| comparative xylose metabolism among the ascomycetes c. albicans, s. stipitis and s. cerevisiae. | the ascomycetes candida albicans, saccharomyces cerevisiae and scheffersomyces stipitis metabolize the pentose sugar xylose very differently. s. cerevisiae fails to grow on xylose, while c. albicans can grow, and s. stipitis can both grow and ferment xylose to ethanol. however, all three species contain highly similar genes that encode potential xylose reductases and xylitol dehydrogenases required to convert xylose to xylulose, and xylulose supports the growth of all three fungi. we have create ... | 2013 | 24236198 |
| overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism. | the psychrophilic, hydrocarbonoclastic microorganism colwellia psychrerythraea is important in global nutrient cycling and bioremediation. in order to investigate how this organism can live so efficiently at low temperatures (~4°c), thermal denaturation studies of a small electron transfer protein from colwellia were performed. colwellia cytochrome c552 was overexpressed in escherichia coli, isolated, purified, and characterized by uv-visible absorption spectroscopy. the melting temperature (tm) ... | 2013 | 24275750 |
| overexpression, purification, and enthalpy of unfolding of ferricytochrome c552 from a psychrophilic microorganism. | the psychrophilic, hydrocarbonoclastic microorganism colwellia psychrerythraea is important in global nutrient cycling and bioremediation. in order to investigate how this organism can live so efficiently at low temperatures (~4°c), thermal denaturation studies of a small electron transfer protein from colwellia were performed. colwellia cytochrome c552 was overexpressed in escherichia coli, isolated, purified, and characterized by uv-visible absorption spectroscopy. the melting temperature (tm) ... | 2013 | 24275750 |
| biosynthesis of rare hexoses using microorganisms and related enzymes. | rare sugars, referred to as monosaccharides and their derivatives that rarely exist in nature, can be applied in many areas ranging from foodstuffs to pharmaceutical and nutrition industry, or as starting materials for various natural products and drug candidates. unfortunately, an important factor restricting the utilization of rare sugars is their limited availability, resulting from limited synthetic methods. nowadays, microbial and enzymatic transformations have become a very powerful tool i ... | 2013 | 24367410 |
| structure and assembly of an inner membrane platform for initiation of type iv pilus biogenesis. | type iv pili are long fibers that are assembled by polymerization of a major pilin protein in the periplasm of a wide range of bacteria and archaea. they play crucial roles in pathogenesis, dna transformation, and motility, and are capable of rapid retraction, generating powerful motor forces. piln and pilo are integral inner membrane proteins that are essential for type iv pilus formation. here, we show that piln and pilo from thermus thermophilus can be isolated as a complex with pilm, a cytop ... | 2013 | 24218553 |
| a structured-based model for the decreased activity of ala222val and glu429ala methylenetetrahydrofolate reductase (mthfr) mutants. | the structure of human methylenetetrahydrofolate reductase (mthfr) is not known either by nmr or by x-ray methods. phosphorylation seems to play an important role in the functioning of this flavoprotein. mthfr catalyzes an irreversible reaction in homocysteine metabolism. phosphorylation decreases the activity of mthfr by enhancing the sensitivity of the enzyme to sadenosylmethione. two common polymorphisms in mthfr, ala222val and glu429ala, can result in a number of vascular diseases. effects o ... | 2013 | 24307772 |
| architecture and gene repertoire of the flexible genome of the extreme acidophile acidithiobacillus caldus. | acidithiobacillus caldus is a sulfur oxidizing extreme acidophile and the only known mesothermophile within the acidithiobacillales. as such, it is one of the preferred microbes for mineral bioprocessing at moderately high temperatures. in this study, we explore the genomic diversity of a. caldus strains using a combination of bioinformatic and experimental techniques, thus contributing first insights into the elucidation of the species pangenome. | 2013 | 24250794 |
| niche specialization of novel thaumarchaeota to oxic and hypoxic acidic geothermal springs of yellowstone national park. | novel lineages of the phylum thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. the primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °c), acidic (ph~3) iron oxide and sulfur sediment environments of yellowstone national park (ynp). metabolic reconstruction ... | 2013 | 24196321 |
| niche specialization of novel thaumarchaeota to oxic and hypoxic acidic geothermal springs of yellowstone national park. | novel lineages of the phylum thaumarchaeota are endemic to thermal habitats, and may exhibit physiological capabilities that are not yet observed in members of this phylum. the primary goals of this study were to conduct detailed phylogenetic and functional analyses of metagenome sequence assemblies of two different thaumarchaeal populations found in high-temperature (65-72 °c), acidic (ph~3) iron oxide and sulfur sediment environments of yellowstone national park (ynp). metabolic reconstruction ... | 2013 | 24196321 |
| aminoacylation of plasmodium falciparum trna(asn) and insights in the synthesis of asparagine repeats. | genome sequencing revealed an extreme at-rich genome and a profusion of asparagine repeats associated with low complexity regions (lcrs) in proteins of the malarial parasite plasmodium falciparum. despite their abundance, the function of these lcrs remains unclear. because they occur in almost all families of plasmodial proteins, the occurrence of lcrs cannot be associated with any specific metabolic pathway; yet their accumulation must have given selective advantages to the parasite. translatio ... | 2013 | 24196969 |
| in silico insights of l-glutamate: structural features in vacuum and in complex with its receptor. | structural properties of the glutamate in vacuum and in complex with its receptor were analyzed. the analysis was focused on global properties, attempting to characterize features such as overall flexibility and common trends in the conformation set. the glutamate, as other ligands in complex with the receptor, adopts a spatial conformation that corresponds to one of the possible molecular equilibrium states in physiological conditions. the glutamate forms an extended structure for all cases, bu ... | 2013 | 24307941 |
| correlation between supercoiling and conformational motions of the bacterial flagellar filament. | the bacterial flagellar filament is a very large macromolecular assembly of a single protein, flagellin. various supercoiled states of the filament exist, which are formed by two structurally different conformations of flagellin in different ratios. we investigated the correlation between supercoiling of the protofilaments and molecular dynamics in the flagellar filament using quasielastic and elastic incoherent neutron scattering on the picosecond and nanosecond timescales. thermal fluctuations ... | 2013 | 24209861 |
| rigidity analysis of protein biological assemblies and periodic crystal structures. | we initiate in silico rigidity-theoretical studies of biological assemblies and small crystals for protein structures. the goal is to determine if, and how, the interactions among neighboring cells and subchains affect the flexibility of a molecule in its crystallized state. we use experimental x-ray crystallography data from the protein data bank (pdb). the analysis relies on an effcient graph-based algorithm. computational experiments were performed using new protein rigidity analysis tools av ... | 2013 | 24564201 |
