| chemical engineering of the peptidyl transferase center reveals an important role of the 2'-hydroxyl group of a2451. | the main enzymatic reaction of the large ribosomal subunit is peptide bond formation. ribosome crystallography showed that a2451 of 23s rrna makes the closest approach to the attacking amino group of aminoacyl-trna. mutations of a2451 had relatively small effects on transpeptidation and failed to unequivocally identify the crucial functional group(s). here, we employed an in vitro reconstitution system for chemical engineering the peptidyl transferase center by introducing non-natural nucleoside ... | 2005 | 15767286 |
| participation of the trna a76 hydroxyl groups throughout translation. | the free 2'-3' cis-diol at the 3'-terminus of trna provides a unique juxtaposition of functional groups that play critical roles during protein synthesis. the translation process involves universally conserved chemistry at almost every stage of this multistep procedure, and the 2'- and 3'-ohs are in the immediate vicinity of chemistry at each step. the cis-diol contribution affects steps ranging from trna aminoacylation to peptide bond formation. the contributions have been studied in assays rel ... | 2006 | 16681365 |
| structural perspective on mutations affecting the function of multisubunit rna polymerases. | high-resolution crystallographic structures of multisubunit rna polymerases (rnaps) have increased our understanding of transcriptional mechanisms. based on a thorough review of the literature, we have compiled the mutations affecting the function of multisubunit rna polymerases, many of which having been generated and studied prior to the publication of the first high-resolution structure, and highlighted the positions of the altered amino acids in the structures of both the prokaryotic and euk ... | 2006 | 16524917 |
| recognition of aminoacyl-trna: a common molecular mechanism revealed by cryo-em. | the accuracy of ribosomal translation is achieved by an initial selection and a proofreading step, mediated by ef-tu, which forms a ternary complex with aminoacyl(aa)-trna. to study the binding modes of different aa-trnas, we compared cryo-em maps of the kirromycin-stalled ribosome bound with ternary complexes containing phe-trna(phe), trp-trna(trp), or leu-trna(leui). the three maps suggest a common binding manner of cognate aa-trnas in their specific binding with both the ribosome and ef-tu. a ... | 2008 | 19020518 |
| organization of an activator-bound rna polymerase holoenzyme. | transcription initiation involves the conversion from closed promoter complexes, comprising rna polymerase (rnap) and double-stranded promoter dna, to open complexes, in which the enzyme is able to access the dna template in a single-stranded form. the complex between bacterial rnap and its major variant sigma factor sigma(54) remains as a closed complex until atp hydrolysis-dependent remodeling by activator proteins occurs. this remodeling facilitates dna melting and allows the transition to th ... | 2008 | 18995832 |
| rifamycins do not function by allosteric modulation of binding of mg2+ to the rna polymerase active center. | rifamycin antibacterial agents inhibit bacterial rna polymerase (rnap) by binding to a site adjacent to the rnap active center and preventing synthesis of rna products >2-3 nt in length. recently, artsimovitch et al. [(2005) cell 122:351-363] proposed that rifamycins function by allosteric modulation of binding of mg(2+) to the rnap active center and presented three lines of biochemical evidence consistent with this proposal. here, we show that rifamycins do not affect the affinity of binding of ... | 2008 | 18787125 |
| enzymes used in molecular biology: a useful guide. | since molecular cloning has become routine laboratory technique, manufacturers offer countless sources of enzymes to generate and manipulate nucleic acids. thus, selecting the appropriate enzyme for a specific task may seem difficult to the novice. this review aims at providing the readers with some cues for understanding the function and specificities of the different sources of polymerases, ligases, nucleases, phosphatases, methylases, and topoisomerases used for molecular cloning. we provide ... | 2008 | 18766469 |
| advances in bacterial promoter recognition and its control by factors that do not bind dna. | early work identified two promoter regions, the -10 and -35 elements, that interact sequence specifically with bacterial rna polymerase (rnap). however, we now know that several additional promoter elements contact rnap and influence transcription initiation. furthermore, our picture of promoter control has evolved beyond one in which regulation results solely from activators and repressors that bind to dna sequences near the rnap binding site: many important transcription factors bind directly ... | 2008 | 18521075 |
| on helicases and other motor proteins. | helicases are molecular machines that utilize energy derived from atp hydrolysis to move along nucleic acids and to separate base-paired nucleotides. the movement of the helicase can also be described as a stationary helicase that pumps nucleic acid. recent structural data for the hexameric e1 helicase of papillomavirus in complex with single-stranded dna and mgadp has provided a detailed atomic and mechanistic picture of its atp-driven dna translocation. the structural and mechanistic features ... | 2008 | 18329872 |
| "hot cores" in proteins: comparative analysis of the apolar contact area in structures from hyper/thermophilic and mesophilic organisms. | a wide variety of stabilizing factors have been invoked so far to elucidate the structural basis of protein thermostability. these include, amongst the others, a higher number of ion-pairs interactions and hydrogen bonds, together with a better packing of hydrophobic residues. it has been frequently observed that packing of hydrophobic side chains is improved in hyperthermophilic proteins, when compared to their mesophilic counterparts. in this work, protein crystal structures from hyper/thermop ... | 2008 | 18312638 |
