| hemq: an iron-coproporphyrin oxidative decarboxylase for protoheme synthesis in firmicutes and actinobacteria. | genes for chlorite dismutase-like proteins are found widely among heme-synthesizing bacteria and some archaea. it is now known that among the firmicutes and actinobacteria these proteins do not possess chlorite dismutase activity but instead are essential for heme synthesis. these proteins, named hemq, are iron-coproporphyrin (coproheme) decarboxylases that catalyze the oxidative decarboxylation of coproheme iii into protoheme ix. as purified, hemqs do not contain bound heme, but readily bind ex ... | 2015 | 25711532 |
| aida: ab initio domain assembly for automated multi-domain protein structure prediction and domain-domain interaction prediction. | most proteins consist of multiple domains, independent structural and evolutionary units that are often reshuffled in genomic rearrangements to form new protein architectures. template-based modeling methods can often detect homologous templates for individual domains, but templates that could be used to model the entire query protein are often not available. | 2015 | 25701568 |
| structure of escherichia coli dgtp triphosphohydrolase: a hexameric enzyme with dna effector molecules. | the escherichia coli dgt gene encodes a dgtp triphosphohydrolase whose detailed role still remains to be determined. deletion of dgt creates a mutator phenotype, indicating that the dgtpase has a fidelity role, possibly by affecting the cellular dntp pool. in the present study, we have investigated the structure of the dgt protein at 3.1-å resolution. one of the obtained structures revealed a protein hexamer that contained two molecules of single-stranded dna. the presence of dna caused signific ... | 2015 | 25694425 |
| 2-thiouracil deprived of thiocarbonyl function preferentially base pairs with guanine rather than adenine in rna and dna duplexes. | 2-thiouracil-containing nucleosides are essential modified units of natural and synthetic nucleic acids. in particular, the 5-substituted-2-thiouridines (s2us) present in trna play an important role in tuning the translation process through codon-anticodon interactions. the enhanced thermodynamic stability of s2u-containing rna duplexes and the preferred s2u-a versus s2u-g base pairing are appreciated characteristics of s2u-modified molecular probes. recently, we have demonstrated that 2-thiouri ... | 2015 | 25690900 |
| rna polymerase-induced remodelling of nusa produces a pause enhancement complex. | pausing during transcription elongation is a fundamental activity in all kingdoms of life. in bacteria, the essential protein nusa modulates transcriptional pausing, but its mechanism of action has remained enigmatic. by combining structural and functional studies we show that a helical rearrangement induced in nusa upon interaction with rna polymerase is the key to its modulatory function. this conformational change leads to an allosteric re-positioning of conserved basic residues that could en ... | 2015 | 25690895 |
| synergistic effects of atp and rna binding to human dead-box protein ddx1. | rna helicases of the dead-box protein family form the largest group of helicases. the human dead-box protein 1 (ddx1) plays an important role in trna and mrna processing, is involved in tumor progression and is also hijacked by several virus families such as hiv-1 for replication and nuclear export. although important in many cellular processes, the mechanism of ddx1's enzymatic function is unknown. we have performed equilibrium titrations and transient kinetics to determine affinities for nucle ... | 2015 | 25690890 |
| identification of a second gtp-bound magnesium ion in archaeal initiation factor 2. | eukaryotic and archaeal translation initiation processes involve a heterotrimeric gtpase e/aif2 crucial for accuracy of start codon selection. in eukaryotes, the gtpase activity of eif2 is assisted by a gtpase-activating protein (gap), eif5. in archaea, orthologs of eif5 are not found and aif2 gtpase activity is thought to be non-assisted. however, no in vitro gtpase activity of the archaeal factor has been reported to date. here, we show that aif2 significantly hydrolyses gtp in vitro. within a ... | 2015 | 25690901 |
| arginine-rhamnosylation as new strategy to activate translation elongation factor p. | ribosome stalling at polyproline stretches is common and fundamental. in bacteria, translation elongation factor p (ef-p) rescues such stalled ribosomes, but only when it is post-translationally activated. in escherichia coli, activation of ef-p is achieved by (r)-β-lysinylation and hydroxylation of a conserved lysine. here we have unveiled a markedly different modification strategy in which a conserved arginine of ef-p is rhamnosylated by a glycosyltransferase (earp) using dtdp-l-rhamnose as a ... | 2015 | 25686373 |
| a prokaryotic twist on argonaute function. | argonaute proteins can be found in all three domains of life. in eukaryotic organisms, argonaute is, as the functional core of the rna-silencing machinery, critically involved in the regulation of gene expression. despite the mechanistic and structural similarities between archaeal, bacterial and eukaryotic argonaute proteins, the biological function of bacterial and archaeal argonautes has remained elusive. this review discusses new findings in the field that shed light on the structure and fun ... | 2015 | 25692904 |
| eukaryotic lyr proteins interact with mitochondrial protein complexes. | in eukaryotic cells, mitochondria host ancient essential bioenergetic and biosynthetic pathways. lyr (leucine/tyrosine/arginine) motif proteins (lyrms) of the complex1_lyr-like superfamily interact with protein complexes of bacterial origin. many lyr proteins function as extra subunits (lyrm3 and lyrm6) or novel assembly factors (lyrm7, lyrm8, acn9 and fmc1) of the oxidative phosphorylation (oxphos) core complexes. structural insights into complex i accessory subunits lyrm6 and lyrm3 have been p ... | 2015 | 25686363 |
| novel flp pilus biogenesis-dependent natural transformation. | natural transformation has been described in bacterial species spread through nearly all major taxonomic groups. however, the current understanding of the structural components and the regulation of competence development is derived from only a few model organisms. although natural transformation was discovered in members of the actinobacteria (high gc gram-positive bacteria) more than four decades ago, the structural components or the regulation of the competence system have not been studied in ... | 2015 | 25713572 |
| the bypass of zipa by overexpression of ftsn requires a previously unknown conserved ftsn motif essential for ftsa-ftsn interaction supporting a model in which ftsa monomers recruit late cell division proteins to the z ring. | assembly of the divisome in escherichia coli occurs in two temporally distinct steps. first, ftsz filaments attached to the membrane through interaction with ftsa and zipa coalesce into a z ring at midcell. then, additional proteins are recruited to the z ring in a hierarchical manner to form a complete divisome, activated by the arrival of ftsn. recently, we proposed that the interaction of ftsa with itself competes with its ability to recruit downstream division proteins (both require the ic d ... | 2015 | 25496259 |