| mechanisms of copper homeostasis in bacteria. | copper is an important micronutrient required as a redox co-factor in the catalytic centers of enzymes. however, free copper is a potential hazard because of its high chemical reactivity. consequently, organisms exert a tight control on cu(+) transport (entry-exit) and traffic through different compartments, ensuring the homeostasis required for cuproprotein synthesis and prevention of toxic effects. recent studies based on biochemical, bioinformatics, and metalloproteomics approaches, reveal a ... | 2013 | 24205499 |
| sequence, structure, and stacking: specifics of trna anchoring to the t box riboswitch. | the term riboswitch usually refers to small molecule sensing regulatory modules in the 5' untranslated regions of a mrna. they are typically comprised of separate ligand binding and regulatory domains. the t box riboswitch is unique from other identified riboswitches because its effector is an essential macromolecule, trna. it senses the aminoacylation state of trna to regulate genes involved in a variety of functions relating to amino acid metabolism and trna aminoacylation. t box riboswitches ... | 2013 | 24356646 |
| insights into protein allostery in the csor/rcnr family of transcriptional repressors. | csor/rcnr transcriptional repressors adopt a disc-shaped, all α-helical dimer of dimers tetrameric architecture, with a four-helix bundle the key structural feature of the dimer. individual members of this large family of repressors coordinate cu(i) or ni(ii)/co(ii) or perform cysteine sulfur chemistry in mitigating the effects of metal or metabolite toxicity, respectively. here we highlight recent insights into the functional diversity of this fascinating family of repressors. | 2013 | 24695963 |
| insights into protein allostery in the csor/rcnr family of transcriptional repressors. | csor/rcnr transcriptional repressors adopt a disc-shaped, all α-helical dimer of dimers tetrameric architecture, with a four-helix bundle the key structural feature of the dimer. individual members of this large family of repressors coordinate cu(i) or ni(ii)/co(ii) or perform cysteine sulfur chemistry in mitigating the effects of metal or metabolite toxicity, respectively. here we highlight recent insights into the functional diversity of this fascinating family of repressors. | 2013 | 24695963 |
| purification, crystallization and preliminary crystallographic analysis of katb, a manganese catalase from anabaena pcc 7120. | catalases are enzymes that play an important role in the detoxification of hydrogen peroxide (h2o2) in aerobic organisms. among catalases, haem-containing catalases are ubiquitously distributed and their enzymatic mechanism is very well understood. on the other hand, manganese catalases that contain a bimanganese core in the active site have been less well characterized and their mode of action is not fully understood. the genome of anabaena pcc 7120 does not show the presence of a haem catalase ... | 2013 | 24192374 |
| cloning, expression, purification, crystallization and preliminary crystallographic analysis of the putative nlpc/p60 endopeptidase, ttha0266, from thermus thermophilus hb8. | autolysins belong to a protein family involved in peptidoglycan degradation and remodelling. within this family, nlpc/p60 endopeptidases are involved in the hydrolysis of the peptide arm of peptidoglycan. in this work, the putative nlpc/p60 endopeptidase ttha0266 from thermus thermophilus hb8 was overexpressed, purified and crystallized. the crystals diffracted to 2.4 å resolution and belonged to the hexagonal space group p6(1), with unit-cell parameters a = b = 71.19, c = 198.68 å, γ = 120°. se ... | 2013 | 24192372 |
| cloning, overexpression, purification and crystallization of malate dehydrogenase from thermus thermophilus. | malate dehydrogenase (mdh) has been used as a conjugate for enzyme immunoassay of a wide variety of compounds, such as drugs of abuse, drugs used in repetitive therapeutic application and hormones. in consideration of the various biotechnological applications of mdh, investigations of mdh from thermus thermophilus were carried out to further understand the properties of this enzyme. the dna fragment containing the open reading frame of mdh was amplified from the genomic dna of t. thermophilus an ... | 2013 | 24192361 |
| biophysical characterization of a recombinant aminopeptidase ii from the thermophilic bacterium bacillus stearothermophilus. | in the present study, the biophysical properties of his6-tagged bacillus stearothermophilus aminopeptidase ii (his6-tagged bsampii) are characterized in detail by gel-filtration, analytical ultracentrifugation, and various spectroscopic techniques. using size-exclusion chromatography and analytical ultracentrifugation, we demonstrate that his6-tagged bsampii exists predominantly as a dimer in solution. the enzyme is active and stable at phs ranging from 6.5 to 8.5. far-uv circular dichroism anal ... | 2013 | 24165863 |
| biophysical characterization of a recombinant aminopeptidase ii from the thermophilic bacterium bacillus stearothermophilus. | in the present study, the biophysical properties of his6-tagged bacillus stearothermophilus aminopeptidase ii (his6-tagged bsampii) are characterized in detail by gel-filtration, analytical ultracentrifugation, and various spectroscopic techniques. using size-exclusion chromatography and analytical ultracentrifugation, we demonstrate that his6-tagged bsampii exists predominantly as a dimer in solution. the enzyme is active and stable at phs ranging from 6.5 to 8.5. far-uv circular dichroism anal ... | 2013 | 24165863 |
| metagenomic approach for the isolation of a thermostable β-galactosidase with high tolerance of galactose and glucose from soil samples of turpan basin. | β-galactosidases can be used to produce low-lactose milk and dairy products for lactose intolerant people. although commercial β-galactosidases have outstanding lactose hydrolysis ability, their thermostability is low, and reaction products have strong inhibition to these enzymes. in addition, the β-galactosidases possessing simultaneously high thermostability and tolerance of galactose and glucose are still seldom reported until now. therefore, identification of novel β-galactosidases with high ... | 2013 | 24156692 |
| translational regulation of yersinia enterocolitica mrna encoding a type iii secretion substrate. | yersinia enterocolitica type iii secretion machines transport yopq and other yop effectors into host immune cells. yopd and its chaperone lcrh are essential components of the yersinia type iii pathway, enabling effector translocation into host cells. yopd, lcrh, and yscm1 also regulate yop expression post-transcriptionally in response to environmental signals; however, the molecular mechanisms for this regulation and yop secretion are unknown. we show here that yopd associates with 30 s ribosoma ... | 2013 | 24158443 |
| a comparative study of ribosomal proteins: linkage between amino acid distribution and ribosomal assembly. | assembly of the ribosome from its protein and rna constituents must occur quickly and efficiently in order to synthesize the proteins necessary for all cellular activity. since the early 1960's, certain characteristics of possible assembly pathways have been elucidated, yet the mechanisms that govern the precise recognition events remain unclear.we utilize a comparative analysis to investigate the amino acid composition of ribosomal proteins (r-proteins) with respect to their role in the assembl ... | 2013 | 24152303 |
