Publications

road rules for traffic on dna-systematic analysis of transcriptional roadblocking in vivo.	genomic dna is bound by many proteins that could potentially impede elongation of rna polymerase (rnap), but the factors determining the magnitude of transcriptional roadblocking in vivo are poorly understood. through systematic experiments and modeling, we analyse how roadblocking by the lac repressor (laci) in escherichia coli cells is controlled by promoter firing rate, the concentration and affinity of the roadblocker protein, the transcription-coupled repair protein mfd, and promoter-roadbl ...	2014	25034688
stability curve prediction of homologous proteins using temperature-dependent statistical potentials.	the unraveling and control of protein stability at different temperatures is a fundamental problem in biophysics that is substantially far from being quantitatively and accurately solved, as it requires a precise knowledge of the temperature dependence of amino acid interactions. in this paper we attempt to gain insight into the thermal stability of proteins by designing a tool to predict the full stability curve as a function of the temperature for a set of 45 proteins belonging to 11 homologou ...	2014	25032839
examining the gm18 and m(1)g modification positions in trna sequences.	the trna structure contains conserved modifications that are responsible for its stability and are involved in the initiation and accuracy of the translation process. trna modification enzymes are prevalent in bacteria, archaea, and eukaryotes. trna gm18 methyltransferase (trmh) and trna m(1)g37 methyltransferase (trmd) are prevalent and essential enzymes in bacterial populations. trmh involves itself in methylation process at the 2'-oh group of ribose at the 18th position of guanosine (g) in tr ...	2014	25031570
an update on complex i assembly: the assembly of players.	defects in complex i assembly is one of the emerging underlying causes of severe mitochondrial disorders. the assembly of complex i has been difficult to understand due to its large size, dual genetic control and the number of proteins involved. mutations in complex i subunits as well as assembly factors have been reported to hinder its assembly and give rise to a range of mitochondria disorders. in this review, we summarize the recent progress made in understanding the complex i assembly pathwa ...	2014	25030182
the hypusine-containing translation factor eif5a.	in addition to the small and large ribosomal subunits, aminoacyl-trnas, and an mrna, cellular protein synthesis is dependent on translation factors. the eukaryotic translation initiation factor 5a (eif5a) and its bacterial ortholog elongation factor p (ef-p) were initially characterized based on their ability to stimulate methionyl-puromycin (met-pmn) synthesis, a model assay for protein synthesis; however, the function of these factors in cellular protein synthesis has been difficult to resolve ...	2014	25029904
inteins as indicators of gene flow in the halobacteria.	this research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the halobacteria. we surveyed 118 genomes representing 26 genera of halobacteria for intein sequences. we then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. we identified 24 proteins in the halobacteria that hav ...	2014	25018750
reverse gyrase--recent advances and current mechanistic understanding of positive dna supercoiling.	reverse gyrases are topoisomerases that introduce positive supercoils into dna in an atp-dependent reaction. they consist of a helicase domain and a topoisomerase domain that closely cooperate in catalysis. the mechanism of the functional cooperation of these domains has remained elusive. recent studies have shown that the helicase domain is a nucleotide-regulated conformational switch that alternates between an open conformation with a low affinity for double-stranded dna, and a closed state wi ...	2014	25013168
phages preying on bacillus anthracis, bacillus cereus, and bacillus thuringiensis: past, present and future.	many bacteriophages (phages) have been widely studied due to their major role in virulence evolution of bacterial pathogens. however, less attention has been paid to phages preying on bacteria from the bacillus cereus group and their contribution to the bacterial genetic pool has been disregarded. therefore, this review brings together the main information for the b. cereus group phages, from their discovery to their modern biotechnological applications. a special focus is given to phages infect ...	2014	25010767
molecular characterization of the na+/h+-antiporter nhaa from salmonella typhimurium.	na+/h+ antiporters are integral membrane proteins that are present in almost every cell and in every kingdom of life. they are essential for the regulation of intracellular ph-value, na+-concentration and cell volume. these secondary active transporters exchange sodium ions against protons via an alternating access mechanism, which is not understood in full detail. na+/h+ antiporters show distinct species-specific transport characteristics and regulatory properties that correlate with respective ...	2014	25010413
function and evolution of the sox multienzyme complex in the marine gammaproteobacterium congregibacter litoralis.	core sets of sox genes were detected in several genome sequenced members of the environmental important om60/nor5 clade of marine gammaproteobacteria. however, emendation of media with thiosulfate did not result in stimulation of growth in two of these strains and cultures of congregibacter litoralis dsm 17192(t) did not oxidize thiosulfate to sulfate in concentrations of one mmol l(-1) or above. on the other hand, a significant production of sulfate was detected upon growth with the organic sul ...	2014	25006520
preliminary x-ray crystallographic analysis of an engineered glutamyl-trna synthetase from escherichia coli.	the nature of interaction between glutamyl-trna synthetase (glurs) and its trna substrate is unique in bacteria in that many bacterial glurs are capable of recognizing two trna substrates: trnaglu and trnagln. to properly understand this distinctive glurs-trna interaction it is important to pursue detailed structure-function studies; however, because of the fact that trna-glurs interaction in bacteria is also associated with phylum-specific idiosyncrasies, the structure-function correlation stud ...	2014	25005090
structure of pneumococcal peptidoglycan hydrolase lytb reveals insights into the bacterial cell wall remodeling and pathogenesis.	streptococcus pneumoniae causes a series of devastating infections in humans. previous studies have shown that the endo-β-n-acetylglucosaminidase lytb is critical for pneumococcal cell division and nasal colonization, but the biochemical mechanism of lytb action remains unknown. here we report the 1.65 å crystal structure of the catalytic domain (residues lys-375-asp-658) of lytb (termed lytbcat), excluding the choline binding domain. lytbcat consists of three structurally independent modules: s ...	2014	25002590