| activity of select dehydrogenases with sepharose-immobilized n(6)-carboxymethyl-nad. | n(6)-carboxymethyl-nad (n(6)-cm-nad) can be used to immobilize nad onto a substrate containing terminal primary amines. we previously immobilized n(6)-cm-nad onto sepharose beads and showed that thermotoga maritima glycerol dehydrogenase could use the immobilized cofactor with cofactor recycling. we now show that saccharomyces cerevisiae alcohol dehydrogenase, rabbit muscle l-lactate dehydrogenase (type xi), bovine liver l-glutamic dehydrogenase (type iii), leuconostoc mesenteroides glucose-6-ph ... | 2015 | 25611453 |
| structural basis for transcription reactivation by rapa. | rna polymerase (rnap) loses activity during transcription as it stalls at various inactive states due to erratic translocation. reactivation of these stalled rnaps is essential for efficient rna synthesis. here we report a 4.7-å resolution crystal structure of the escherichia coli rnap core enzyme in complex with atpase rapa that is involved in reactivating stalled rnaps. the structure reveals that rapa binds at the rna exit channel of the rnap and makes the channel unable to accommodate the for ... | 2015 | 25646438 |
| distinct pathways of rna polymerase regulation by a phage-encoded factor. | transcription antitermination is a common strategy of gene expression regulation, but only a few transcription antitermination factors have been studied in detail. here, we dissect the transcription antitermination mechanism of xanthomonas oryzae virus xp10 protein p7, which binds host rna polymerase (rnap) and regulates both transcription initiation and termination. we show that p7 suppresses intrinsic termination by decreasing rnap pausing and increasing the transcription complex stability, in ... | 2015 | 25646468 |
| diversity in (p)ppgpp metabolism and effectors. | bacteria produce guanosine tetraphosphate and pentaphosphate, collectively named (p)ppgpp, in response to a variety of environmental stimuli. these two remarkable molecules regulate many cellular processes, including the central dogma processes and metabolism, to ensure survival and adaptation. work in escherichia coli laid the foundation for understanding the molecular details of (p)ppgpp and its cellular functions. as recent studies expand to other species, it is apparent that there exists con ... | 2015 | 25636134 |
| mutations in ribosomal proteins, rpl4 and rack1, suppress the phenotype of a thermospermine-deficient mutant of arabidopsis thaliana. | thermospermine acts in negative regulation of xylem differentiation and its deficient mutant of arabidopsis thaliana, acaulis5 (acl5), shows excessive xylem formation and severe dwarfism. studies of two dominant suppressors of acl5, sac51-d and sac52-d, have revealed that sac51 and sac52 encode a transcription factor and a ribosomal protein l10 (rpl10), respectively, and these mutations enhance translation of the sac51 mrna, which contains conserved upstream open reading frames in the 5' leader. ... | 2015 | 25625317 |
| advancing the development of glycated protein biosensing technology: next-generation sensing molecules. | research advances in biochemical molecules have led to the development of convenient and reproducible biosensing molecules for glycated proteins, such as those based on the enzymes fructosyl amino acid oxidase (faox) or fructosyl peptide oxidase (fpox). recently, more attractive biosensing molecules with potential applications in next-generation biosensing of glycated proteins have been aggressively reported. we review 2 such molecules, fructosamine 6-kinase (fn6k) and fructosyl amino acid-bindi ... | 2015 | 25627465 |
| role of δ1-pyrroline-5-carboxylate dehydrogenase supports mitochondrial metabolism and host-cell invasion of trypanosoma cruzi. | proline is crucial for energizing critical events throughout the life cycle of trypanosoma cruzi, the etiological agent of chagas disease. the proline breakdown pathway consists of two oxidation steps, both of which produce reducing equivalents as follows: the conversion of proline to δ(1)-pyrroline-5-carboxylate (p5c), and the subsequent conversion of p5c to glutamate. we have identified and characterized the δ(1)-pyrroline-5-carboxylate dehydrogenase from t. cruzi (tcp5cdh) and report here on ... | 2015 | 25623067 |
| engineering the genome of thermus thermophilus using a counterselectable marker. | thermus thermophilus is an extremely thermophilic bacterium that is widely used as a model thermophile, in large part due to its amenability to genetic manipulation. here we describe a system for the introduction of genomic point mutations or deletions using a counterselectable marker consisting of a conditionally lethal mutant allele of phes encoding the phenylalanyl-trna synthetase α-subunit. mutant phes with an a294g amino acid substitution renders cells sensitive to the phenylalanine analog ... | 2015 | 25605305 |
| structural insights into mis-regulation of protein kinase a in human tumors. | the extensively studied camp-dependent protein kinase a (pka) is involved in the regulation of critical cell processes, including metabolism, gene expression, and cell proliferation; consequentially, mis-regulation of pka signaling is implicated in tumorigenesis. recent genomic studies have identified recurrent mutations in the catalytic subunit of pka in tumors associated with cushing's syndrome, a kidney disorder leading to excessive cortisol production, and also in tumors associated with fibr ... | 2015 | 25605907 |
| redox state of flavin adenine dinucleotide drives substrate binding and product release in escherichia coli succinate dehydrogenase. | the complex ii family of enzymes, comprising respiratory succinate dehydrogenases and fumarate reductases, catalyzes reversible interconversion of succinate and fumarate. in contrast to the covalent flavin adenine dinucleotide (fad) cofactor assembled in these enzymes, soluble fumarate reductases (e.g., those from shewanella frigidimarina) that assemble a noncovalent fad cannot catalyze succinate oxidation but retain the ability to reduce fumarate. in this study, an sdha-h45a variant that elimin ... | 2015 | 25569225 |
| substrate trna recognition mechanism of eubacterial trna (m1a58) methyltransferase (trmi). | trmi generates n(1)-methyladenosine at position 58 (m(1)a58) in trna. the thermus thermophilus trna(phe) transcript was methylated efficiently by t. thermophilus trmi, whereas the yeast trna(phe) transcript was poorly methylated. fourteen chimeric trna transcripts derived from these two trnas revealed that trmi recognized the combination of aminoacyl stem, variable region, and t-loop. this was confirmed by 10 deletion trna variants: trmi methylated transcripts containing the aminoacyl stem, vari ... | 2015 | 25593312 |
| conformational changes of elongation factor g on the ribosome during trna translocation. | the universally conserved gtpase elongation factor g (ef-g) catalyzes the translocation of trna and mrna on the ribosome after peptide bond formation. despite numerous studies suggesting that ef-g undergoes extensive conformational rearrangements during translocation, high-resolution structures exist for essentially only one conformation of ef-g in complex with the ribosome. here, we report four atomic-resolution crystal structures of ef-g bound to the ribosome programmed in the pre- and posttra ... | 2015 | 25594181 |
| hydrazidase, a novel amidase signature enzyme that hydrolyzes acylhydrazides. | the degradation mechanisms of natural and artificial hydrazides have been elucidated. here we screened and isolated bacteria that utilize the acylhydrazide 4-hydroxybenzoic acid 1-phenylethylidene hydrazide (hbph) from soils. physiological and phylogenetic studies identified one bacterium as microbacterium sp. strain hm58-2, from which we purified intracellular hydrazidase, cloned its gene, and prepared recombinant hydrazidase using an escherichia coli expression system. the microbacterium sp. h ... | 2015 | 25583978 |