| structure of the secy channel during initiation of protein translocation. | many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic secy or eukaryotic sec61 complexes, and are translocated across the membrane during their synthesis. crystal structures of the inactive channel show that the secy subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. the closed channel has an empty ... | 2013 | 24153188 |
| structure of the secy channel during initiation of protein translocation. | many secretory proteins are targeted by signal sequences to a protein-conducting channel, formed by prokaryotic secy or eukaryotic sec61 complexes, and are translocated across the membrane during their synthesis. crystal structures of the inactive channel show that the secy subunit of the heterotrimeric complex consists of two halves that form an hourglass-shaped pore with a constriction in the middle of the membrane and a lateral gate that faces the lipid phase. the closed channel has an empty ... | 2013 | 24153188 |
| crystal structure of a bioactive pactamycin analog bound to the 30s ribosomal subunit. | biosynthetically and chemically derived analogs of the antibiotic pactamycin and de-6-methylsalicylyl (msa)-pactamycin have attracted recent interest as potential antiprotozoal and antitumor drugs. here, we report a 3.1-å crystal structure of de-6-msa-pactamycin bound to its target site on the thermus thermophilus 30s ribosomal subunit. although de-6-msa-pactamycin lacks the msa moiety, it shares the same binding site as pactamycin and induces a displacement of nucleic acid template bound at the ... | 2013 | 23702293 |
| evolution of crispr rna recognition and processing by cas6 endonucleases. | in many bacteria and archaea, small rnas derived from clustered regularly interspaced short palindromic repeats (crisprs) associate with crispr-associated (cas) proteins to target foreign dna for destruction. in type i and iii crispr/cas systems, the cas6 family of endoribonucleases generates functional crispr-derived rnas by site-specific cleavage of repeat sequences in precursor transcripts. crispr repeats differ widely in both sequence and structure, with varying propensity to form hairpin fo ... | 2013 | 24150936 |
| evolution of crispr rna recognition and processing by cas6 endonucleases. | in many bacteria and archaea, small rnas derived from clustered regularly interspaced short palindromic repeats (crisprs) associate with crispr-associated (cas) proteins to target foreign dna for destruction. in type i and iii crispr/cas systems, the cas6 family of endoribonucleases generates functional crispr-derived rnas by site-specific cleavage of repeat sequences in precursor transcripts. crispr repeats differ widely in both sequence and structure, with varying propensity to form hairpin fo ... | 2013 | 24150936 |
| 12-fold symmetry of the putative portal protein from the thermus thermophilus bacteriophage g20c determined by x-ray analysis. | in tailed bacteriophages and several animal viruses, the portal protein forms the gateway through which viral dna is translocated into the head structure during viral particle assembly. in the mature virion the portal protein exists as a dodecamer, while recombinant portal proteins from several phages, including spp1 and cnph82, have been shown to form 13-subunit assemblies. a putative portal protein from the thermostable bacteriophage g20c has been cloned, overexpressed and purified. crystals o ... | 2013 | 24192358 |
| crystallization and preliminary x-ray study of alanine dehydrogenase from bacillus pseudofirmus of4. | alanine dehydrogenase (of4ald) from the alkaliphilic bacillus pseudofirmus of4 was expressed and purified with a his6 tag in a form suitable for x-ray crystallographic analysis. crystals were grown by the hanging-drop vapour-diffusion method at 289 k using a solution consisting of 0.1 m tris-hcl ph 8.0, 0.2 m liso4, 22%(w/v) peg 3350. x-ray diffraction data were collected to 2.8 å resolution. the crystal belonged to the triclinic space group p1, with unit-cell parameters a = 88.04, b = 105.59, c ... | 2013 | 24192355 |
| crystallization and preliminary x-ray diffraction studies of staphylococcus aureus homoserine dehydrogenase. | staphylococcus aureus is a gram-positive nosocomial pathogen. the prevalence of multidrug-resistant s. aureus strains in both hospital and community settings makes it imperative to characterize new drug targets to combat s. aureus infections. in this context, enzymes involved in cell-wall maintenance and essential amino-acid biosynthesis are significant drug targets. homoserine dehydrogenase (hsd) is an oxidoreductase that is involved in the reversible conversion of l-aspartate semialdehyde to l ... | 2013 | 24192352 |
| temperature dependence of the dna double helix at the nanoscale: structure, elasticity, and fluctuations. | biological organisms exist over a broad temperature range of -15°c to +120°c, where many molecular processes involving dna depend on the nanoscale properties of the double helix. here, we present results of extensive molecular dynamics simulations of dna oligomers at different temperatures. we show that internal basepair conformations are strongly temperature-dependent, particularly in the stretch and opening degrees of freedom whose harmonic fluctuations can be considered the initial steps of t ... | 2013 | 24138866 |
| structure of the homodimeric glycine decarboxylase p-protein from synechocystis sp. pcc 6803 suggests a mechanism for redox regulation. | glycine decarboxylase, or p-protein, is a pyridoxal 5'-phosphate (plp)-dependent enzyme in one-carbon metabolism of all organisms, in the glycine and serine catabolism of vertebrates, and in the photorespiratory pathway of oxygenic phototrophs. p-protein from the cyanobacterium synechocystis sp. pcc 6803 is an α2 homodimer with high homology to eukaryotic p-proteins. the crystal structure of the apoenzyme shows the c terminus locked in a closed conformation by a disulfide bond between cys(972) i ... | 2013 | 24121504 |
| structure and activity of the rna-targeting type iii-b crispr-cas complex of thermus thermophilus. | the crispr-cas system is a prokaryotic host defense system against genetic elements. the type iii-b crispr-cas system of the bacterium thermus thermophilus, the ttcmr complex, is composed of six different protein subunits (cmr1-6) and one crrna with a stoichiometry of cmr112131445361:crrna1. the ttcmr complex copurifies with crrna species of 40 and 46 nt, originating from a distinct subset of crispr loci and spacers. the ttcmr complex cleaves the target rna at multiple sites with 6 nt intervals ... | 2013 | 24119403 |
| cloning and expression of dnak gene from bacillus pumilus of hot water spring origin. | a set of thermotolerant strains isolated from hot springs of manikaran and bakreshwar (india) were selected with an aim to isolate dnak gene which encodes dnak protein. the gene dnak along with its flanking region was successfully amplified from 5 different strains (4 from bakreshwar and one from manikaran). restriction fragment length polymorphism (rflp) revealed that amplicons were almost identical in sequence. the dnak gene from one representative, bacillus pumilus strain b3 isolated from bak ... | 2013 | 27275408 |