| macromolecular micromovements: how rna polymerase translocates. | multi-subunit dna-dependent rna polymerases synthesize rna molecules thousands of nucleotides long. the reiterative reaction of nucleotide condensation occurs at rates of tens of nucleotides per second, invariably linked to the translocation of the enzyme along the dna template, or threading of the dna and the nascent rna molecule through the enzyme. reiteration of the nucleotide addition/translocation cycle without dissociation from the dna and rna requires both isomorphic and metamorphic confo ... | 2009 | 19889534 |
| elongation in translation as a dynamic interaction among the ribosome, trna, and elongation factors ef-g and ef-tu. | the ribosome is a complex macromolecular machine that translates the message encoded in the messenger rna and synthesizes polypeptides by linking the individual amino acids carried by the cognate transfer rnas (trnas). the protein elongation cycle, during which the trnas traverse the ribosome in a coordinated manner along a path of more than 100 a, is facilitated by large-scale rearrangements of the ribosome. these rearrangements go hand in hand with conformational changes of trna as well as elo ... | 2009 | 20025795 |
| hydrogen bonding and packing density are factors most strongly connected to limiting sites of high flexibility in the 16s rrna in the 30s ribosome. | conformational flexibility in structured rna frequently is critical to function. the 30s ribosomal subunit exists in different conformations in different functional states due to changes in the central part of the 16s rrna. we are interested in evaluating the factors that might be responsible for restricting flexibility to specific parts of the 16s rrna using biochemical data obtained from the 30s subunit in solution. this problem was approached taking advantage of the observation that there mus ... | 2009 | 19643000 |
| rna polymerase active center: the molecular engine of transcription. | rna polymerase (rnap) is a complex molecular machine that governs gene expression and its regulation in all cellular organisms. to accomplish its function of accurately producing a full-length rna copy of a gene, rnap performs a plethora of chemical reactions and undergoes multiple conformational changes in response to cellular conditions. at the heart of this machine is the active center, the engine, which is composed of distinct fixed and moving parts that serve as the ultimate acceptor of reg ... | 2009 | 19489723 |
| the nucleotide addition cycle of rna polymerase is controlled by two molecular hinges in the bridge helix domain. | cellular rna polymerases (rnaps) are complex molecular machines that combine catalysis with concerted conformational changes in the active center. previous work showed that kinking of a hinge region near the c-terminus of the bridge helix (bh-h(c)) plays a critical role in controlling the catalytic rate. | 2010 | 21034443 |
| the architecture of rna polymerase fidelity. | the basis for transcriptional fidelity by rna polymerase is not understood, but the 'trigger loop', a conserved structural element that is rearranged in the presence of correct substrate nucleotides, is thought to be critical. a study just published in bmc biology sheds new light on the ways in which the trigger loop may promote selection of correct nucleotide triphosphate substrates. see research article http://www.biomedcentral.com/1741-7007/8/54. | 2010 | 20598112 |
| modulation of rna polymerase activity through the trigger loop folding. | folding of the trigger loop of rna polymerase promotes nucleotide addition through creating a closed, catalytically competent conformation of the active center. here, we discuss the impact of adjacent rna polymerase elements, including the f loop and the jaw domain, as well as external regulatory factors on the trigger loop folding and catalysis. | 2010 | 21326898 |
| stepwise mechanism for transcription fidelity. | transcription is the first step of gene expression and is characterized by a high fidelity of rna synthesis. during transcription, the rna polymerase active centre discriminates against not just non-complementary ribo ntp substrates but also against complementary 2'- and 3'-deoxy ntps. a flexible domain of the rna polymerase active centre, the trigger loop, was shown to play an important role in this process, but the mechanisms of this participation remained elusive. | 2010 | 20459653 |
| non-canonical dna transcription enzymes and the conservation of two-barrel rna polymerases. | dna transcription depends on multimeric rna polymerases that are exceptionally conserved in all cellular organisms, with an active site region of >500 amino acids mainly harboured by their rpb1 and rpb2 subunits. together with the distantly related eukaryotic rna-dependent polymerases involved in gene silencing, they form a monophyletic family of ribonucleotide polymerases with a similarly organized active site region based on two double-psi barrels. recent viral and phage genome sequencing have ... | 2010 | 20360047 |
| the bridge helix of rna polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement. | the availability of in vitro assembly systems to produce recombinant archaeal rna polymerases (rnaps) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying rnap function. over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. the bridge helix domain, which appears in numerous ... | 2011 | 22312317 |
| the bridge helix of rna polymerase acts as a central nanomechanical switchboard for coordinating catalysis and substrate movement. | the availability of in vitro assembly systems to produce recombinant archaeal rna polymerases (rnaps) offers one of the most powerful experimental tools for investigating the still relatively poorly understood molecular mechanisms underlying rnap function. over the last few years, we pioneered new robot-based high-throughput mutagenesis approaches to study structure/function relationships within various domains surrounding the catalytic center. the bridge helix domain, which appears in numerous ... | 2011 | 22312317 |