| structural biology. division of labor in transhydrogenase by alternating proton translocation and hydride transfer. | nadph/nadp(+) (the reduced form of nadp(+)/nicotinamide adenine dinucleotide phosphate) homeostasis is critical for countering oxidative stress in cells. nicotinamide nucleotide transhydrogenase (th), a membrane enzyme present in both bacteria and mitochondria, couples the proton motive force to the generation of nadph. we present the 2.8 å crystal structure of the transmembrane proton channel domain of th from thermus thermophilus and the 6.9 å crystal structure of the entire enzyme (holo-th). ... | 2015 | 25574024 |
| identification of fah domain-containing protein 1 (fahd1) as oxaloacetate decarboxylase. | fumarylacetoacetate hydrolase (fah) domain-containing proteins occur in both prokaryotes and eukaryotes, where they carry out diverse enzymatic reactions, probably related to structural differences in their respective fah domains; however, the precise relationship between structure of the fah domain and the associated enzyme function remains elusive. in mammals, three fah domain-containing proteins, fahd1, fahd2a, and fahd2b, are known; however, their enzymatic function, if any, remains to be de ... | 2015 | 25575590 |
| enzyme dynamics from nmr spectroscopy. | conspectus: biological activities of enzymes, including regulation or coordination of mechanistic stages preceding or following the chemical step, may depend upon kinetic or equilibrium changes in protein conformations. exchange of more open or flexible conformational states with more closed or constrained states can influence inhibition, allosteric regulation, substrate recognition, formation of the michaelis complex, side reactions, and product release. nmr spectroscopy has long been applied t ... | 2015 | 25574774 |
| specific and non-specific interactions of parb with dna: implications for chromosome segregation. | the segregation of many bacterial chromosomes is dependent on the interactions of parb proteins with centromere-like dna sequences called pars that are located close to the origin of replication. in this work, we have investigated the binding of bacillus subtilis parb to dna in vitro using a variety of biochemical and biophysical techniques. we observe tight and specific binding of a parb homodimer to the pars sequence. binding of parb to non-specific dna is more complex and displays apparent po ... | 2015 | 25572315 |
| association between intrinsic disorder and serine/threonine phosphorylation in mycobacterium tuberculosis. | serine/threonine phosphorylation is an important mechanism that is involved in the regulation of protein function. in eukaryotes, phosphorylation occurs predominantly in intrinsically disordered regions of proteins. though serine/threonine phosphorylation and protein disorder are much less prevalent in prokaryotes, some bacteria have high levels of serine/threonine phosphorylation and disorder, including the medically important m. tuberculosis. here i show that serine/threonine phosphorylation s ... | 2015 | 25648268 |
| nucleoid occlusion protein noc recruits dna to the bacterial cell membrane. | to proliferate efficiently, cells must co-ordinate division with chromosome segregation. in bacillus subtilis, the nucleoid occlusion protein noc binds to specific dna sequences (nbss) scattered around the chromosome and helps to protect genomic integrity by coupling the initiation of division to the progression of chromosome replication and segregation. however, how it inhibits division has remained unclear. here, we demonstrate that noc associates with the cell membrane via an n-terminal amphi ... | 2015 | 25568309 |
| cdc45 (cell division cycle protein 45) guards the gate of the eukaryote replisome helicase stabilizing leading strand engagement. | dna replication licensing is now understood to be the pathway that leads to the assembly of double hexamers of minichromosome maintenance (mcm2-7) at origin sites. cell division control protein 45 (cdc45) and gins proteins activate the latent mcm2-7 helicase by inducing allosteric changes through binding, forming a cdc45/mcm2-7/gins (cmg) complex that is competent to unwind duplex dna. the cmg has an active gate between subunits mcm2 and mcm5 that opens and closes in response to nucleotide bindi ... | 2015 | 25561522 |
| production of dioxygen in the dark: dismutases of oxyanions. | o₂-generating reactions are exceedingly rare in biology and difficult to mimic synthetically. perchlorate-respiring bacteria enzymatically detoxify chlorite (clo₂(-) ), the end product of the perchlorate (clo(4)(-) ) respiratory pathway, by rapidly converting it to dioxygen (o₂) and chloride (cl(-)). this reaction is catalyzed by a heme-containing protein, called chlorite dismutase (cld), which bears no structural or sequence relationships with known peroxidases or other heme proteins and is par ... | 2015 | 25707466 |
| high throughput screen identifies natural product inhibitor of phenylalanyl-trna synthetase from pseudomonas aeruginosa and streptococcus pneumoniae. | pseudomonas aeruginosa and streptococcus pneumoniae are causative agents in a wide range of infections. genes encoding proteins corresponding to phenylalanyl-trna synthetase (phers) were cloned from both bacteria. the two forms of phers were kinetically evaluated and the k(m)'s for p. aeruginosa phers with its three substrates, phenylalanine, atp and trna(phe) were determined to be 48, 200, and 1.2 µm, respectively, while the k(m)'s for s. pneumoniae phers with respect to phenylalanine, atp and ... | 2015 | 25601215 |
| crystallization and preliminary x-ray analysis of the nad+-reducing [nife] hydrogenase from hydrogenophilus thermoluteolus th-1. | nad+-reducing [nife] hydrogenases catalyze the oxidoreduction of dihydrogen concomitant with the interconversion of nad+ and nadh. here, the isolation, purification and crystallization of the nad+-reducing [nife] hydrogenase from hydrogenophilus thermoluteolus th-1 are reported. crystals of the nad+-reducing [nife] hydrogenase were obtained within one week from a solution containing polyethylene glycol using the sitting-drop vapour-diffusion method and micro-seeding. the crystal diffracted to 2. ... | 2015 | 25615977 |
| in pursuit of an accurate spatial and temporal model of biomolecules at the atomistic level: a perspective on computer simulation. | despite huge advances in the computational techniques available for simulating biomolecules at the quantum-mechanical, atomistic and coarse-grained levels, there is still a widespread perception amongst the experimental community that these calculations are highly specialist and are not generally applicable by researchers outside the theoretical community. in this article, the successes and limitations of biomolecular simulation and the further developments that are likely in the near future are ... | 2015 | 25615870 |
| metagenomic analysis of hot springs in central india reveals hydrocarbon degrading thermophiles and pathways essential for survival in extreme environments. | extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. india harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. the aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central india namel ... | 2016 | 28105025 |