| cloning and expression of dnak gene from bacillus pumilus of hot water spring origin. | a set of thermotolerant strains isolated from hot springs of manikaran and bakreshwar (india) were selected with an aim to isolate dnak gene which encodes dnak protein. the gene dnak along with its flanking region was successfully amplified from 5 different strains (4 from bakreshwar and one from manikaran). restriction fragment length polymorphism (rflp) revealed that amplicons were almost identical in sequence. the dnak gene from one representative, bacillus pumilus strain b3 isolated from bak ... | 2013 | 27275408 |
| 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 |
| staphylococcus epidermidis csm1 is a 3'-5' exonuclease. | clustered regularly interspaced short palindromic repeats (crispr) offer an adaptive immune system that protects bacteria and archaea from nucleic acid invaders through an rna-mediated nucleic acid cleavage mechanism. our knowledge of nucleic acid cleavage mechanisms is limited to three examples of widely different ribonucleoprotein particles that target either dna or rna. staphylococcus epidermidis belongs to the type iii-a crispr system and has been shown to interfere with invading dna in vivo ... | 2013 | 24121684 |
| staphylococcus epidermidis csm1 is a 3'-5' exonuclease. | clustered regularly interspaced short palindromic repeats (crispr) offer an adaptive immune system that protects bacteria and archaea from nucleic acid invaders through an rna-mediated nucleic acid cleavage mechanism. our knowledge of nucleic acid cleavage mechanisms is limited to three examples of widely different ribonucleoprotein particles that target either dna or rna. staphylococcus epidermidis belongs to the type iii-a crispr system and has been shown to interfere with invading dna in vivo ... | 2013 | 24121684 |
| conformational and thermodynamic hallmarks of dna operator site specificity in the copper sensitive operon repressor from streptomyces lividans. | metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. the copper sensitive operon repressor (csor) family is widely distributed in bacteria and controls the expression of copper efflux systems. csor operator sites consist of g-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. here, we use a structurally characterized csor from streptomyces li ... | 2013 | 24121681 |
| conformational and thermodynamic hallmarks of dna operator site specificity in the copper sensitive operon repressor from streptomyces lividans. | metal ion homeostasis in bacteria relies on metalloregulatory proteins to upregulate metal resistance genes and enable the organism to preclude metal toxicity. the copper sensitive operon repressor (csor) family is widely distributed in bacteria and controls the expression of copper efflux systems. csor operator sites consist of g-tract containing pseudopalindromes of which the mechanism of operator binding is poorly understood. here, we use a structurally characterized csor from streptomyces li ... | 2013 | 24121681 |
| menaquinone biosynthesis: formation of aminofutalosine requires a unique radical sam enzyme. | menaquinone (mk, vitamin k2) is a lipid-soluble molecule that participates in the bacterial electron transport chain. in mammalian cells, mk functions as an essential vitamin for the activation of various proteins involved in blood clotting and bone metabolism. recently, a new pathway for the biosynthesis of this cofactor was discovered in streptomyces coelicolor a3(2) in which chorismate is converted to aminofutalosine in a reaction catalyzed by mqna and an unidentified enzyme. here, we reconst ... | 2013 | 24083939 |
| construction of an in vitro bypassed pyruvate decarboxylation pathway using thermostable enzyme modules and its application to n-acetylglutamate production. | metabolic engineering has emerged as a practical alternative to conventional chemical conversion particularly in biocommodity production processes. however, this approach is often hampered by as yet unidentified inherent mechanisms of natural metabolism. one of the possible solutions for the elimination of the negative effects of natural regulatory mechanisms on artificially engineered metabolic pathway is to construct an in vitro pathway using a limited number of enzymes. employment of thermost ... | 2013 | 24099461 |
| minimal mechanistic model of sirna-dependent target rna slicing by recombinant human argonaute 2 protein. | argonaute (ago) proteins are the key component of the rna-induced silencing complex and mediate rna interference (rnai) in association with small rnas. although overall the mechanism of rnai is well understood, many molecular details of this complex process are not. here we report about in-depth steady-state and, in particular, pre-steady-state characterization of sirna binding, target rna recognition, sequence-specific cleavage and product release by recombinant human ago 2 (hago2). in combinin ... | 2013 | 24101500 |
| archaeal ubiquitin-like samp3 is isopeptide-linked to proteins via a ubaa-dependent mechanism. | samp1 and samp2 are ubiquitin-like proteins that function as protein modifiers and are required for the production of sulfur-containing biomolecules in the archaeon haloferax volcanii. here we report a novel small archaeal modifier protein (named samp3) with a β-grasp fold and c-terminal diglycine motif characteristic of ubiquitin that is functional in protein conjugation in hfx. volcanii. samp3 conjugates were dependent on the ubiquitin-activating e1 enzyme homolog of archaea (ubaa) for synthes ... | 2013 | 24097257 |
| archaeal ubiquitin-like samp3 is isopeptide-linked to proteins via a ubaa-dependent mechanism. | samp1 and samp2 are ubiquitin-like proteins that function as protein modifiers and are required for the production of sulfur-containing biomolecules in the archaeon haloferax volcanii. here we report a novel small archaeal modifier protein (named samp3) with a β-grasp fold and c-terminal diglycine motif characteristic of ubiquitin that is functional in protein conjugation in hfx. volcanii. samp3 conjugates were dependent on the ubiquitin-activating e1 enzyme homolog of archaea (ubaa) for synthes ... | 2013 | 24097257 |
| crystal structure of human seryl-trna synthetase and ser-sa complex reveals a molecular lever specific to higher eukaryotes. | seryl-trna synthetase (serrs), an essential enzyme for translation, also regulates vascular development. this "gain-of-function" has been linked to the une-s domain added to vertebrate serrs during evolution. however, the significance of two insertions also specific to higher eukaryotic serrs remains elusive. here, we determined the crystal structure of human serrs in complex with ser-sa, an aminoacylation reaction intermediate analog, at 2.9 å resolution. despite a 70 å distance, binding of ser ... | 2013 | 24095058 |
| thermal adaptation of conformational dynamics in ribonuclease h. | the relationship between inherent internal conformational processes and enzymatic activity or thermodynamic stability of proteins has proven difficult to characterize. the study of homologous proteins with differing thermostabilities offers an especially useful approach for understanding the functional aspects of conformational dynamics. in particular, ribonuclease hi (rnase h), an 18 kd globular protein that hydrolyzes the rna strand of rna:dna hybrid substrates, has been extensively studied by ... | 2013 | 24098095 |
