -type cytochrome c oxidase and copper homeostasis in rhodobacter capsulatus.	copper (cu) is an essential micronutrient that functions as a cofactor in several important enzymes, such as respiratory heme-copper oxygen reductases. yet, cu is also toxic and therefore cells engage a highly coordinated cu uptake and delivery system to prevent the accumulation of toxic cu concentrations. in this study, we analyzed cu delivery to the cbb3 -type cytochrome c oxidase (cbb3 -cox) of rhodobacter capsulatus. we identified the pcua c-like periplasmic chaperone pcca and analyzed its c ...	2016	26718481
energy conversion, redox catalysis and generation of reactive oxygen species by respiratory complex i.	complex i (nadh:ubiquinone oxidoreductase) is critical for respiration in mammalian mitochondria. it oxidizes nadh produced by the krebs' tricarboxylic acid cycle and β-oxidation of fatty acids, reduces ubiquinone, and transports protons to contribute to the proton-motive force across the inner membrane. complex i is also a significant contributor to cellular oxidative stress. in complex i, nadh oxidation by a flavin mononucleotide, followed by intramolecular electron transfer along a chain of i ...	2016	26721206
short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations.	mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ...	2015	26721932
short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations.	mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ...	2015	26721932
redirection of the reaction specificity of a thermophilic acetolactate synthase toward acetaldehyde formation.	acetolactate synthase and pyruvate decarboxylase are thiamine pyrophosphate-dependent enzymes that convert pyruvate into acetolactate and acetaldehyde, respectively. although the former are encoded in the genomes of many thermophiles and hyperthermophiles, the latter has been found only in mesophilic organisms. in this study, the reaction specificity of acetolactate synthase from thermus thermophilus was redirected to catalyze acetaldehyde formation to develop a thermophilic pyruvate decarboxyla ...	2016	26731734
gbtools: interactive visualization of metagenome bins in r.	improvements in dna sequencing technology have increased the amount and quality of sequences that can be obtained from metagenomic samples, making it practical to extract individual microbial genomes from metagenomic assemblies ("binning"). however, while many tools and methods exist for unsupervised binning with various statistical algorithms, there are few options for visualizing the results, even though visualization is vital to exploratory data analysis. we have developed gbtools, a software ...	2015	26732662
lineage-specific variations in the trigger loop modulate rna proofreading by bacterial rna polymerases.	rna cleavage by bacterial rna polymerase (rnap) has been implicated in transcriptional proofreading and reactivation of arrested transcription elongation complexes but its molecular mechanism is less understood than the mechanism of nucleotide addition, despite both reactions taking place in the same active site. rnap from the radioresistant bacterium deinococcus radiodurans is characterized by highly efficient intrinsic rna cleavage in comparison with escherichia coli rnap. we find that the enh ...	2016	26733581
a model for genesis of transcription systems.	repeating sequences generated from rna gene fusions/ligations dominate ancient life, indicating central importance of building structural complexity in evolving biological systems. a simple and coherent story of life on earth is told from tracking repeating motifs that generate α/β proteins, 2-double-ψ-β-barrel (dpbb) type rna polymerases (rnaps), general transcription factors (gtfs), and promoters. a general rule that emerges is that biological complexity that arises through generation of repea ...	2016	26735411
comparing residue clusters from thermophilic and mesophilic enzymes reveals adaptive mechanisms.	understanding how proteins adapt to function at high temperatures is important for deciphering the energetics that dictate protein stability and folding. while multiple principles important for thermostability have been identified, we lack a unified understanding of how internal protein structural and chemical environment determine qualitative or quantitative impact of evolutionary mutations. in this work we compare equivalent clusters of spatially neighboring residues between paired thermophili ...	2016	26741367
the bioactive secondary metabolites from talaromyces species.	the focus of this review is placed on the chemical structures from the species of the genus talaromyces reported with reference to their biological activities. 221 secondary metabolites, including 43 alkaloids and peptides, 88 esters, 31 polyketides, 19 quinones, 15 steroid and terpenoids, and 25 other structure type compounds, have been included, and 66 references are cited.	2016	26746215
n(6)-methyladenosine in mrna disrupts trna selection and translation-elongation dynamics.	n(6)-methylation of adenosine (forming m(6)a) is the most abundant post-transcriptional modification within the coding region of mrna, but its role during translation remains unknown. here, we used bulk kinetic and single-molecule methods to probe the effect of m(6)a in mrna decoding. although m(6)a base-pairs with uridine during decoding, as shown by x-ray crystallographic analyses of thermus thermophilus ribosomal complexes, our measurements in an escherichia coli translation system revealed t ...	2016	26751643
two-dimensional crystallization of monomeric bovine cytochrome c oxidase with bound cytochrome c in reconstituted lipid membranes.	mitochondrial cytochrome c oxidase utilizes electrons provided by cytochrome c for the active vectorial transport of protons across the inner mitochondrial membrane through the reduction of molecular oxygen to water. direct structural evidence on the transient cytochrome c oxidase-cytochrome c complex thus far, however, remains elusive and its physiological relevant oligomeric form is unclear. here, we report on the 2d crystallization of monomeric bovine cytochrome c oxidase with tightly bound c ...	2016	26754561