| metagenomic analysis of hot springs in central india reveals hydrocarbon degrading thermophiles and pathways essential for survival in extreme environments. | extreme ecosystems such as hot springs are of great interest as a source of novel extremophilic species, enzymes, metabolic functions for survival and biotechnological products. india harbors hundreds of hot springs, the majority of which are not yet explored and require comprehensive studies to unravel their unknown and untapped phylogenetic and functional diversity. the aim of this study was to perform a large-scale metagenomic analysis of three major hot springs located in central india namel ... | 2016 | 28105025 |
| editorial: filamentous bacteriophage in bio/nano/technology, bacterial pathogenesis and ecology. | | 2016 | 28066406 |
| coupled atpase-adenylate kinase activity in abc transporters. | atp-binding cassette (abc) transporters, a superfamily of integral membrane proteins, catalyse the translocation of substrates across the cellular membrane by atp hydrolysis. here we demonstrate by nucleotide turnover and binding studies based on (31)p solid-state nmr spectroscopy that the abc exporter and lipid a flippase msba can couple atp hydrolysis to an adenylate kinase activity, where adp is converted into amp and atp. single-point mutations reveal that both atpase and adenylate kinase me ... | 2016 | 28004795 |
| mapping the membrane proteome of anaerobic gut fungi identifies a wealth of carbohydrate binding proteins and transporters. | engineered cell factories that convert biomass into value-added compounds are emerging as a timely alternative to petroleum-based industries. although often overlooked, integral membrane proteins such as solute transporters are pivotal for engineering efficient microbial chassis. anaerobic gut fungi, adapted to degrade raw plant biomass in the intestines of herbivores, are a potential source of valuable transporters for biotechnology, yet very little is known about the membrane constituents of t ... | 2016 | 27998268 |
| homology-based modeling of universal stress protein from listeria innocua up-regulated under acid stress conditions. | an universal stress protein (usp) expressed under acid stress condition by listeria innocua atcc 33090 was investigated. the usp was up-regulated not only in the stationary phase but also during the exponential growth phase. the three dimensional (3d) structure of usp was predicted using a combined proteomic and bioinformatics approach. phylogenetic analysis showed that the usp from listeria detected in our study was distant from the usps of other bacteria (such as pseudomonas spp., escherichia ... | 2016 | 28066336 |
| comparison of lipases and glycoside hydrolases as catalysts in synthesis reactions. | lipases and glycoside hydrolases have large similarities concerning reaction mechanisms. acyl-enzyme intermediates are formed during lipase-catalyzed reactions and in an analogous way, retaining glycoside hydrolases form glycosyl-enzyme intermediates during catalysis. in both cases, the covalent enzyme intermediates can react with water or other nucleophiles containing hydroxyl groups. simple alcohols are accepted as nucleophiles by both types of enzymes. lipases are used very successfully in sy ... | 2016 | 27995311 |
| comparison of lipases and glycoside hydrolases as catalysts in synthesis reactions. | lipases and glycoside hydrolases have large similarities concerning reaction mechanisms. acyl-enzyme intermediates are formed during lipase-catalyzed reactions and in an analogous way, retaining glycoside hydrolases form glycosyl-enzyme intermediates during catalysis. in both cases, the covalent enzyme intermediates can react with water or other nucleophiles containing hydroxyl groups. simple alcohols are accepted as nucleophiles by both types of enzymes. lipases are used very successfully in sy ... | 2016 | 27995311 |
| systematic analysis of the lysine acetylome in fusarium graminearum. | lysine acetylation in proteins is a ubiquitous and conserved post-translational modification, playing a critical regulatory role in almost every aspect of living cells. although known for many years, its function remains elusive in fusarium graminearum, one of the most important necrotrophic plant pathogens with huge economic impact. | 2016 | 27964708 |
| the mechanism of a formaldehyde-sensing transcriptional regulator. | most organisms are exposed to the genotoxic chemical formaldehyde, either from endogenous or environmental sources. therefore, biology has evolved systems to perceive and detoxify formaldehyde. the frmra(b) operon that is present in many bacteria represents one such system. the frmr protein is a transcriptional repressor that is specifically inactivated in the presence of formaldehyde, permitting expression of the formaldehyde detoxification machinery (frma and frmb, when the latter is present). ... | 2016 | 27934966 |
| dynamic complexes in the chaperonin-mediated protein folding cycle. | the groel-groes chaperonin system is probably one of the most studied chaperone systems at the level of the molecular mechanism. since the first reports of a bacterial gene involved in phage morphogenesis in 1972, these proteins have stimulated intensive research for over 40 years. during this time, detailed structural and functional studies have yielded constantly evolving concepts of the chaperonin mechanism of action. despite of almost three decades of research on this oligomeric protein, cer ... | 2016 | 28008398 |
| structure of the 40s ribosomal subunit of plasmodium falciparum by homology and de novo modeling. | generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. this is especially the case if a homologous crystal structure is already available. high-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of sc ... | 2016 | 28119814 |
| structure of the 40s ribosomal subunit of plasmodium falciparum by homology and de novo modeling. | generation of three dimensional structures of macromolecules using in silico structural modeling technologies such as homology and de novo modeling has improved dramatically and increased the speed by which tertiary structures of organisms can be generated. this is especially the case if a homologous crystal structure is already available. high-resolution structures can be rapidly created using only their sequence information as input, a process that has the potential to increase the speed of sc ... | 2016 | 28119814 |
| pb(2+) effects on growth, lipids, and protein and dna profiles of the thermophilic bacterium thermus thermophilus. | extremophiles are organisms able to thrive in extreme environmental conditions and some of them show the ability to survive high doses of heavy metals thanks to defensive mechanisms provided by primary and secondary metabolic products, i.e., extremolytes, lipids, and extremozymes. this is why there is a growing scientific and industrial interest in the use of thermophilic bacteria in a host of tasks, from the environmental detoxification of heavy metal to industrial activities, such as bio-machi ... | 2016 | 27929414 |
| improved in-cell structure determination of proteins at near-physiological concentration. | investigating three-dimensional (3d) structures of proteins in living cells by in-cell nuclear magnetic resonance (nmr) spectroscopy opens an avenue towards understanding the structural basis of their functions and physical properties under physiological conditions inside cells. in-cell nmr provides data at atomic resolution non-invasively, and has been used to detect protein-protein interactions, thermodynamics of protein stability, the behavior of intrinsically disordered proteins, etc. in cel ... | 2016 | 27910948 |