| the role of the mitochondrial ribosome in human disease: searching for mutations in 12s mitochondrial rrna with high disruptive potential. | mutations of mitochondrial dna are linked to many human diseases. despite the identification of a large number of variants in the mitochondrially encoded rrna (mt-rrna) genes, the evidence supporting their pathogenicity is, at best, circumstantial. establishing the pathogenicity of these variations is of major diagnostic importance. here, we aim to estimate the disruptive effect of mt-rrna variations on the function of the mitochondrial ribosome. in the absence of direct biochemical methods to s ... | 2013 | 24092330 |
| the role of the mitochondrial ribosome in human disease: searching for mutations in 12s mitochondrial rrna with high disruptive potential. | mutations of mitochondrial dna are linked to many human diseases. despite the identification of a large number of variants in the mitochondrially encoded rrna (mt-rrna) genes, the evidence supporting their pathogenicity is, at best, circumstantial. establishing the pathogenicity of these variations is of major diagnostic importance. here, we aim to estimate the disruptive effect of mt-rrna variations on the function of the mitochondrial ribosome. in the absence of direct biochemical methods to s ... | 2013 | 24092330 |
| ndufaf7 methylates arginine 85 in the ndufs2 subunit of human complex i. | complex i (nadh ubiquinone oxidoreductase) in mammalian mitochondria is an l-shaped assembly of 44 subunits. one arm is embedded in the inner membrane with the other protruding ∼100 å into the matrix of the organelle. the extrinsic arm contains binding sites for nadh and the primary electron acceptor fmn, and it provides a scaffold for seven iron-sulfur clusters that form an electron pathway linking fmn to the terminal electron acceptor, ubiquinone, which is bound in the region of the junction b ... | 2013 | 24089531 |
| basic properties of rotary dynamics of the molecular motor enterococcus hirae v1-atpase. | v-atpases are rotary molecular motors that generally function as proton pumps. we recently solved the crystal structures of the v1 moiety of enterococcus hirae v-atpase (ehv1) and proposed a model for its rotation mechanism. here, we characterized the rotary dynamics of ehv1 using single-molecule analysis employing a load-free probe. ehv1 rotated in a counterclockwise direction, exhibiting two distinct rotational states, namely clear and unclear, suggesting unstable interactions between the roto ... | 2013 | 24089518 |
| protein folding on the ribosome studied using nmr spectroscopy. | nmr spectroscopy is a powerful tool for the investigation of protein folding and misfolding, providing a characterization of molecular structure, dynamics and exchange processes, across a very wide range of timescales and with near atomic resolution. in recent years nmr methods have also been developed to study protein folding as it might occur within the cell, in a de novo manner, by observing the folding of nascent polypeptides in the process of emerging from the ribosome during synthesis. des ... | 2013 | 24083462 |
| nanometer scale pores similar in size to the entrance of the ribosomal exit cavity are a common feature of large rnas. | the highly conserved peptidyl transferase center (ptc) of the ribosome contains an rna pore that serves as the entrance to the exit tunnel. analysis of available ribosome crystal structures has revealed the presence of multiple additional well-defined pores of comparable size in the ribosomal (rrna) rnas. these typically have dimensions of 1-2 nm, with a total area of ∼100 å(2) or more, and most are associated with one or more ribosomal proteins. the ptc example and the other rrna pores result f ... | 2013 | 23940386 |
| s6:s18 ribosomal protein complex interacts with a structural motif present in its own mrna. | prokaryotic ribosomal protein genes are typically grouped within highly conserved operons. in many cases, one or more of the encoded proteins not only bind to a specific site in the ribosomal rna, but also to a motif localized within their own mrna, and thereby regulate expression of the operon. in this study, we computationally predicted an rna motif present in many bacterial phyla within the 5' untranslated region of operons encoding ribosomal proteins s6 and s18. we demonstrated that the s6:s ... | 2013 | 23980204 |
| automated classification of rna 3d motifs and the rna 3d motif atlas. | the analysis of atomic-resolution rna three-dimensional (3d) structures reveals that many internal and hairpin loops are modular, recurrent, and structured by conserved non-watson-crick base pairs. structurally similar loops define rna 3d motifs that are conserved in homologous rna molecules, but can also occur at nonhomologous sites in diverse rnas, and which often vary in sequence. to further our understanding of rna motif structure and sequence variability and to provide a useful resource for ... | 2013 | 23970545 |
| mechanisms of eukaryotic transcription. | a report on the cold spring harbor laboratory mechanisms of eukaryotic transcription meeting, cold spring harbor, new york, usa, august 27–31, 2013. | 2013 | 24079829 |
| fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome. | determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. ... | 2013 | 24081579 |
| fast fitting to low resolution density maps: elucidating large-scale motions of the ribosome. | determining the conformational rearrangements of large macromolecules is challenging experimentally and computationally. case in point is the ribosome; it has been observed by high-resolution crystallography in several states, but many others are known only from low-resolution methods including cryo-electron microscopy. combining these data into dynamical trajectories that may aid understanding of its largest-scale conformational changes has so far remained out of reach of computational methods. ... | 2013 | 24081579 |
| crystallization and preliminary crystallographic analysis of ganb, a gh42 intracellular β-galactosidase from geobacillus stearothermophilus. | geobacillus stearothermophilus t-6 is a gram-positive thermophilic soil bacterium that contains a multi-enzyme system for the utilization of plant cell-wall polysaccharides, including xylan, arabinan and galactan. the bacterium uses a number of endo-acting extracellular enzymes that break down the high-molecular-weight polysaccharides into decorated oligosaccharides. these oligosaccharides enter the cell and are further hydrolyzed into sugar monomers by a set of intracellular glycoside hydrolase ... | 2013 | 24100561 |
| a nondiscriminating glutamyl-trna synthetase in the plasmodium apicoplast: the first enzyme in an indirect aminoacylation pathway. | the malaria parasite plasmodium falciparum and related organisms possess a relict plastid known as the apicoplast. apicoplast protein synthesis is a validated drug target in malaria because antibiotics that inhibit translation in prokaryotes also inhibit apicoplast protein synthesis and are sometimes used for malaria prophylaxis or treatment. we identified components of an indirect aminoacylation pathway for gln-trna(gln) biosynthesis in plasmodium that we hypothesized would be essential for api ... | 2013 | 24072705 |
| comparative analysis of barophily-related amino acid content in protein domains of pyrococcus abyssi and pyrococcus furiosus. | amino acid substitution patterns between the nonbarophilic pyrococcus furiosus and its barophilic relative p. abyssi confirm that hydrostatic pressure asymmetry indices reflect the extent to which amino acids are preferred by barophilic archaeal organisms. substitution patterns in entire protein sequences, shared protein domains defined at fold superfamily level, domains in homologous sequence pairs, and domains of very ancient and very recent origin now provide further clues about the environme ... | 2013 | 24187517 |