impact of different target sequences on type iii crispr-cas immunity.	clustered regularly interspaced short palindromic repeat (crispr) loci encode an adaptive immune system of prokaryotes. within these loci, sequences intercalated between repeats known as "spacers" specify the targets of crispr immunity. the majority of spacers match sequences present in phages and plasmids; however, it is not known whether there are differences in the immunity provided against these diverse invaders. we studied this issue using the staphylococcus epidermidis crispr system, which ...	2016	26755632
structural basis for the endoribonuclease activity of the type iii-a crispr-associated protein csm6.	prokaryotic crispr-cas systems provide an rna-guided mechanism for genome defense against mobile genetic elements such as viruses and plasmids. in type iii-a crispr-cas systems, the rna-guided multisubunit csm effector complex targets both single-stranded rnas and double-stranded dnas. in addition to the csm complex, efficient anti-plasmid immunity mediated by type iii-a systems also requires the crispr-associated protein csm6. here we report the crystal structure of csm6 from thermus thermophil ...	2016	26763118
a comprehensive benchmarking study of protocols and sequencing platforms for 16s rrna community profiling.	in the last 5 years, the rapid pace of innovations and improvements in sequencing technologies has completely changed the landscape of metagenomic and metagenetic experiments. therefore, it is critical to benchmark the various methodologies for interrogating the composition of microbial communities, so that we can assess their strengths and limitations. the most common phylogenetic marker for microbial community diversity studies is the 16s ribosomal rna gene and in the last 10 years the field h ...	2016	26763898
bacterial transcription as a target for antibacterial drug development.	transcription, the first step of gene expression, is carried out by the enzyme rna polymerase (rnap) and is regulated through interaction with a series of protein transcription factors. rnap and its associated transcription factors are highly conserved across the bacterial domain and represent excellent targets for broad-spectrum antibacterial agent discovery. despite the numerous antibiotics on the market, there are only two series currently approved that target transcription. the determination ...	2016	26764017
a target-protection mechanism of antibiotic resistance at atomic resolution: insights into fusb-type fusidic acid resistance.	antibiotic resistance in clinically important bacteria can be mediated by proteins that physically associate with the drug target and act to protect it from the inhibitory effects of an antibiotic. we present here the first detailed structural characterization of such a target protection mechanism mediated through a protein-protein interaction, revealing the architecture of the complex formed between the fusb fusidic acid resistance protein and the drug target (ef-g) it acts to protect. binding ...	2016	26781961
centers of motion associated with ef-tu binding to the ribosome.	structural centers of motion (pivot points) in the ribosome have recently been identified by measurement of conformational changes in rrna resulting from ef-g gtp hydrolysis. this series of measurements is extended here to the ribosome's interactions with the cofactor ef-tu. four recent ef-tu bound ribosome structures were compared to unbound structures. a total of 16 pivots were identified, of which 4 are unique to the ef-tu interaction. pivots in the gtpase associated center and the sarcin-ric ...	2016	26786136
the dna polymerase iii holoenzyme contains γ and is not a trimeric polymerase.	there is widespread agreement that the clamp loader of the escherichia coli replicase has the composition dnax3δδ'χψ. two dnax proteins exist in e. coli, full length τ and a truncated γ that is created by ribosomal frameshifting. τ binds dna polymerase iii tightly; γ does not. there is a controversy as to whether or not dna polymerase iii holoenzyme (pol iii he) contains γ. a three-τ form of pol iii he would contain three pol iiis. proponents of the three-τ hypothesis have claimed that γ found i ...	2016	26786318
functional determinants of metal ion transport and selectivity in paralogous cation diffusion facilitator transporters czcd and mnte in streptococcus pneumoniae.	cation diffusion facilitators (cdfs) are a large family of divalent metal transporters that collectively possess broad metal specificity and contribute to intracellular metal homeostasis and virulence in bacterial pathogens. streptococcus pneumoniae expresses two homologous cdf efflux transporters, mnte and czcd. cells lacking mnte or czcd are sensitive to manganese (mn) or zinc (zn) toxicity, respectively, and specifically accumulate mn or zn, respectively, thus suggesting that mnte selectively ...	2016	26787764
cysteine biosynthesis in lactobacillus casei: identification and characterization of a serine acetyltransferase.	in bacteria, cysteine can be synthesized from serine by two steps involving an l-serine o-acetyltransferase (sat) and a cysteine synthase (cysk). while cysk is found in the publicly available annotated genome from lactobacillus casei atcc 334, a gene encoding sat (cyse) is missing. in this study, we found that various strains of l. casei grew in a chemically defined medium containing sulfide as the sole sulfur source, indicating the presence of a serine o-acetyltransferase. the gene lying upstre ...	2016	26790714
novel base-pairing interactions at the trna wobble position crucial for accurate reading of the genetic code.	posttranscriptional modifications at the wobble position of transfer rnas play a substantial role in deciphering the degenerate genetic code on the ribosome. the number and variety of modifications suggest different mechanisms of action during messenger rna decoding, of which only a few were described so far. here, on the basis of several 70s ribosome complex x-ray structures, we demonstrate how escherichia coli trna(lys)(uuu) with hypermodified 5-methylaminomethyl-2-thiouridine (mnm(5)s(2)u) at ...	2016	26791911