| identification of a highly conserved hypothetical protein ton_0340 as a probable manganese-dependent phosphatase. | a hypothetical protein ton_0340 of a thermococcus species is a protein conserved in a variety of organisms including human. herein, we present four different crystal structures of ton_0340, leading to the identification of an active-site cavity harboring a metal-binding site composed of six invariant aspartate and glutamate residues that coordinate one to three metal ions. biochemical and mutational analyses involving many phosphorous compounds show that ton_0340 is a mn2+-dependent phosphatase. ... | 2016 | 27907125 |
| structures of type iv pilins from thermus thermophilus demonstrate similarities with type ii secretion system pseudopilins. | type iv pilins are proteins which form polymers that extend from the surface of the bacterial cell; they are involved in mediating a wide variety of functions, including adhesion, motility and natural competence. here we describe the determination of the crystal structures of three type iva pilins proteins from the thermophile thermus thermophilus. they form part of a cluster of pilus-like proteins within the genome; our results show that one, tt1222, is very closely related to the main structur ... | 2016 | 27612581 |
| structural basis for the disaggregase activity and regulation of hsp104. | the hsp104 disaggregase is a two-ring atpase machine that rescues various forms of non-native proteins including the highly resistant amyloid fibers. the structural-mechanistic underpinnings of how the recovery of toxic protein aggregates is promoted and how this potent unfolding activity is prevented from doing collateral damage to cellular proteins are not well understood. here, we present structural and biochemical data revealing the organization of hsp104 from chaetomium thermophilum at 3.7 ... | 2016 | 27901467 |
| thermotoga maritima nusg: domain interaction mediates autoinhibition and thermostability. | nusg, the only universally conserved transcription factor, comprises an n- and a c-terminal domain (ntd, ctd) that are flexibly connected and move independently in escherichia coli and other organisms. in nusg from the hyperthermophilic bacterium thermotoga maritima (tmnusg), however, ntd and ctd interact tightly. this closed state stabilizes the ctd, but masks the binding sites for the interaction partners rho, nuse and rna polymerase (rnap), suggesting that tmnusg is autoinhibited. furthermore ... | 2016 | 27899597 |
| thermotoga maritima nusg: domain interaction mediates autoinhibition and thermostability. | nusg, the only universally conserved transcription factor, comprises an n- and a c-terminal domain (ntd, ctd) that are flexibly connected and move independently in escherichia coli and other organisms. in nusg from the hyperthermophilic bacterium thermotoga maritima (tmnusg), however, ntd and ctd interact tightly. this closed state stabilizes the ctd, but masks the binding sites for the interaction partners rho, nuse and rna polymerase (rnap), suggesting that tmnusg is autoinhibited. furthermore ... | 2016 | 27899597 |
| redox cofactors insertion in prokaryotic molybdoenzymes occurs via a conserved folding mechanism. | a major gap of knowledge in metalloproteins is the identity of the prefolded state of the protein before cofactor insertion. this holds for molybdoenzymes serving multiple purposes for life, especially in energy harvesting. this large group of prokaryotic enzymes allows for coordination of molybdenum or tungsten cofactors (mo/w-bispgd) and fe/s clusters. here we report the structural data on a cofactor-less enzyme, the nitrate reductase respiratory complex and characterize the conformational cha ... | 2016 | 27886223 |
| computing and applying atomic regulons to understand gene expression and regulation. | understanding gene function and regulation is essential for the interpretation, prediction, and ultimate design of cell responses to changes in the environment. an important step toward meeting the challenge of understanding gene function and regulation is the identification of sets of genes that are always co-expressed. these gene sets, atomic regulons (ars), represent fundamental units of function within a cell and could be used to associate genes of unknown function with cellular processes an ... | 2016 | 27933038 |
| a thermostable bilirubin-oxidizing enzyme from activated sludge isolated by a metagenomic approach. | a gene coding for a multicopper oxidase (bopa) was identified through the screening of a metagenomic library constructed from wastewater treatment activated sludge. the recombinant bopa protein produced in escherichia coli exhibited oxidation activity toward 2,2'-azino-bis-(3-ethylbenzothiazoline-6-sulfonate) (abts) in the presence of copper, suggesting that bopa is laccase. a bioinformatic analysis of the bopa gene sequence indicated that it has a phylogenetically bacterial origin, possibly der ... | 2016 | 27885197 |
| beyond antibodies: development of a novel protein scaffold based on human chaperonin 10. | human chaperonin 10 (hcpn10) was utilised as a novel scaffold for presenting peptides of therapeutic and diagnostic significance. molecular dynamic simulations and protein sizing analyses identified a peptide linker (p1) optimal for the formation of the quarternary hcpn10 heptamer structure. hcpn10 scaffold displaying peptides targeting factor viia (ce76-p1) and cd44 (cp7) were expressed in e. coli. functional studies of ce76-p1 indicated nanomolar affinity for factor viia (3 nm) similar to the ... | 2016 | 27874025 |
| first resistance mechanisms characterization in glyphosate-resistant leptochloa virgata. | leptochloa virgata (l.) p. beauv. is an annual weed common in citrus groves in the states of puebla and veracruz, mexico limiting their production. since 2010, several l. virgata populations were identified as being resistant to glyphosate, but studies of their resistance mechanisms developed by this species have been conducted. in this work, three glyphosate-resistant populations (r8, r14, and r15) collected in citrus orchards from mexico, were used to study their resistance mechanisms comparin ... | 2016 | 27917189 |
| a natural light-driven inward proton pump. | light-driven outward h(+) pumps are widely distributed in nature, converting sunlight energy into proton motive force. here we report the characterization of an oppositely directed h(+) pump with a similar architecture to outward pumps. a deep-ocean marine bacterium, parvularcula oceani, contains three rhodopsins, one of which functions as a light-driven inward h(+) pump when expressed in escherichia coli and mouse neural cells. detailed mechanistic analyses of the purified proteins reveal that ... | 2016 | 27853152 |
| boosting functionality of synthetic dna circuits with tailored deactivation. | molecular programming takes advantage of synthetic nucleic acid biochemistry to assemble networks of reactions, in vitro, with the double goal of better understanding cellular regulation and providing information-processing capabilities to man-made chemical systems. the function of molecular circuits is deeply related to their topological structure, but dynamical features (rate laws) also play a critical role. here we introduce a mechanism to tune the nonlinearities associated with individual no ... | 2016 | 27845324 |
| two proofreading steps amplify the accuracy of genetic code translation. | aminoacyl-trnas (aa-trnas) are selected by the messenger rna programmed ribosome in ternary complex with elongation factor tu (ef-tu) and gtp and then, again, in a proofreading step after gtp hydrolysis on ef-tu. we use trna mutants with different affinities for ef-tu to demonstrate that proofreading of aa-trnas occurs in two consecutive steps. first, aa-trnas in ternary complex with ef-tu·gdp are selected in a step where the accuracy increases linearly with increasing aa-trna affinity to ef-tu. ... | 2016 | 27837019 |