| single mutations that redirect internal proton transfer in the ba3 oxidase from thermus thermophilus. | the ba3-type cytochrome c oxidase from thermus thermophilus is a membrane-bound proton pump. results from earlier studies have shown that with the aa3-type oxidases proton uptake to the catalytic site and "pump site" occurs simultaneously. however, with ba3 oxidase the pump site is loaded before proton transfer to the catalytic site because the proton transfer to the latter is slower than that with the aa3 oxidases. in addition, the timing of formation and decay of catalytic intermediates is dif ... | 2013 | 24004023 |
| structural, biochemical and genetic characterization of dissimilatory atp sulfurylase from allochromatium vinosum. | atp sulfurylase (atps) catalyzes a key reaction in the global sulfur cycle by reversibly converting inorganic sulfate (so4 (2-)) with atp to adenosine 5'-phosphosulfate (aps) and pyrophosphate (ppi). in this work we report on the sat encoded dissimilatory atp sulfurylase from the sulfur-oxidizing purple sulfur bacterium allochromatium vinosum. in this organism, the sat gene is located in one operon and co-transcribed with the aprmba genes for membrane-bound aps reductase. like aps reductase, sat ... | 2013 | 24073218 |
| mutations in gtp binding protein obg of mycoplasma synoviae vaccine strain ms-h: implications in temperature-sensitivity phenotype. | mycoplasma synoviae strain ms-h, developed by chemical mutagenesis of the australian field strain 86079/7ns, is a live temperature-sensitive (ts (+)) vaccine used for control of m. synoviae infection in poultry worldwide. genetic basis of temperature sensitivity and attenuation of ms-h has not been revealed thus far. comparison of the complete genome sequence of ms-h, its parent strain 86079/7ns and two non-temperature sensitive (ts (-)) reisolates of ms-h revealed a mutation in a highly conserv ... | 2013 | 24069254 |
| loose binding of the df axis with the a3b3 complex stimulates the initial activity of enterococcus hirae v1-atpase. | vacuolar atpases (v-atpases) function as proton pumps in various cellular membrane systems. the hydrophilic v1 portion of the v-atpase is a rotary motor, in which a central-axis df complex rotates inside a hexagonally arranged catalytic a3b3 complex by using atp hydrolysis energy. we have previously reported crystal structures of enterococcushirae v-atpase a3b3 and a3b3df (v1) complexes; the result suggested that the df axis induces structural changes in the a3b3 complex through extensive protei ... | 2013 | 24058539 |
| an ftsh protease is recruited to the mitochondrion of plasmodium falciparum. | the two organelles, apicoplast and mitochondrion, of the malaria parasite plasmodium falciparum have unique morphology in liver and blood stages; they undergo complex branching and looping prior to division and segregation into daughter merozoites. little is known about the molecular processes and proteins involved in organelle biogenesis in the parasite. we report the identification of an aaa+/ftsh protease homolog (pfftsh1) that exhibits atp- and zn(2+)-dependent protease activity. pfftsh1 und ... | 2013 | 24058559 |
| chaperone machines for protein folding, unfolding and disaggregation. | molecular chaperones are diverse families of multidomain proteins that have evolved to assist nascent proteins to reach their native fold, protect subunits from heat shock during the assembly of complexes, prevent protein aggregation or mediate targeted unfolding and disassembly. their increased expression in response to stress is a key factor in the health of the cell and longevity of an organism. unlike enzymes with their precise and finely tuned active sites, chaperones are heavy-duty molecul ... | 2013 | 24026055 |
| bacterial argonaute samples the transcriptome to identify foreign dna. | eukaryotic argonautes bind small rnas and use them as guides to find complementary rna targets and induce gene silencing. though homologs of eukaryotic argonautes are present in many bacteria and archaea, their small rna partners and functions are unknown. we found that the argonaute of rhodobacter sphaeroides (rsago) associates with 15-19 nt rnas that correspond to the majority of transcripts. rsago also binds single-stranded 22-24 nt dna molecules that are complementary to the small rnas and e ... | 2013 | 24034694 |
| involvement of protein if2 n domain in ribosomal subunit joining revealed from architecture and function of the full-length initiation factor. | translation initiation factor 2 (if2) promotes 30s initiation complex (ic) formation and 50s subunit joining, which produces the 70s ic. the architecture of full-length if2, determined by small angle x-ray diffraction and cryo electron microscopy, reveals a more extended conformation of if2 in solution and on the ribosome than in the crystal. the n-terminal domain is only partially visible in the 30s ic, but in the 70s ic, it stabilizes interactions between if2 and the l7/l12 stalk of the 50s, a ... | 2013 | 24029017 |
| initiation factor 2 crystal structure reveals a different domain organization from eukaryotic initiation factor 5b and mechanism among translational gtpases. | the initiation of protein synthesis uses initiation factor 2 (if2) in prokaryotes and a related protein named eukaryotic initiation factor 5b (eif5b) in eukaryotes. if2 is a gtpase that positions the initiator trna on the 30s ribosomal initiation complex and stimulates its assembly to the 50s ribosomal subunit to make the 70s ribosome. the 3.1-å resolution x-ray crystal structures of the full-length thermus thermophilus apo if2 and its complex with gdp presented here exhibit two different confor ... | 2013 | 24029018 |
| systematic mutational analysis of the putative hydrolase pqse: toward a deeper molecular understanding of virulence acquisition in pseudomonas aeruginosa. | pseudomonas aeruginosa is an important opportunistic human pathogen that can establish bacterial communication by synchronizing the behavior of individual cells in a molecular phenomenon known as "quorum sensing". through an elusive mechanism involving gene products of the pqs operon, the pqse enzyme is absolutely required for the synthesis of extracellular phenazines, including the toxic blue pigment pyocyanin, effectively allowing cells to achieve full-fledged virulence. despite several functi ... | 2013 | 24040042 |
| complete genomic dna sequence of the east asian spotted fever disease agent rickettsia japonica. | rickettsia japonica is an obligate intracellular alphaproteobacteria that causes tick-borne japanese spotted fever, which has spread throughout east asia. we determined the complete genomic dna sequence of r. japonica type strain yh (vr-1363), which consists of 1,283,087 base pairs (bp) and 971 protein-coding genes. comparison of the genomic dna sequence of r. japonica with other rickettsiae in the public databases showed that 2 regions (4,323 and 216 bp) were conserved in a very narrow range of ... | 2013 | 24039725 |
| aminoacylation of trna 2'- or 3'-hydroxyl by phosphoseryl- and pyrrolysyl-trna synthetases. | class i and ii aminoacyl-trna synthetases (aarss) attach amino acids to the 2'- and 3'-oh of the trna terminal adenosine, respectively. one exception is phenylalanyl-trna synthetase (phers), which belongs to class ii but attaches phenylalanine to the 2'-oh. here we show that two class ii aarss, o-phosphoseryl- (seprs) and pyrrolysyl-trna (pylrs) synthetases, aminoacylate the 2'- and 3'-oh, respectively. structure-based-phylogenetic analysis reveals that seprs is more closely related to phers tha ... | 2013 | 24021645 |