evidence for a hexaheteromeric methylenetetrahydrofolate reductase in moorella thermoacetica.	moorella thermoacetica can grow with h₂ and co₂, forming acetic acid from 2 co₂ via the wood-ljungdahl pathway. all enzymes involved in this pathway have been characterized to date, except for methylenetetrahydrofolate reductase (metf). we report here that the m. thermoacetica gene that putatively encodes this enzyme, metf, is part of a transcription unit also containing the genes hdrcba, mvhd, and metv. metf copurified with the other five proteins encoded in the unit in a hexaheteromeric comple ...	2014	25002540
ancient translation factor is essential for trna-dependent cysteine biosynthesis in methanogenic archaea.	methanogenic archaea lack cysteinyl-trna synthetase; they synthesize cys-trna and cysteine in a trna-dependent manner. two enzymes are required: phosphoseryl-trna synthetase (seprs) forms phosphoseryl-trna(cys) (sep-trna(cys)), which is converted to cys-trna(cys) by sep-trna:cys-trna synthase (sepcyss). this represents the ancestral pathway of cys biosynthesis and coding in archaea. here we report a translation factor, sepcyse, essential for methanococcal cys biosynthesis; its deletion in methan ...	2014	25002468
proteomic mapping of the human mitochondrial intermembrane space in live cells via ratiometric apex tagging.	obtaining complete protein inventories for subcellular regions is a challenge that often limits our understanding of cellular function, especially for regions that are impossible to purify and are therefore inaccessible to traditional proteomic analysis. we recently developed a method to map proteomes in living cells with an engineered peroxidase (apex) that bypasses the need for organellar purification when applied to membrane-bound compartments; however, it was insufficiently specific when app ...	2014	25002142
free-energy landscape of reverse trna translocation through the ribosome analyzed by electron microscopy density maps and molecular dynamics simulations.	to understand the mechanism of reverse trna translocation in the ribosome, all-atom molecular dynamics simulations of the ribosome-trnas-mrna-efg complex were performed. the complex at the post-translocational state was directed towards the translocational and pre-translocational states by fitting the complex into cryo-em density maps. between a series of the fitting simulations, umbrella sampling simulations were performed to obtain the free-energy landscape. multistep structural changes, such ...	2014	24999999
inhibition of the 4fe-4s proteins ispg and isph: an epr, endor and hyscore investigation.	ispg and isph are proteins that are involved in isoprenoid biosynthesis in most bacteria as well as in malaria parasites and are important drug targets. they contain cubane-type 4fe-4s clusters that are involved in unusual 2h(+)/2e(-) reductions. here, we report the results of electron paramagnetic resonance spectroscopic investigations of the binding of amino- and thiolo-hmbpp (hmbpp=e-1-hydroxy-2-methyl-but-2-enyl 4-diphosphate) isph substrate-analog inhibitors to both proteins, as well as the ...	2014	24999381
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
the pathway of o₂to the active site in heme-copper oxidases.	the route of o₂to and from the high-spin heme in heme-copper oxidases has generally been believed to emulate that of carbon monoxide (co). time-resolved and stationary infrared experiments in our laboratories of the fully reduced co-bound enzymes, as well as transient optical absorption saturation kinetics studies as a function of co pressure, have provided strong support for co binding to cub⁺ on the pathway to and from the high-spin heme. the presence of co on cub⁺ suggests that o₂binding may ...	2014	24998308
regulation of the mammalian elongation cycle by subunit rolling: a eukaryotic-specific ribosome rearrangement.	the extent to which bacterial ribosomes and the significantly larger eukaryotic ribosomes share the same mechanisms of ribosomal elongation is unknown. here, we present subnanometer resolution cryoelectron microscopy maps of the mammalian 80s ribosome in the posttranslocational state and in complex with the eukaryotic eef1a⋅val-trna⋅gmppnp ternary complex, revealing significant differences in the elongation mechanism between bacteria and mammals. surprisingly, and in contrast to bacterial riboso ...	2014	24995983
prokaryotic ubiquitin-like protein modification.	prokaryotes form ubiquitin (ub)-like isopeptide bonds on the lysine residues of proteins by at least two distinct pathways that are reversible and regulated. in mycobacteria, the c-terminal gln of pup (prokaryotic ubiquitin-like protein) is deamidated and isopeptide linked to proteins by a mechanism distinct from ubiquitylation in enzymology yet analogous to ubiquitylation in targeting proteins for destruction by proteasomes. ub-fold proteins of archaea (samps, small archaeal modifier proteins) ...	2014	24995873
veillonella, firmicutes: microbes disguised as gram negatives.	the firmicutes represent a major component of the intestinal microflora. the intestinal firmicutes are a large, diverse group of organisms, many of which are poorly characterized due to their anaerobic growth requirements. although most firmicutes are gram positive, members of the class negativicutes, including the genus veillonella, stain gram negative. veillonella are among the most abundant organisms of the oral and intestinal microflora of animals and humans, in spite of being strict anaerob ...	2013	24976898
oral manifestations of hepatitis c virus infection.	extrahepatic manifestations (ehms) of hepatitis c virus (hcv) infection can affect a variety of organ systems with significant morbidity and mortality. some of the most frequently reported ehm of hcv infection, involve the oral region predominantly or exclusively. oral lichen planus (olp) is a chronic inflammatory condition that is potentially malignant and represents cell-mediated reaction to a variety of extrinsic antigens, altered self-antigens, or super antigens. robust epidemiological evide ...	2014	24976694
magnesium-dependent processes are targets of bacterial manganese toxicity.	a bradyrhizobium japonicum mutant defective in the gene encoding the high-affinity mn(2+) transporter mnth has a severe growth phenotype under manganese limitation. here, we isolated suppressor mutants of an mnth strain that grew under manganese limitation, and activities of high-affinity mn(2+) transport and mn(2+) -dependent enzymes were partially rescued. the suppressor strains harbour gain-of-function mutations in the gene encoding the mg(2+) channel mgte. the mgte variants likely allow mn(2 ...	2014	24975873
structural basis of transcription initiation by bacterial rna polymerase holoenzyme.	the bacterial rna polymerase (rnap) holoenzyme containing σ factor initiates transcription at specific promoter sites by de novo rna priming, the first step of rna synthesis where rnap accepts two initiating ribonucleoside triphosphates (intps) and performs the first phosphodiester bond formation. we present the structure of de novo transcription initiation complex that reveals unique contacts of the intps bound at the transcription start site with the template dna and also with rnap and demonst ...	2014	24973216
misfolding of amyloidogenic proteins and their interactions with membranes.	in this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. many of these proteins are implicated in serious illnesses such as alzheimer's disease and parkinson's disease. misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membran ...	2013	24970204