| identification of ybey-protein interactions involved in 16s rrna maturation and stress regulation in escherichia coli. | ybey is part of a core set of rnases in escherichia coli and other bacteria. this highly conserved endoribonuclease has been implicated in several important processes such as 16s rrna 3' end maturation, 70s ribosome quality control, and regulation of mrnas and small noncoding rnas, thereby affecting cellular viability, stress tolerance, and pathogenic and symbiotic behavior of bacteria. thus, ybey likely interacts with numerous protein or rna partners that are involved in various aspects of cell ... | 2016 | 27834201 |
| cryo-em study of start codon selection during archaeal translation initiation. | eukaryotic and archaeal translation initiation complexes have a common structural core comprising e/aif1, e/aif1a, the ternary complex (tc, e/aif2-gtp-met-trnai(met)) and mrna bound to the small ribosomal subunit. e/aif2 plays a crucial role in this process but how this factor controls start codon selection remains unclear. here, we present cryo-em structures of the full archaeal 30s initiation complex showing two conformational states of the tc. in the first state, the tc is bound to the riboso ... | 2016 | 27819266 |
| identification of essential genes in the salmonella phage spn3us reveals novel insights into giant phage head structure and assembly. | giant tailed bacterial viruses, or phages, such as pseudomonas aeruginosa phage ϕkz, have long genomes packaged into large, atypical virions. many aspects of ϕkz and related phage biology are poorly understood, mostly due to the fact that the functions of the majority of their proteins are unknown. we hypothesized that the salmonella enterica phage spn3us could be a useful model phage to address this gap in knowledge. the 240-kb spn3us genome shares a core set of 91 genes with ϕkz and related ph ... | 2016 | 27605673 |
| the hemq coprohaem decarboxylase generates reactive oxygen species: implications for the evolution of classical haem biosynthesis. | bacteria require a haem biosynthetic pathway for the assembly of a variety of protein complexes, including cytochromes, peroxidases, globins, and catalase. haem is synthesised via a series of tetrapyrrole intermediates, including non-metallated porphyrins, such as protoporphyrin ix, which is well known to generate reactive oxygen species in the presence of light and oxygen. staphylococcus aureus has an ancient haem biosynthetic pathway that proceeds via the formation of coproporphyrin iii, a les ... | 2016 | 27597779 |
| crystal structures of the atp-binding and adp-release dwells of the v1 rotary motor. | v1-atpases are highly conserved atp-driven rotary molecular motors found in various membrane systems. we recently reported the crystal structures for the enterococcus hirae a3b3df (v1) complex, corresponding to the catalytic dwell state waiting for atp hydrolysis. here we present the crystal structures for two other dwell states obtained by soaking nucleotide-free v1 crystals in adp. in the presence of 20 μm adp, two adp molecules bind to two of three binding sites and cooperatively induce confo ... | 2016 | 27807367 |
| avilamycin and evernimicin induce structural changes in rproteins ul16 and ctc that enhance the inhibition of a-site trna binding. | two structurally unique ribosomal antibiotics belonging to the orthosomycin family, avilamycin and evernimicin, possess activity against enterococci, staphylococci, and streptococci, and other gram-positive bacteria. here, we describe the high-resolution crystal structures of the eubacterial large ribosomal subunit in complex with them. their extended binding sites span the a-trna entrance corridor, thus inhibiting protein biosynthesis by blocking the binding site of the a-trna elbow, a mechanis ... | 2016 | 27791159 |
| structure of the 70s ribosome from human pathogen staphylococcus aureus. | comparative structural studies of ribosomes from various organisms keep offering exciting insights on how species-specific or environment-related structural features of ribosomes may impact translation specificity and its regulation. although the importance of such features may be less obvious within more closely related organisms, their existence could account for vital yet species-specific mechanisms of translation regulation that would involve stalling, cell survival and antibiotic resistance ... | 2016 | 27906650 |
| structures and stabilization of kinetoplastid-specific split rrnas revealed by comparing leishmanial and human ribosomes. | the recent success in ribosome structure determination by cryoem has opened the door to defining structural differences between ribosomes of pathogenic organisms and humans and to understand ribosome-targeting antibiotics. here, by direct electron-counting cryoem, we have determined the structures of the leishmania donovani and human ribosomes at 2.9 å and 3.6 å, respectively. our structure of the leishmanial ribosome elucidates the organization of the six fragments of its large subunit rrna (as ... | 2016 | 27752045 |
| characterization of a highly thermostable and organic solvent-tolerant copper-containing polyphenol oxidase with dye-decolorizing ability from kurthia huakuii lam0618t. | laccases are green biocatalysts that possess attractive advantages for the treatment of resistant environmental pollutants and dye effluents. a putative laccase-like gene, laclk, encoding a protein of 29.3 kda and belonging to the cu-oxidase_4 superfamily, was cloned and overexpressed in escherichia coli. the purified recombinant protein laclk (laclk) was able to oxidize typical laccase substrates such as 2,6-dimethoxyphenol and l-dopamine. the characteristic adsorption maximums of typical lacca ... | 2016 | 27741324 |
| microcystin-bound protein patterns in different cultures of microcystis aeruginosa and field samples. | micocystin (mc) exists in microcystis cells in two different forms, free and protein-bound. we examined the dynamic change in extracellular free mcs, intracellular free mcs and protein-bound mcs in both batch cultures and semi-continuous cultures, using high performance liquid chromatography and western blot. the results showed that the free mc per cell remained constant, while the quantity of protein-bound mcs increased with the growth of microcystis cells in both kinds of culture. significant ... | 2016 | 27754336 |
| functional characterization of a csor-cuea divergon in bradyrhizobium liaoningense ccnwsx0360, involved in copper, zinc and cadmium cotolerance. | random mutagenesis in a symbiotic nitrogen-fixing bradyrhizobium liaoningense ccnwsx0360 (bln0360) using tn5 identified five copper (cu) resistance-related genes. they were functionally sorted into three groups: transmembrane transport (cuea and tolc); oxidation (copa); and protection of the membrane barrier (lpte and ctpa). the gene cuea, together with the upstream csor (cu-sensitive operon repressor), constituted a csor-cuea divergon which plays a crucial role in cu homeostasis. deletion of cu ... | 2016 | 27725778 |
| structural characterization of antibiotic self-immunity trna synthetase in plant tumour biocontrol agent. | antibiotic-producing microbes evolved self-resistance mechanisms to avoid suicide. the biocontrol agrobacterium radiobacter k84 secretes the trojan horse antibiotic agrocin 84 that is selectively transported into the plant pathogen a. tumefaciens and processed into the toxin tm84. we previously showed that tm84 employs a unique trna-dependent mechanism to inhibit leucyl-trna synthetase (leurs), while the tm84-producer prevents self-poisoning by expressing a resistant leurs agnb2. we now identify ... | 2016 | 27713402 |