| significance of neuropilin-1 expression in acute myeloid leukemia. | neuropilin-1 is a vascular endothelial growth factor receptor that acts as a mediator of angiogenesis. its importance in hematological malignancies such as acute myeloid leukemia (aml) remains to be elucidated. the aim of this study was to evaluate the significance of neuropilin-1 expression in aml patients by both flow cytometry and real-time polymerase chain reaction (pcr) in regard to its diagnostic and prognostic values. | 2013 | 24385810 |
| the uve1 endonuclease is regulated by the white collar complex to protect cryptococcus neoformans from uv damage. | the pathogenic fungus cryptococcus neoformans uses the bwc1-bwc2 photoreceptor complex to regulate mating in response to light, virulence and ultraviolet radiation tolerance. how the complex controls these functions is unclear. here, we identify and characterize a gene in cryptococcus, uve1, whose mutation leads to a uv hypersensitive phenotype. the homologous gene in fission yeast schizosaccharomyces pombe encodes an apurinic/apyrimidinic endonuclease acting in the uvde-dependent excision repai ... | 2013 | 24039606 |
| splicefinder - a fast and easy screening method for active protein trans-splicing positions. | split intein enabled protein trans-splicing (pts) is a powerful method for the ligation of two protein fragments, thereby paving the way for various protein modification or protein function control applications. pts activity is strongly influenced by the amino acids directly flanking the splice junctions. however, to date no reliable prediction can be made whether or not a split intein is active in a particular foreign extein context. here we describe splicefinder, a pcr-based method, allowing f ... | 2013 | 24023792 |
| a two-domain elevator mechanism for sodium/proton antiport. | sodium/proton (na(+)/h(+)) antiporters, located at the plasma membrane in every cell, are vital for cell homeostasis. in humans, their dysfunction has been linked to diseases, such as hypertension, heart failure and epilepsy, and they are well-established drug targets. the best understood model system for na(+)/h(+) antiport is nhaa from escherichia coli, for which both electron microscopy and crystal structures are available. nhaa is made up of two distinct domains: a core domain and a dimeriza ... | 2013 | 23995679 |
| physiological role of acyl coenzyme a synthetase homologs in lipid metabolism in neurospora crassa. | acyl coenzyme a (coa) synthetase (acs) enzymes catalyze the activation of free fatty acids (fas) to coa esters by a two-step thioesterification reaction. activated fas participate in a variety of anabolic and catabolic lipid metabolic pathways, including de novo complex lipid biosynthesis, fa β-oxidation, and lipid membrane remodeling. analysis of the genome sequence of the filamentous fungus neurospora crassa identified seven putative fatty acss (acs-1 through acs-7). acs-3 was found to be the ... | 2013 | 23873861 |
| genome-wide transcriptional profiling of the purple sulfur bacterium allochromatium vinosum dsm 180t during growth on different reduced sulfur compounds. | the purple sulfur bacterium allochromatium vinosum dsm 180(t) is one of the best-studied sulfur-oxidizing anoxygenic phototrophic bacteria, and it has been developed into a model organism for laboratory-based studies of oxidative sulfur metabolism. here, we took advantage of the organism's high metabolic versatility and performed whole-genome transcriptional profiling to investigate the response of a. vinosum cells upon exposure to sulfide, thiosulfate, elemental sulfur, or sulfite compared to p ... | 2013 | 23873913 |
| sensitive and specific quantitative detection of rotavirus a by one-step real-time reverse transcription-pcr assay without antecedent double-stranded-rna denaturation. | a real-time quantitative reverse transcription-pcr (qrt-pcr) assay using the recombinant thermostable thermus thermophilus (rtth) enzyme was developed to detect and quantify rotavirus a (rva). by using rtth polymerase, significant improvement was achieved over the existing real-time rt-pcr assays, which require denaturation of the rva double-stranded rna (dsrna) prior to assay setup. using a dsrna transcript for segment 7, which encodes the assay target nsp3 gene, the limit of detection for the ... | 2013 | 23850952 |
| two atp-binding cassette transporters involved in (s)-2-aminoethyl-cysteine uptake in thermus thermophilus. | thermus thermophilus exhibits hypersensitivity to a lysine analog, (s)-2-aminoethyl-cysteine (aec). cosmid libraries were constructed using genomes from two aec-resistant mutants, at10 and at14, and the cosmids that conferred aec resistance on the wild-type strain were isolated. when the cosmid library for mutant at14 was screened, two independent cosmids, conferring partial aec resistance to the wild type, were obtained. two cosmids carried a common genomic region from ttc0795 to ttc0810. this ... | 2013 | 23794618 |
| polysaccharide-degrading thermophiles generated by heterologous gene expression in geobacillus kaustophilus hta426. | thermophiles have important advantages over mesophiles as host organisms for high-temperature bioprocesses, functional production of thermostable enzymes, and efficient expression of enzymatic activities in vivo. to capitalize on these advantages of thermophiles, we describe here a new inducible gene expression system in the thermophile geobacillus kaustophilus hta426. six promoter regions in the hta426 genome were identified and analyzed for expression profiles using β-galactosidase reporter as ... | 2013 | 23793634 |
| mechanism of activation of elongation factor tu by ribosome: catalytic histidine activates gtp by protonation. | elongation factor tu (ef-tu) is central to prokaryotic protein synthesis as it has the role of delivering amino-acylated trnas to the ribosome. release of ef-tu, after correct binding of the ef-tu:aa-trna complex to the ribosome, is initiated by gtp hydrolysis. this reaction, whose mechanism is uncertain, is catalyzed by ef-tu, but requires activation by the ribosome. there have been a number of mechanistic proposals, including those spurred by a recent x-ray crystallographic analysis of a ribos ... | 2013 | 23864225 |
| translation of cga codon repeats in yeast involves quality control components and ribosomal protein l1. | translation of cga codon repeats in the yeast saccharomyces cerevisiae is inefficient, resulting in dose-dependent reduction in expression and in production of an mrna cleavage product, indicative of a stalled ribosome. here, we use genetics and translation inhibitors to understand how ribosomes respond to cga repeats. we find that cga codon repeats result in a truncated polypeptide that is targeted for degradation by ltn1, an e3 ubiquitin ligase involved in nonstop decay, although deletion of l ... | 2013 | 23825054 |
| an insertion peptide in yeast glycyl-trna synthetase facilitates both productive docking and catalysis of cognate trnas. | the yeast saccharomyces cerevisiae possesses two distinct glycyl-trna synthetase (glyrs) genes: grs1 and grs2. grs1 is dually functional, encoding both cytoplasmic and mitochondrial activities, while grs2 is dysfunctional and not required for growth. the protein products of these two genes, glyrs1 and glyrs2, are much alike but are distinguished by an insertion peptide of glyrs1, which is absent from glyrs2 and other eukaryotic homologues. we show that deletion or mutation of the insertion pepti ... | 2013 | 23816885 |