misfolding of amyloidogenic proteins and their interactions with membranes.	in this paper, we discuss amyloidogenic proteins, their misfolding, resulting structures, and interactions with membranes, which lead to membrane damage and subsequent cell death. many of these proteins are implicated in serious illnesses such as alzheimer's disease and parkinson's disease. misfolding of amyloidogenic proteins leads to the formation of polymorphic oligomers and fibrils. oligomeric aggregates are widely thought to be the toxic species, however, fibrils also play a role in membran ...	2013	24970204
improvement of biocatalysts for industrial and environmental purposes by saturation mutagenesis.	laboratory evolution techniques are becoming increasingly widespread among protein engineers for the development of novel and designed biocatalysts. the palette of different approaches ranges from complete randomized strategies to rational and structure-guided mutagenesis, with a wide variety of costs, impacts, drawbacks and relevance to biotechnology. a technique that convincingly compromises the extremes of fully randomized vs. rational mutagenesis, with a high benefit/cost ratio, is saturatio ...	2013	24970191
angling for uniqueness in enzymatic preparation of glycosides.	in the early days of biocatalysis, limitations of an enzyme modeled the enzymatic applications; nowadays the enzyme can be engineered to be suitable for the process requirements. this is a general bird's-eye view and as such cannot be specific for articulated situations found in different classes of enzymes or for selected enzymatic processes. as far as the enzymatic preparation of glycosides is concerned, recent scientific literature is awash with examples of uniqueness related to the features ...	2013	24970171
the evolution of respiratory o2/no reductases: an out-of-the-phylogenetic-box perspective.	complex life on our planet crucially depends on strong redox disequilibria afforded by the almost ubiquitous presence of highly oxidizing molecular oxygen. however, the history of o2-levels in the atmosphere is complex and prior to the great oxidation event some 2.3 billion years ago, the amount of o2 in the biosphere is considered to have been extremely low as compared with present-day values. therefore the evolutionary histories of life and of o2-levels are likely intricately intertwined. the ...	2014	24968694
card integrates three functional modules to promote efficient transcription, antibiotic tolerance, and pathogenesis in mycobacteria.	although the basic mechanisms of prokaryotic transcription are conserved, it has become evident that some bacteria require additional factors to allow for efficient gene transcription. card is an rna polymerase (rnap)-binding protein conserved in numerous bacterial species and essential in mycobacteria. despite the importance of card, its function at transcription complexes remains unclear. we have generated a panel of mutations that individually target three independent functional modules of ca ...	2014	24962732
macrolide antibiotics allosterically predispose the ribosome for translation arrest.	translation arrest directed by nascent peptides and small cofactors controls expression of important bacterial and eukaryotic genes, including antibiotic resistance genes, activated by binding of macrolide drugs to the ribosome. previous studies suggested that specific interactions between the nascent peptide and the antibiotic in the ribosomal exit tunnel play a central role in triggering ribosome stalling. however, here we show that macrolides arrest translation of the truncated ermdl regulato ...	2014	24961372
linking chemical electron-proton transfer to proton pumping in cytochrome c oxidase: broken-symmetry dft exploration of intermediates along the catalytic reaction pathway of the iron-copper dinuclear complex.	after a summary of the problem of coupling electron and proton transfer to proton pumping in cytochrome c oxidase, we present the results of our earlier and recent density functional theory calculations for the dinuclear fe-a3-cub reaction center in this enzyme. a specific catalytic reaction wheel diagram is constructed from the calculations, based on the structures and relative energies of the intermediate states of the reaction cycle. a larger family of tautomers/protonation states is generate ...	2014	24960612
acetyl coenzyme a synthetase is acetylated on multiple lysine residues by a protein acetyltransferase with a single gcn5-type n-acetyltransferase (gnat) domain in saccharopolyspora erythraea.	reversible lysine acetylation (rla) is used by cells of all domains of life to modulate protein function. to date, bacterial acetylation/deacetylation systems have been studied in a few bacteria (e.g., salmonella enterica, bacillus subtilis, escherichia coli, erwinia amylovora, mycobacterium tuberculosis, and geobacillus kaustophilus), but little is known about rla in antibiotic-producing actinomycetes. here, we identify the gcn5-like protein acetyltransferase acua of saccharopolyspora erythraea ...	2014	24957627
life-history constraints on the mechanisms that control the rate of ros production.	the quest to understand why and how we age has led to numerous lines of investigation that have gradually converged to consider mitochondrial metabolism as a major player. during mitochondrial respiration a small and variable amount of the consumed oxygen is converted to reactive species of oxygen (ros). for many years, these ros have been perceived as harmful by-products of respiration. however, evidence from recent years indicates that ros fulfill important roles as cellular messengers. result ...	2014	24955029
identification of promiscuous ene-reductase activity by mining structural databases using active site constellations.	the exploitation of catalytic promiscuity and the application of de novo design have recently opened the access to novel, non-natural enzymatic activities. here we describe a structural bioinformatic method for predicting catalytic activities of enzymes based on three-dimensional constellations of functional groups in active sites ('catalophores'). as a proof-of-concept we identify two enzymes with predicted promiscuous ene-reductase activity (reduction of activated c-c double bonds) and compare ...	2014	24954722
building a stable rna u-turn with a protonated cytidine.	the u-turn is a classical three-dimensional rna folding motif first identified in the anticodon and t-loops of trnas. it also occurs frequently as a building block in other functional rna structures in many different sequence and structural contexts. u-turns induce sharp changes in the direction of the rna backbone and often conform to the 3-nt consensus sequence 5'-unr-3' (n = any nucleotide, r = purine). the canonical u-turn motif is stabilized by a hydrogen bond between the n3 imino group of ...	2014	24951555
characterization of two homologous 2'-o-methyltransferases showing different specificities for their trna substrates.	the 2'-o-methylation of the nucleoside at position 32 of trna is found in organisms belonging to the three domains of life. unrelated enzymes catalyzing this modification in bacteria (trmj) and eukarya (trm7) have already been identified, but until now, no information is available for the archaeal enzyme. in this work we have identified the methyltransferase of the archaeon sulfolobus acidocaldarius responsible for the 2'-o-methylation at position 32. this enzyme is a homolog of the bacterial tr ...	2014	24951554