| in vitro engineering of novel bioactivity in the natural enzymes. | enzymes catalyze various biochemical functions with high efficiency and specificity. in vitro design of the enzyme leads to novel bioactivity in this natural biomolecule that give answers of some vital questions like crucial residues in binding with substrate, molecular evolution, cofactor specificity etc. enzyme engineering technology involves directed evolution, rational designing, semi-rational designing, and structure-based designing using chemical modifications. similarly, combined computat ... | 2016 | 27774447 |
| mechanism of ph-dependent activation of the sodium-proton antiporter nhaa. | escherichia coli nhaa is a prototype sodium-proton antiporter, which has been extensively characterized by x-ray crystallography, biochemical and biophysical experiments. however, the identities of proton carriers and details of ph-regulated mechanism remain controversial. here we report constant ph molecular dynamics data, which reveal that nhaa activation involves a net charge switch of a ph sensor at the entrance of the cytoplasmic funnel and opening of a hydrophobic gate at the end of the fu ... | 2016 | 27708266 |
| nusg inhibits rna polymerase backtracking by stabilizing the minimal transcription bubble. | universally conserved factors from nusg family bind at the upstream fork junction of transcription elongation complexes and modulate rna synthesis in response to translation, processing, and folding of the nascent rna. escherichia coli nusg enhances transcription elongation in vitro by a poorly understood mechanism. here we report that e. coli nusg slows gre factor-stimulated cleavage of the nascent rna, but does not measurably change the rates of single nucleotide addition and translocation by ... | 2016 | 27697152 |
| target and non-target site mechanisms developed by glyphosate-resistant hairy beggarticks (bidens pilosa l.) populations from mexico. | in 2014 hairy beggarticks (bidens pilosa l.) has been identified as being glyphosate-resistant in citrus orchards from mexico. the target and non-target site mechanisms involved in the response to glyphosate of two resistant populations (r1 and r2) and one susceptible (s) were studied. experiments of dose-response, shikimic acid accumulation, uptake-translocation, enzyme activity and 5-enolpyruvyl shikimate-3-phosphate synthase (epsps) gene sequencing were carried out in each population. the r1 ... | 2016 | 27752259 |
| a cascade of thermophilic enzymes as an approach to the synthesis of modified nucleotides. | we propose a new approach for the synthesis of biologically important nucleotides which includes a multi-enzymatic cascade conversion of d-pentoses into purine nucleotides. the approach exploits nucleic acid exchange enzymes from thermophilic microorganisms: ribokinase, phosphoribosylpyrophosphate synthetase, and adenine phosphoribosyltransferase. we cloned the ribokinase gene from thermus sp. 2.9, as well as two different genes of phosphoribosylpyrophosphate synthetase (prpp-synthetase) and the ... | 2016 | 28050269 |
| ns-μs time-resolved step-scan ftir of ba₃ oxidoreductase from thermus thermophilus: protonic connectivity of w941-w946-w927. | time-resolved step-scan ftir spectroscopy has been employed to probe the dynamics of the ba₃ oxidoreductase from thermus thermophilus in the ns-μs time range and in the ph/pd 6-9 range. the data revealed a ph/pd sensitivity of the d372 residue and of the ring-a propionate of heme a₃. based on the observed transient changes a model in which the protonic connectivity of w941-w946-927 to the d372 and the ring-a propionate of heme a₃ is described. | 2016 | 27690021 |
| birth of archaeal cells: molecular phylogenetic analyses of g1p dehydrogenase, g3p dehydrogenases, and glycerol kinase suggest derived features of archaeal membranes having g1p polar lipids. | bacteria and eukarya have cell membranes with sn-glycerol-3-phosphate (g3p), whereas archaeal membranes contain sn-glycerol-1-phosphate (g1p). determining the time at which cells with either g3p-lipid membranes or g1p-lipid membranes appeared is important for understanding the early evolution of terrestrial life. to clarify this issue, we reconstructed molecular phylogenetic trees of g1pdh (g1p dehydrogenase; egsa/aram) which is responsible for g1p synthesis and g3pdhs (g3p dehydrogenase; gpsa a ... | 2016 | 27774041 |
| unexpected functional implication of a stable succinimide in the structural stability of methanocaldococcus jannaschii glutaminase. | protein ageing is often mediated by the formation of succinimide intermediates. these short-lived intermediates derive from asparaginyl deamidation and aspartyl dehydration and are rapidly converted into β-aspartyl or d-aspartyl residues. here we report the presence of a highly stable succinimide intermediate in the glutaminase subunit of gmp synthetase from the hyperthermophile methanocaldoccocus jannaschii. by comparing the biophysical properties of the wild-type protein and of several mutants ... | 2016 | 27677693 |
| analysis of the core genome and pan-genome of autotrophic acetogenic bacteria. | acetogens are obligate anaerobic bacteria capable of reducing carbon dioxide (co2) to multicarbon compounds coupled to the oxidation of inorganic substrates, such as hydrogen (h2) or carbon monoxide (co), via the wood-ljungdahl pathway. owing to the metabolic capability of co2 fixation, much attention has been focused on understanding the unique pathways associated with acetogens, particularly their metabolic coupling of co2 fixation to energy conservation. most known acetogens are phylogenetica ... | 2016 | 27733845 |
| uniformity of peptide release is maintained by methylation of release factors. | termination of protein synthesis on the ribosome is catalyzed by release factors (rfs), which share a conserved glycine-glycine-glutamine (ggq) motif. the glutamine residue is methylated in vivo, but a mechanistic understanding of its contribution to hydrolysis is lacking. here, we show that the modification, apart from increasing the overall rate of termination on all dipeptides, substantially increases the rate of peptide release on a subset of amino acids. in the presence of unmethylated rfs, ... | 2016 | 27681416 |
| quantifying the biases in metagenome mining for realistic assessment of microbial ecology of naturally fermented foods. | cultivation-independent investigation of microbial ecology is biased by the dna extraction methods used. we aimed to quantify those biases by comparative analysis of the metagenome mined from four diverse naturally fermented foods (bamboo shoot, milk, fish, soybean) using eight different dna extraction methods with different cell lysis principles. our findings revealed that the enzymatic lysis yielded higher eubacterial and yeast metagenomic dna from the food matrices compared to the widely used ... | 2016 | 27669673 |
| metagenomics of thermophiles with a focus on discovery of novel thermozymes. | microbial populations living in environments with temperatures above 50°c (thermophiles) have been widely studied, increasing our knowledge in the composition and function of these ecological communities. since these populations express a broad number of heat-resistant enzymes (thermozymes), they also represent an important source for novel biocatalysts that can be potentially used in industrial processes. the integrated study of the whole-community dna from an environment, known as metagenomics ... | 2016 | 27729905 |