| divergent contributions of conserved active site residues to transcription by eukaryotic rna polymerases i and ii. | multisubunit rna polymerases (msrnaps) exhibit high sequence and structural homology, especially within their active sites, which is generally thought to result in msrnap functional conservation. however, we show that mutations in the trigger loop (tl) in the largest subunit of rna polymerase i (pol i) yield phenotypes unexpected from studies of pol ii. for example, a well-characterized gain-of-function mutation in pol ii results in loss of function in pol i (pol ii: rpb1- e1103g; pol i: rpa190- ... | 2013 | 23994471 |
| ppr-smrs: ancient proteins with enigmatic functions. | a small subset of the large pentatricopeptide repeat (ppr) protein family in higher plants contain a c-terminal small muts-related (smr) domain. although few in number, they figure prominently in the chloroplast biogenesis and retrograde signaling literature due to their striking mutant phenotypes. in this review, we summarize current knowledge of ppr-smr proteins focusing on arabidopsis and maize proteomic and mutant studies. we also examine their occurrence in other organisms and have determin ... | 2013 | 24004908 |
| the temperature sensitivity of a mutation in the essential trna modification enzyme trna methyltransferase d (trmd). | conditional temperature-sensitive (ts) mutations are important reagents to study essential genes. although it is commonly assumed that the ts phenotype of a specific mutation arises from thermal denaturation of the mutant enzyme, the possibility also exists that the mutation decreases the enzyme activity to a certain level at the permissive temperature and aggravates the negative effect further upon temperature upshifts. resolving these possibilities is important for exploiting the ts mutation f ... | 2013 | 23986443 |
| exploration of freely available web-interfaces for comparative homology modelling of microbial proteins. | this study was conducted to find the best suited freely available software for modelling of proteins by taking a few sample proteins. the proteins used were small to big in size with available crystal structures for the purpose of benchmarking. key players like phyre2, swiss-model, cphmodels-3.0, homer, (ps)2, (ps)(2)-v(2), modweb were used for the comparison and model generation. | 2013 | 24023424 |
| generation of a mouse model with down-regulated u50 snorna (snord50) expression and its organ-specific phenotypic modulation. | box c/d-type small nucleolar rnas (snornas) are functional rnas responsible for mediating 2'-o-ribose methylation of ribosomal rnas (rrnas) within the nucleolus. in the past years, evidence for the involvement of human u50 snorna in tumorigenesis has been accumulating. we previously identified u50hg, a non-protein-coding gene that hosted a box c/d-type u50 snorna, in a chromosomal breakpoint in a human b-cell lymphoma. mouse genome analysis revealed four mouse u50 (mu50) host-genes: three mu50hg ... | 2013 | 23991050 |
| reca protein recruits structural maintenance of chromosomes (smc)-like recn protein to dna double-strand breaks. | escherichia coli recn is an smc (structural maintenance of chromosomes) family protein that is required for dna double-strand break (dsb) repair. previous studies show that gfp-recn forms nucleoid-associated foci in response to dna damage, but the mechanism by which recn is recruited to the nucleoid is unknown. here, we show that the assembly of gfp-recn foci on the nucleoid in response to dna damage involves a functional interaction between recn and reca. a novel reca allele identified in this ... | 2013 | 23974212 |
| crystal structure of ruvc resolvase in complex with holliday junction substrate. | the key intermediate in genetic recombination is the holliday junction (hj), a four-way dna structure. at the end of recombination, hjs are cleaved by specific nucleases called resolvases. in gram-negative bacteria, this cleavage is performed by ruvc, a dimeric endonuclease that belongs to the retroviral integrase superfamily. here, we report the first crystal structure of ruvc in complex with a synthetic hj solved at 3.75 å resolution. the junction in the complex is in an unfolded 2-fold symmet ... | 2013 | 23980027 |
| structural phylogenomics retrodicts the origin of the genetic code and uncovers the evolutionary impact of protein flexibility. | the genetic code shapes the genetic repository. its origin has puzzled molecular scientists for over half a century and remains a long-standing mystery. here we show that the origin of the genetic code is tightly coupled to the history of aminoacyl-trna synthetase enzymes and their interactions with trna. a timeline of evolutionary appearance of protein domain families derived from a structural census in hundreds of genomes reveals the early emergence of the 'operational' rna code and the late i ... | 2013 | 23991065 |
| discovery of a potent benzoxaborole-based anti-pneumococcal agent targeting leucyl-trna synthetase. | streptococcus pneumoniae causes bacterial pneumonia with high mortality and morbidity. the emergency of multidrug-resistant bacteria threatens the treatment of the disease. leucyl-trna synthetase (leurs) plays an essential role in cellular translation and is an attractive drug target for antimicrobial development. here we report the compound zcl039, a benzoxaborole-based derivative of an2690, as a potent anti-pneumococcal agent that inhibits s. pneumoniae leurs (spleurs) activity. we show using ... | 2013 | 23959225 |
| the legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments. | legionella pneumophila uses aquatic protozoa as replication niche and protection from harsh environments. although l. pneumophila is not known to have a circadian clock, it encodes homologues of the kaibc proteins of cyanobacteria that regulate circadian gene expression. we show that l. pneumophila kaib, kaic and the downstream gene lpp1114, are transcribed as a unit under the control of the stress sigma factor rpos. kaic and kaib of l. pneumophila do not interact as evidenced by yeast and bacte ... | 2013 | 23957615 |
| the legionella pneumophila kai operon is implicated in stress response and confers fitness in competitive environments. | legionella pneumophila uses aquatic protozoa as replication niche and protection from harsh environments. although l. pneumophila is not known to have a circadian clock, it encodes homologues of the kaibc proteins of cyanobacteria that regulate circadian gene expression. we show that l. pneumophila kaib, kaic and the downstream gene lpp1114, are transcribed as a unit under the control of the stress sigma factor rpos. kaic and kaib of l. pneumophila do not interact as evidenced by yeast and bacte ... | 2013 | 23957615 |
| serial femtosecond x-ray diffraction of 30s ribosomal subunit microcrystals in liquid suspension at ambient temperature using an x-ray free-electron laser. | high-resolution ribosome structures determined by x-ray crystallography have provided important insights into the mechanism of translation. such studies have thus far relied on large ribosome crystals kept at cryogenic temperatures to reduce radiation damage. here, the application of serial femtosecond x-ray crystallography (sfx) using an x-ray free-electron laser (xfel) to obtain diffraction data from ribosome microcrystals in liquid suspension at ambient temperature is described. 30s ribosomal ... | 2013 | 23989164 |