gla-rich protein is a potential new vitamin k target in cancer: evidences for a direct grp-mineral interaction.	gla-rich protein (grp) was described in sturgeon as a new vitamin-k-dependent protein (vkdp) with a high density of gla residues and associated with ectopic calcifications in humans. although vkdps function has been related with γ-carboxylation, the gla status of grp in humans is still unknown. here, we investigated the expression of recently identified grp spliced transcripts, the γ-carboxylation status, and its association with ectopic calcifications, in skin basal cell and breast carcinomas. ...	2014	24949434
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27.	thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ...	2014	24948436
life at the border: adaptation of proteins to anisotropic membrane environment.	this review discusses main features of transmembrane (tm) proteins which distinguish them from water-soluble proteins and allow their adaptation to the anisotropic membrane environment. we overview the structural limitations on membrane protein architecture, spatial arrangement of proteins in membranes and their intrinsic hydrophobic thickness, co-translational and post-translational folding and insertion into lipid bilayers, topogenesis, high propensity to form oligomers, and large-scale confor ...	2014	24947665
synthesis of water-soluble dinuclear mn-porphyrin with multiple antioxidative activities.	superoxide dismutase (sod) and catalase activities of a drug are of great importance for its effective protection against reactive oxygen species (ros)-induced injury. achievement of catalase activity of a synthetic compound remains a challenge. water-soluble mn-porphyrins have high sod and peroxynitrite (onoo(-)) reducing activities, but not catalase-like activity. herein, we are able to retain the fair sod-like activity of a mononuclear mn-5-(n-methylpyridinium-4-yl)-10,15,20-triphenyl porphyr ...	2014	24944735
conjugation with polyamines enhances the antibacterial and anticancer activity of chloramphenicol.	chloramphenicol (cam) is a broad-spectrum antibiotic, limited to occasional only use in developed countries because of its potential toxicity. to explore the influence of polyamines on the uptake and activity of cam into cells, a series of polyamine-cam conjugates were synthesized. both polyamine architecture and the position of cam-scaffold substitution were crucial in augmenting the antibacterial and anticancer potency of the synthesized conjugates. compounds 4 and 5, prepared by replacement o ...	2014	24939899
the flavoprotein mcap0476 (rlmfo) catalyzes m5u1939 modification in mycoplasma capricolum 23s rrna.	efficient protein synthesis in all organisms requires the post-transcriptional methylation of specific ribosomal ribonucleic acid (rrna) and transfer rna (trna) nucleotides. the methylation reactions are almost invariably catalyzed by enzymes that use s-adenosylmethionine (adomet) as the methyl group donor. one noteworthy exception is seen in some bacteria, where the conserved trna methylation at m5u54 is added by the enzyme trmfo using flavin adenine dinucleotide together with n5,n10-methylenet ...	2014	24939895
lysine propionylation is a prevalent post-translational modification in thermus thermophilus.	recent studies of protein post-translational modifications revealed that various types of lysine acylation occur in eukaryotic and bacterial proteins. lysine propionylation, a newly discovered type of acylation, occurs in several proteins, including some histones. in this study, we identified 361 propionylation sites in 183 mid-exponential phase and late stationary phase proteins from thermus thermophilus hb8, an extremely thermophilic eubacterium. functional classification of the propionylprote ...	2014	24938286
conserved glycine 232 in the ligand channel of ba3 cytochrome oxidase from thermus thermophilus.	knowing how the protein environment modulates ligand pathways and redox centers in the respiratory heme-copper oxidases is fundamental for understanding the relationship between the structure and function of these enzymes. in this study, we investigated the reactions of o2 and no with the fully reduced g232v mutant of ba3 cytochrome c oxidase from thermus thermophilus (tt ba3) in which a conserved glycine residue in the o2 channel of the enzyme was replaced with a bulkier valine residue. previou ...	2014	24937405
the role of a novel auxiliary pocket in bacterial phenylalanyl-trna synthetase druggability.	the antimicrobial activity of phenyl-thiazolylurea-sulfonamides against staphylococcus aureus phers are dependent upon phenylalanine levels in the extracellular fluids. inhibitor efficacy in animal models of infection is substantially diminished by dietary phenylalanine intake, thereby reducing the perceived clinical utility of this inhibitor class. the search for novel antibacterial compounds against gram-negative pathogens led to a re-evaluation of this phenomenon, which is shown here to be un ...	2014	24936059
conserved evolutionary units in the heme-copper oxidase superfamily revealed by novel homologous protein families.	the heme-copper oxidase (hco) superfamily includes hcos in aerobic respiratory chains and nitric oxide reductases (nors) in the denitrification pathway. the hco/nor catalytic subunit has a core structure consisting of 12 transmembrane helices (tmhs) arranged in three-fold rotational pseudosymmetry, with six conserved histidines for heme and metal binding. using sensitive sequence similarity searches, we detected a number of novel hco/nor homologs and named them hco homology (hcoh) proteins. seve ...	2014	24931479
biochemical and cellular analysis of human variants of the dyt1 dystonia protein, torsina/tor1a.	early-onset dystonia is associated with the deletion of one of a pair of glutamic acid residues (c.904_906delgag/c.907_909delgag; p.glu302del/glu303del; δe 302/303) near the carboxyl-terminus of torsina, a member of the aaa(+) protein family that localizes to the endoplasmic reticulum lumen and nuclear envelope. this deletion commonly underlies early-onset dyt1 dystonia. while the role of the disease-causing mutation, torsinaδe, has been established through genetic association studies, it is muc ...	2014	24930953
genomic and phenotypic attributes of novel salinivibrios from stromatolites, sediment and water from a high altitude lake.	salinivibrios are moderately halophilic bacteria found in salted meats, brines and hypersaline environments. we obtained three novel conspecific salinivibrio strains closely related to s. costicola, from socompa lake, a high altitude hypersaline andean lake (approx. 3,570 meters above the sea level).	2014	24927949
condensation and localization of the partitioning protein parb on the bacterial chromosome.	the parabs system mediates chromosome segregation and plasmid partitioning in many bacteria. as part of the partitioning mechanism, parb proteins form a nucleoprotein complex at pars sites. the biophysical basis underlying parb-dna complex formation and localization remains elusive. specifically, it is unclear whether parb spreads in 1d along dna or assembles into a 3d protein-dna complex. we show that a combination of 1d spreading bonds and a single 3d bridging bond between parb proteins consti ...	2014	24927534
modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant mycobacterium tuberculosis.	rifamycin b, a product of amycolatopsis mediterranei s699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and aids-related mycobacterial infections. however, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of mycobacterium tuberculosis. as part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of ...	2014	24923585
crystallization and preliminary x-ray crystallographic analysis of a bacterial asn-transamidosome.	most canonical aminoacyl-trnas are synthesized directly by their cognate aminoacyl-trna synthetases (aarss), but glutaminyl-trna(gln) and asparaginyl-trna(asn) are synthesized indirectly by two-step processes. these processes are catalyzed by the transamidosome, a large ribonucleoprotein particle composed of gata, gatb, gatc, aars and trna. in this study, the asn-transamidosome from pseudomonas aeruginosa was reconstructed and crystallized by mixing purified gatcab complex, asprs and trna(asn). ...	2014	24915095
structural and bioinformatic characterization of an acinetobacter baumannii type ii carrier protein.	microorganisms produce a variety of natural products via secondary metabolic biosynthetic pathways. two of these types of synthetic systems, the nonribosomal peptide synthetases (nrpss) and polyketide synthases (pkss), use large modular enzymes containing multiple catalytic domains in a single protein. these multidomain enzymes use an integrated carrier protein domain to transport the growing, covalently bound natural product to the neighboring catalytic domains for each step in the synthesis. i ...	2014	24914982
determination of kinetics and the crystal structure of a novel type 2 isopentenyl diphosphate: dimethylallyl diphosphate isomerase from streptococcus pneumoniae.	isopentenyl diphosphate isomerase (idi) is a key enzyme in the isoprenoid biosynthetic pathway and is required for all organisms that synthesize isoprenoid metabolites from mevalonate. type 1 idi (idi-1) is a metalloprotein that is found in eukaryotes, whereas the type 2 isoform (idi-2) is a flavoenzyme found in bacteria that is completely absent from human. idi-2 from the pathogenic bacterium streptococcus pneumoniae was recombinantly expressed in escherichia coli. steady-state kinetic studies ...	2014	24910111
the structural basis of transfer rna mimicry and conformational plasticity by a viral rna.	rna is arguably the most functionally diverse biological macromolecule. in some cases a single discrete rna sequence performs multiple roles, and this can be conferred by a complex three-dimensional structure. such multifunctionality can also be driven or enhanced by the ability of a given rna to assume different conformational (and therefore functional) states. despite its biological importance, a detailed structural understanding of the paradigm of rna structure-driven multifunctionality is la ...	2014	24909993
unravelling the structural and mechanistic basis of crispr-cas systems.	bacteria and archaea have evolved sophisticated adaptive immune systems, known as crispr-cas (clustered regularly interspaced short palindromic repeats-crispr-associated proteins) systems, which target and inactivate invading viruses and plasmids. immunity is acquired by integrating short fragments of foreign dna into crispr loci, and following transcription and processing of these loci, the crispr rnas (crrnas) guide the cas proteins to complementary invading nucleic acid, which results in targ ...	2014	24909109
the crystal structure of pyrimidine/thiamin biosynthesis precursor-like domain-containing protein cae31940 from proteobacterium bordetella bronchiseptica rb50, and evolutionary insight into the nmt1/thi5 family.	we report a 2.0 å structure of the cae31940 protein, a proteobacterial nmt1/thi5-like domain-containing protein. we also discuss the primary and tertiary structure similarity with its homologs. the highly conserved fggxmp motif was identified in cae31940, which corresponds to the gcccx motif located in the vicinity of the active center characteristic for thi5-like proteins found in yeast. this suggests that the fggxmp motif may be a unique hallmark of proteobacterial nmt1/thi5-like proteins.	2014	24908050
a third subunit in ancestral cytochrome c-dependent nitric oxide reductases.	reduction of no to n2o by denitrifiying bacteria is catalyzed either by a monomeric quinol-nitric oxide reductase (qnor) or by a heterodimeric cytochrome c-dependent nitric oxide reductase (cnor). in ancient thermophilic bacteria belonging to the thermales and aquificales phylogenetic groups, the cluster encoding the cnor includes a small third gene (norh), in addition to those encoding homologues to the subunits of a typical cnor (norc and norb). we show in thermus thermophilus that the three g ...	2014	24907324
archaeal tuc1/ncs6 homolog required for wobble uridine trna thiolation is associated with ubiquitin-proteasome, translation, and rna processing system homologs.	while cytoplasmic trna 2-thiolation protein 1 (tuc1/ncs6) and ubiquitin-related modifier-1 (urm1) are important in the 2-thiolation of 5-methoxycarbonylmethyl-2-thiouridine (mcm5s2u) at wobble uridines of trnas in eukaryotes, the biocatalytic roles and properties of ncs6/tuc1 and its homologs are poorly understood. here we present the first report of an ncs6 homolog of archaea (ncsa of haloferax volcanii) that is essential for maintaining cellular pools of thiolated trna(lys)uuu and for growth a ...	2014	24906001
methylated nucleosides in trna and trna methyltransferases.	to date, more than 90 modified nucleosides have been found in trna and the biosynthetic pathways of the majority of trna modifications include a methylation step(s). recent studies of the biosynthetic pathways have demonstrated that the availability of methyl group donors for the methylation in trna is important for correct and efficient protein synthesis. in this review, i focus on the methylated nucleosides and trna methyltransferases. the primary functions of trna methylations are linked to t ...	2014	24904644
evidence for a catalytically and kinetically competent enzyme-substrate cross-linked intermediate in catalysis by lipoyl synthase.	lipoyl synthase (ls) catalyzes the final step in lipoyl cofactor biosynthesis: the insertion of two sulfur atoms at c6 and c8 of an (n(6)-octanoyl)-lysyl residue on a lipoyl carrier protein (lcp). ls is a member of the radical sam superfamily, enzymes that use a [4fe-4s] cluster to effect the reductive cleavage of s-adenosyl-l-methionine (sam) to l-methionine and a 5'-deoxyadenosyl 5'-radical (5'-da(•)). in the ls reaction, two equivalents of 5'-da(•) are generated sequentially to abstract hydro ...	2014	24901788
structure-based ligand design of novel bacterial rna polymerase inhibitors.	bacterial rna polymerase (rnap) is essential for transcription and is an antibacterial target for small molecule inhibitors. the binding region of myxopyronin b (myxb), a bacterial rnap inhibitor, offers the possibility of new inhibitor design. the molecular design program sprout has been used in conjunction with the x-ray cocrystal structure of thermus thermophilus rnap with myxb to design novel inhibitors based on a substituted pyridyl-benzamide scaffold. a series of molecules, with molecular ...	2011	24900260