| cryptosporidium and toxoplasma parasites are inhibited by a benzoxaborole targeting leucyl-trna synthetase. | the apicomplexan parasites cryptosporidium and toxoplasma are serious threats to human health. cryptosporidiosis is a severe diarrheal disease in malnourished children and immunocompromised individuals, with the only fda-approved drug treatment currently being nitazoxanide. the existing therapies for toxoplasmosis, an important pathology in immunocompromised individuals and pregnant women, also have serious limitations. with the aim of developing alternative therapeutic options to address these ... | 2016 | 27431220 |
| molecular insights into substrate recognition and catalytic mechanism of the chaperone and fkbp peptidyl-prolyl isomerase slyd. | peptidyl-prolyl isomerases (ppiases) catalyze cis/trans isomerization of peptidyl-prolyl bonds, which is often rate-limiting for protein folding. slyd is a two-domain enzyme containing both a ppiase fk506-binding protein (fkbp) domain and an insert-in-flap (if) chaperone domain. to date, the interactions of these domains with unfolded proteins have remained rather obscure, with structural information on binding to the fkbp domain being limited to complexes involving various inhibitor compounds o ... | 2016 | 27664121 |
| large-scale movements of if3 and trna during bacterial translation initiation. | in bacterial translational initiation, three initiation factors (ifs 1-3) enable the selection of initiator trna and the start codon in the p site of the 30s ribosomal subunit. here, we report 11 single-particle cryo-electron microscopy (cryoem) reconstructions of the complex of bacterial 30s subunit with initiator trna, mrna, and ifs 1-3, representing different steps along the initiation pathway. if1 provides key anchoring points for if2 and if3, thereby enhancing their activities. if2 position ... | 2016 | 27662086 |
| avoidance of stochastic rna interactions can be harnessed to control protein expression levels in bacteria and archaea. | a critical assumption of gene expression analysis is that mrna abundances broadly correlate with protein abundance, but these two are often imperfectly correlated. some of the discrepancy can be accounted for by two important mrna features: codon usage and mrna secondary structure. we present a new global factor, called mrna:ncrna avoidance, and provide evidence that avoidance increases translational efficiency. we also demonstrate a strong selection for the avoidance of stochastic mrna:ncrna in ... | 2016 | 27642845 |
| molecular basis of cobalamin-dependent rna modification. | queuosine (q) was discovered in the wobble position of a transfer rna (trna) 47 years ago, yet the final biosynthetic enzyme responsible for q-maturation, epoxyqueuosine (oq) reductase (queg), was only recently identified. queg is a cobalamin (cbl)-dependent, [4fe-4s] cluster-containing protein that produces the hypermodified nucleoside q in situ on four trnas. to understand how queg is able to perform epoxide reduction, an unprecedented reaction for a cbl-dependent enzyme, we have determined a ... | 2016 | 27638883 |
| specific internalisation of gold nanoparticles into engineered porous protein cages via affinity binding. | porous protein cages are supramolecular protein self-assemblies presenting pores that allow the access of surrounding molecules and ions into their core in order to store and transport them in biological environments. protein cages' pores are attractive channels for the internalisation of inorganic nanoparticles and an alternative for the preparation of hybrid bioinspired nanoparticles. however, strategies based on nanoparticle transport through the pores are largely unexplored, due to the diffi ... | 2016 | 27622533 |
| n-acetylgalatosamine-mediated regulation of the aga operon by agar in streptococcus pneumoniae. | here, we analyze the transcriptomic response of streptococcus pneumoniae d39 to n-acetylgalactosamine (naga). transcriptome comparison of s. pneumoniae d39 grown in nagam17 (0.5% naga + m17) to that grown in gm17 (0.5% glucose + m17) revealed the elevated expression of various carbon metabolic genes/operons, including a pts operon (denoted here as the aga operon), which is putatively involved in naga transport and utilization, in the presence of naga. we further studied the role of a gntr-family ... | 2016 | 27672623 |
| inhibition of bacterial rnase p rna by phenothiazine derivatives. | there is a need to identify novel scaffolds and targets to develop new antibiotics. methylene blue is a phenothiazine derivative, and it has been shown to possess anti-malarial and anti-trypanosomal activities. here, we show that different phenothiazine derivatives and pyronine g inhibited the activities of three structurally different bacterial rnase p rnas (rprs), including that from mycobacterium tuberculosis, with ki values in the lower μm range. interestingly, three antipsychotic phenothiaz ... | 2016 | 27618117 |
| purification, characterization, cytotoxicity and anticancer activities of l-asparaginase, anti-colon cancer protein, from the newly isolated alkaliphilic streptomyces fradiae neae-82. | l-asparaginase is an important enzyme as therapeutic agents used in combination with other drugs in the treatment of acute lymphoblastic leukemia. a newly isolated actinomycetes strain, streptomyces sp. neae-82, was potentially producing extracellular l-asparaginase, it was identified as streptomyces fradiae neae-82, sequencing product was deposited in the genbank database under accession number kj467538. l-asparaginase was purified from the crude enzyme using ammonium sulfate precipitation, dia ... | 2016 | 27605431 |
| chemistry and molecular dynamics simulations of heme b-hemq and coproheme-hemq. | recently, a novel pathway for heme b biosynthesis in gram-positive bacteria has been proposed. the final poorly understood step is catalyzed by an enzyme called hemq and includes two decarboxylation reactions leading from coproheme to heme b. coproheme has been suggested to act as both substrate and redox active cofactor in this reaction. in the study presented here, we focus on hemqs from listeria monocytogenes (lmhemq) and staphylococcus aureus (sahemq) recombinantly produced as apoproteins in ... | 2016 | 27599156 |
| atomic structure of an archaeal gan suggests its dual roles as an exonuclease in dna repair and a cmg component in dna replication. | in eukaryotic dna replication initiation, hexameric mcm (mini-chromosome maintenance) unwinds the template double-stranded dna to form the replication fork. mcm is activated by two proteins, cdc45 and gins, which constitute the 'cmg' unwindosome complex together with the mcm core. the archaeal dna replication system is quite similar to that of eukaryotes, but only limited knowledge about the dna unwinding mechanism is available, from a structural point of view. here, we describe the crystal stru ... | 2016 | 27599844 |
| crystal structure of the two-subunit trna m(1)a58 methyltransferase trm6-trm61 from saccharomyces cerevisiae. | the n(1) methylation of adenine at position 58 (m(1)a58) of trna is an important post-transcriptional modification, which is vital for maintaining the stability of the initiator methionine trnai(met). in eukaryotes, this modification is performed by the trm6-trm61 holoenzyme. to understand the molecular mechanism that underlies the cooperation of trm6 and trm61 in the methyl transfer reaction, we determined the crystal structure of trm6-trm61 holoenzyme from saccharomyces cerevisiae in the prese ... | 2016 | 27582183 |