cocrystal structures of glycyl-trna synthetase in complex with trna suggest multiple conformational states in glycylation.	aminoacyl-trna synthetases are an ancient enzyme family that specifically charges trna molecules with cognate amino acids for protein synthesis. glycyl-trna synthetase (glyrs) is one of the most intriguing aminoacyl-trna synthetases due to its divergent quaternary structure and abnormal charging properties. in the past decade, mutations of human glyrs (hglyrs) were also found to be associated with charcot-marie-tooth disease. however, the mechanisms of traditional and alternative functions of hg ...	2014	24898252
crystal structure of trna m(1)a58 methyltransferase trmi from aquifex aeolicus in complex with s-adenosyl-l-methionine.	the n (1)-methyladenosine residue at position 58 of trna is found in the three domains of life, and contributes to the stability of the three-dimensional l-shaped trna structure. in thermophilic bacteria, this modification is important for thermal adaptation, and is catalyzed by the trna m(1)a58 methyltransferase trmi, using s-adenosyl-l-methionine (adomet) as the methyl donor. we present the 2.2 å crystal structure of trmi from the extremely thermophilic bacterium aquifex aeolicus, in complex w ...	2014	24894648
oxidation of cellular amino acid pools leads to cytotoxic mistranslation of the genetic code.	aminoacyl-trna synthetases use a variety of mechanisms to ensure fidelity of the genetic code and ultimately select the correct amino acids to be used in protein synthesis. the physiological necessity of these quality control mechanisms in different environments remains unclear, as the cost vs benefit of accurate protein synthesis is difficult to predict. we show that in escherichia coli, a non-coded amino acid produced through oxidative damage is a significant threat to the accuracy of protein ...	2014	24891238
molecular characterization of novel pyridoxal-5'-phosphate-dependent enzymes from the human microbiome.	pyridoxal-5'-phosphate or plp, the active form of vitamin b6, is a highly versatile cofactor that participates in a large number of mechanistically diverse enzymatic reactions in basic metabolism. plp-dependent enzymes account for ∼1.5% of most prokaryotic genomes and are estimated to be involved in ∼4% of all catalytic reactions, making this an important class of enzymes. here, we structurally and functionally characterize three novel plp-dependent enzymes from bacteria in the human microbiome: ...	2014	24888348
current development in genetic engineering strategies of bacillus species.	the complete sequencing and annotation of the genomes of industrially-important bacillus species has enhanced our understanding of their properties, and allowed advances in genetic manipulations in other bacillus species. post-genomic studies require simple and highly efficient tools to enable genetic manipulation. here, we summarize the recent progress in genetic engineering strategies for bacillus species. we review the available genetic tools that have been developed in bacillus species, as w ...	2014	24885003
the role of ribonucleases in regulating global mrna levels in the model organism thermus thermophilus hb8.	rna metabolism, including rna synthesis and rna degradation, is one of the most conserved biological systems and has been intensively studied; however, the degradation network of ribonucleases (rnases) and rna substrates is not fully understood.	2014	24884843
the amazon continuum dataset: quantitative metagenomic and metatranscriptomic inventories of the amazon river plume, june 2010.	the amazon river is by far the world's largest in terms of volume and area, generating a fluvial export that accounts for about a fifth of riverine input into the world's oceans. marine microbial communities of the western tropical north atlantic ocean are strongly affected by the terrestrial materials carried by the amazon plume, including dissolved (doc) and particulate organic carbon (poc) and inorganic nutrients, with impacts on primary productivity and carbon sequestration.	2014	24883185
loss of quaternary structure is associated with rapid sequence divergence in the osbs family.	the rate of protein evolution is determined by a combination of selective pressure on protein function and biophysical constraints on protein folding and structure. determining the relative contributions of these properties is an unsolved problem in molecular evolution with broad implications for protein engineering and function prediction. as a case study, we examined the structural divergence of the rapidly evolving o-succinylbenzoate synthase (osbs) family, which catalyzes a step in menaquino ...	2014	24872444
xanthomonas campestris rpfb is a fatty acyl-coa ligase required to counteract the thioesterase activity of the rpff diffusible signal factor (dsf) synthase.	in xanthomonas campestris pv. campestris (xcc), the proteins encoded by the rpf (regulator of pathogenicity factor) gene cluster produce and sense a fatty acid signal molecule called diffusible signalling factor (dsf, 2(z)-11-methyldodecenoic acid). rpfb was reported to be involved in dsf processing and was predicted to encode an acyl-coa ligase. we report that rpfb activates a wide range of fatty acids to their coa esters in vitro. moreover, rpfb can functionally replace the paradigm bacterial ...	2014	24866092
intact functional fourteen-subunit respiratory membrane-bound [nife]-hydrogenase complex of the hyperthermophilic archaeon pyrococcus furiosus.	the archaeon pyrococcus furiosus grows optimally at 100 °c by converting carbohydrates to acetate, co2, and h2, obtaining energy from a respiratory membrane-bound hydrogenase (mbh). this conserves energy by coupling h2 production to oxidation of reduced ferredoxin with generation of a sodium ion gradient. mbh is encoded by a 14-gene operon with both hydrogenase and na(+)/h(+) antiporter modules. herein a his-tagged mbh was expressed in p. furiosus and the detergent-solubilized complex purified u ...	2014	24860091
evidence for a dna-relay mechanism in parabs-mediated chromosome segregation.	the widely conserved parabs system plays a major role in bacterial chromosome segregation. how the components of this system work together to generate translocation force and directional motion remains uncertain. here, we combine biochemical approaches, quantitative imaging and mathematical modeling to examine the mechanism by which para drives the translocation of the parb/pars partition complex in caulobacter crescentus. our experiments, together with simulations grounded on experimentally-det ...	2014	24859756
coliphage hk022 nun protein inhibits rna polymerase translocation.	the nun protein of coliphage hk022 arrests rna polymerase (rnap) in vivo and in vitro at pause sites distal to phage λ n-utilization (nut) site rna sequences. we tested the activity of nun on ternary elongation complexes (tecs) assembled with templates lacking the λ nut sequence. we report that nun stabilizes both translocation states of rnap by restricting lateral movement of tec along the dna register. when nun stabilized tec in a pretranslocated register, immediately after nmp incorporation, ...	2014	24853501
reduced ribosomes of the apicoplast and mitochondrion of plasmodium spp. and predicted interactions with antibiotics.	apicomplexan protists such as plasmodium and toxoplasma contain a mitochondrion and a relic plastid (apicoplast) that are sites of protein translation. although there is emerging interest in the partitioning and function of translation factors that participate in apicoplast and mitochondrial peptide synthesis, the composition of organellar ribosomes remains to be elucidated. we carried out an analysis of the complement of core ribosomal protein subunits that are encoded by either the parasite or ...	2014	24850912
structural and evolutionary aspects of antenna chromophore usage by class ii photolyases.	light-harvesting and resonance energy transfer to the catalytic fad cofactor are key roles for the antenna chromophores of light-driven dna photolyases, which remove uv-induced dna lesions. so far, five chemically diverse chromophores have been described for several photolyases and related cryptochromes, but no correlation between phylogeny and used antenna has been found. despite a common protein topology, structural analysis of the distantly related class ii photolyase from the archaeon methan ...	2014	24849603
pcr performance of a thermostable heterodimeric archaeal dna polymerase.	dna polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (pcr), cdna cloning, genome sequencing, and nucleic acid based diagnostics. taking into account the multiple dna amplification techniques in use, different dna polymerases must be optimized for each type of application. one of the current tendencies is to reengineer or to discover new dna polymerases with increased performance and broadened substrate ...	2014	24847315
transcription inhibition by the depsipeptide antibiotic salinamide a.	we report that bacterial rna polymerase (rnap) is the functional cellular target of the depsipeptide antibiotic salinamide a (sal), and we report that sal inhibits rnap through a novel binding site and mechanism. we show that sal inhibits rna synthesis in cells and that mutations that confer sal-resistance map to rnap genes. we show that sal interacts with the rnap active-center 'bridge-helix cap' comprising the 'bridge-helix n-terminal hinge', 'f-loop', and 'link region'. we show that sal inhib ...	2014	24843001
robust and accurate prediction of residue-residue interactions across protein interfaces using evolutionary information.	do the amino acid sequence identities of residues that make contact across protein interfaces covary during evolution? if so, such covariance could be used to predict contacts across interfaces and assemble models of biological complexes. we find that residue pairs identified using a pseudo-likelihood-based method to covary across protein-protein interfaces in the 50s ribosomal unit and 28 additional bacterial protein complexes with known structure are almost always in contact in the complex, pr ...	2014	24842992
specificity and catalytic mechanism in family 5 uracil dna glycosylase.	udgb belongs to family 5 of the uracil dna glycosylase (udg) superfamily. here, we report that family 5 udgb from thermus thermophilus hb8 is not only a uracil dna glycosyase acting on g/u, t/u, c/u, and a/u base pairs, but also a hypoxanthine dna glycosylase acting on g/i, t/i, and a/i base pairs and a xanthine dna glycosylase acting on all double-stranded and single-stranded xanthine-containing dna. analysis of potentials of mean force indicates that the tendency of hypoxanthine base flipping ...	2014	24838246
prokaryotic argonautes defend genomes against invasive dna.	argonaute proteins are central players in small rna-mediated silencing mechanisms such as rna interference (rnai), microrna repression and pirna-mediated transposon silencing. in eukaryotes, argonautes bind small rnas that guide them to rna targets in order to regulate gene expression and repress invasive genomic elements. although argonaute proteins are conserved in all life forms from bacteria to eukaryotes, until now studies have focused on the biological functions of eukaryotic argonautes. h ...	2014	24836995
psychrophily and catalysis.	polar and other low temperature environments are characterized by a low content in energy and this factor has a strong incidence on living organisms which populate these rather common habitats. indeed, low temperatures have a negative effect on ectothermic populations since they can affect their growth, reaction rates of biochemical reactions, membrane permeability, diffusion rates, action potentials, protein folding, nucleic acids dynamics and other temperature-dependent biochemical processes. ...	2013	24832805
a complete landscape of post-transcriptional modifications in mammalian mitochondrial trnas.	in mammalian mitochondria, 22 species of trnas encoded in mitochondrial dna play crucial roles in the translation of 13 essential subunits of the respiratory chain complexes involved in oxidative phosphorylation. following transcription, mitochondrial trnas are modified by nuclear-encoded trna-modifying enzymes. these modifications are required for the proper functioning of mitochondrial trnas (mt trnas), and the absence of these modifications can cause pathological consequences. to date, howeve ...	2014	24831542
cu(i)-mediated allosteric switching in a copper-sensing operon repressor (csor).	the copper-sensing operon repressor (csor) is representative of a major cu(i)-sensing family of bacterial metalloregulatory proteins that has evolved to prevent cytoplasmic copper toxicity. it is unknown how cu(i) binding to tetrameric csors mediates transcriptional derepression of copper resistance genes. a phylogenetic analysis of 227 duf156 protein members, including biochemically or structurally characterized csor/rcnr repressors, reveals that geobacillus thermodenitrificans (gt) csor charac ...	2014	24831014
parb spreading requires dna bridging.	the parabs system is a widely employed mechanism for plasmid partitioning and chromosome segregation in bacteria. parb binds to pars sites on plasmids and chromosomes and associates with broad regions of adjacent dna, a phenomenon known as spreading. although essential for parb function, the mechanism of spreading remains poorly understood. using single-molecule approaches, we discovered that bacillus subtilis parb (spo0j) is able to trap dna loops. point mutants in spo0j that disrupt dna bridgi ...	2014	24829297
allosteric regulation of the human and mouse deoxyribonucleotide triphosphohydrolase sterile α-motif/histidine-aspartate domain-containing protein 1 (samhd1).	the deoxyribonucleotide triphosphohydrolase samhd1 restricts lentiviral infection by depleting the dntps required for viral dna synthesis. in cultured human fibroblasts samhd1 is expressed maximally during quiescence preventing accumulation of dntps outside s phase. sirna silencing of samhd1 increases dntp pools, stops cycling human cells in g1, and blocks dna replication. surprisingly, knock-out of the mouse gene does not affect the well being of the animals. dntps are both substrates and allos ...	2014	24828500
3'-biotin-tagged microrna-27 does not associate with argonaute proteins in cells.	synthetic 3'-biotin-tagged micrornas (mirnas) have often been used to select interacting messenger rna (mrna) and noncoding rna (ncrna) targets. here, we examined the extent of association of 3'-end biotinylated mir-27 with argonaute (ago) proteins in transfected human cells using a coimmunoprecipitation assay followed by northern blot analysis. we report that biotinylated mir-27 does not efficiently associate with ago compared to unmodified mir-27. these results suggest that 3'-end biotin-modif ...	2014	24821854
structural analysis of base substitutions in thermus thermophilus 16s rrna conferring streptomycin resistance.	streptomycin is a bactericidal antibiotic that induces translational errors. it binds to the 30s ribosomal subunit, interacting with ribosomal protein s12 and with 16s rrna through contacts with the phosphodiester backbone. to explore the structural basis for streptomycin resistance, we determined the x-ray crystal structures of 30s ribosomal subunits from six streptomycin-resistant mutants of thermus thermophilus both in the apo form and in complex with streptomycin. base substitutions at highl ...	2014	24820088
bacterial magnetosome biomineralization--a novel platform to study molecular mechanisms of human cdf-related type-ii diabetes.	cation diffusion facilitators (cdf) are part of a highly conserved protein family that maintains cellular divalent cation homeostasis in all organisms. cdfs were found to be involved in numerous human health conditions, such as type-ii diabetes and neurodegenerative diseases. in this work, we established the magnetite biomineralizing alphaproteobacterium magnetospirillum gryphiswaldense as an effective model system to study cdf-related type-ii diabetes. here, we introduced two znt-8 type-ii diab ...	2014	24819161
purification, crystallization and preliminary crystallographic analysis of a ribosome-recycling factor from thermoanaerobacter tengcongensis (tterrf).	ribosome-recycling factor (rrf) plays an essential role in the fourth step of protein synthesis in prokaryotes. rrf combined with elongation factor g (ef-g) disassembles the post-termination ribosome complex and recycles the protein synthesis machine for the next round of translation. a reductive-methylation-modified rrf from thermoanaerobacter tengcongensis (tterrf) has been crystallized using the vapour-diffusion method. the crystal grew in a condition consisting of 0.1 m citric acid ph 3.5, 3 ...	2014	24817715
structure determination of a sugar-binding protein from the phytopathogenic bacterium xanthomonas citri.	the uptake of maltose and related sugars in gram-negative bacteria is mediated by an abc transporter encompassing a periplasmic component (the maltose-binding protein or male), a pore-forming membrane protein (malf and malg) and a membrane-associated atpase (malk). in the present study, the structure determination of the apo form of the putative maltose/trehalose-binding protein (xac-male) from the citrus pathogen xanthomonas citri in space group p6522 is described. the crystals contained two pr ...	2014	24817711
co-opting sulphur-carrier proteins from primary metabolic pathways for 2-thiosugar biosynthesis.	sulphur is an essential element for life and is ubiquitous in living systems. yet how the sulphur atom is incorporated into many sulphur-containing secondary metabolites is poorly understood. for bond formation between carbon and sulphur in primary metabolites, the major ionic sulphur sources are the persulphide and thiocarboxylate groups on sulphur-carrier (donor) proteins. each group is post-translationally generated through the action of a specific activating enzyme. in all reported bacterial ...	2014	24814342
probing the global and local dynamics of aminoacyl-trna synthetases using all-atom and coarse-grained simulations.	coarse-grained simulations have emerged as invaluable tools for studying conformational changes in biomolecules. to evaluate the effectiveness of computationally inexpensive coarse-grained models in studying global and local dynamics of large protein systems like aminoacyl-trna synthetases, we have performed coarse-grained normal mode analysis, as well as principle component analysis on trajectories of all-atom and coarse-grained molecular dynamics simulations for three aminoacyl-trna synthetase ...	2014	24810463
deletion of the cyclic di-amp phosphodiesterase gene (cnpb) in mycobacterium tuberculosis leads to reduced virulence in a mouse model of infection.	tuberculosis (tb) remains a major cause of morbidity and mortality worldwide. the pathogenesis by the causative agent, mycobacterium tuberculosis, is still not fully understood. we have previously reported that m. tuberculosis rv3586 (disa) encodes a diadenylate cyclase, which converts atp to cyclic di-amp (c-di-amp). in this study, we demonstrated that a protein encoded by rv2837c (cnpb) possesses c-di-amp phosphodiesterase activity and cleaves c-di-amp exclusively to amp. our results showed th ...	2014	24806618
sets of covariant residues modulate the activity and thermal stability of gh1 β-glucosidases.	the statistical coupling analysis of 768 β-glucosidases from the gh1 family revealed 23 positions in which the amino acid frequencies are coupled. the roles of these covariant positions in terms of the properties of β-glucosidases were investigated by alanine-screening mutagenesis using the fall armyworm spodoptera frugiperda β-glycosidase (sfβgly) as a model. the effects of the mutations on the sfβgly kinetic parameters (kcat/km) for the hydrolysis of three different p-nitrophenyl β-glycosides ...	2014	24804841
evolution of mitochondria reconstructed from the energy metabolism of living bacteria.	the ancestors of mitochondria, or proto-mitochondria, played a crucial role in the evolution of eukaryotic cells and derived from symbiotic α-proteobacteria which merged with other microorganisms - the basis of the widely accepted endosymbiotic theory. however, the identity and relatives of proto-mitochondria remain elusive. here we show that methylotrophic α-proteobacteria could be the closest living models for mitochondrial ancestors. we reached this conclusion after reconstructing the possibl ...	2014	24804722
the transmembrane channel-like protein family and human papillomaviruses: insights into epidermodysplasia verruciformis and progression to squamous cell carcinoma.	epidermodysplasia verruciformis (ev) is a rare genodermatosis characterized by increased sensitivity to infection by the β-subtype of human papillomaviruses (β-hpvs), causing persistent, tinea versicolor-like dermal lesions. in a majority of affected individuals, these macular lesions progress to invasive cutaneous squamous cell carcinoma (cscc) in sun-exposed areas. while mutations in transmembrane channel-like 6 (tmc6 / ever1) and 8 (tmc8 / ever2) have been causally linked to ev, their molecul ...	2014	24800179
cryo-em structure of the small subunit of the mammalian mitochondrial ribosome.	the mammalian mitochondrial ribosomes (mitoribosomes) are responsible for synthesizing 13 membrane proteins that form essential components of the complexes involved in oxidative phosphorylation or atp generation for the eukaryotic cell. the mammalian 55s mitoribosome contains significantly smaller rrnas and a large mass of mitochondrial ribosomal proteins (mrps), including large mito-specific amino acid extensions and insertions in mrps that are homologous to bacterial ribosomal proteins and an ...	2014	24799711