| transcription initiation factor dksa has diverse effects on rna chain elongation. | bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ... | 2011 | 22210857 |
| transcription initiation factor dksa has diverse effects on rna chain elongation. | bacterial transcription factors dksa and greb belong to a family of coiled-coil proteins that bind within the secondary channel of rna polymerase (rnap). these proteins display structural homology but play different regulatory roles. dksa disrupts rnap interactions with promoter dna and inhibits formation of initiation complexes, sensitizing rrna synthesis to changes in concentrations of ppgpp and ntps. gre proteins remodel the rnap active site and facilitate cleavage of the nascent rna in elong ... | 2011 | 22210857 |
| the dna exonucleases of escherichia coli. | dna exonucleases, enzymes that hydrolyze phosphodiester bonds in dna from a free end, play important cellular roles in dna repair, genetic recombination and mutation avoidance in all organisms. this article reviews the structure, biochemistry, and biological functions of the 17 exonucleases currently identified in the bacterium escherichia coli. these include the exonucleases associated with dna polymerases i (pola), ii (polb), and iii (dnaq/mutd); exonucleases i (xona/sbcb), iii (xtha), iv, vii ... | 2011 | 26442508 |
| enzymatic synthesis of long double-stranded dna labeled with haloderivatives of nucleobases in a precisely pre-determined sequence. | restriction endonucleases are widely applied in recombinant dna technology. among them, enzymes of class iis, which cleave dna beyond recognition sites, are especially useful. we use bsai enzyme for the pinpoint introduction of halogen nucleobases into dna. this has been done for the purpose of anticancer radio- and phototherapy that is our long-term objective. | 2011 | 21864341 |
| genetic tool development underpins recent advances in thermophilic whole-cell biocatalysts. | the environmental value of sustainably producing bioproducts from biomass is now widely appreciated, with a primary target being the economic production of fuels such as bioethanol from lignocellulose. the application of thermophilic prokaryotes is a rapidly developing niche in this field, driven by their known catabolic versatility with lignocellulose-derived carbohydrates. fundamental to the success of this work has been the development of reliable genetic and molecular systems. these technica ... | 2011 | 21310009 |
| microbial ecology of the dark ocean above, at, and below the seafloor. | the majority of life on earth--notably, microbial life--occurs in places that do not receive sunlight, with the habitats of the oceans being the largest of these reservoirs. sunlight penetrates only a few tens to hundreds of meters into the ocean, resulting in large-scale microbial ecosystems that function in the dark. our knowledge of microbial processes in the dark ocean-the aphotic pelagic ocean, sediments, oceanic crust, hydrothermal vents, etc.-has increased substantially in recent decades. ... | 2011 | 21646433 |
| mechanism of bacterial transcription initiation: rna polymerase - promoter binding, isomerization to initiation-competent open complexes, and initiation of rna synthesis. | initiation of rna synthesis from dna templates by rna polymerase (rnap) is a multi-step process, in which initial recognition of promoter dna by rnap triggers a series of conformational changes in both rnap and promoter dna. the bacterial rnap functions as a molecular isomerization machine, using binding free energy to remodel the initial recognition complex, placing downstream duplex dna in the active site cleft and then separating the nontemplate and template strands in the region surrounding ... | 2011 | 21371479 |
| x-ray crystal structures elucidate the nucleotidyl transfer reaction of transcript initiation using two nucleotides. | we have determined the x-ray crystal structures of the pre- and postcatalytic forms of the initiation complex of bacteriophage n4 rna polymerase that provide the complete set of atomic images depicting the process of transcript initiation by a single-subunit rna polymerase. as observed during t7 rna polymerase transcript elongation, substrate loading for the initiation process also drives a conformational change of the o-helix, but only the correct base pairing between the +2 substrate and dna b ... | 2011 | 21321236 |
| rna polymerase-promoter interactions determining different stability of the escherichia coli and thermus aquaticus transcription initiation complexes. | transcription initiation complexes formed by bacterial rna polymerases (rnaps) exhibit dramatic species-specific differences in stability, leading to different strategies of transcription regulation. the molecular basis for this diversity is unclear. promoter complexes formed by rnap from thermus aquaticus (taq) are considerably less stable than escherichia coli rnap promoter complexes, particularly at temperatures below 37°c. here, we used a fluorometric rnap molecular beacon assay to discern p ... | 2012 | 23087380 |
| interplay of dna repair with transcription: from structures to mechanisms. | many dna transactions are crucial for maintaining genomic integrity and faithful transfer of genetic information but remain poorly understood. an example is the interplay between nucleotide excision repair (ner) and transcription, also known as transcription-coupled dna repair (tcr). discovered decades ago, the mechanisms for tcr have remained elusive, not in small part due to the scarcity of structural studies of key players. here we summarize recent structural information on ner/tcr factors, f ... | 2012 | 23084398 |
| altered large-ring cyclodextrin product profile due to a mutation at tyr-172 in the amylomaltase of corynebacterium glutamicum. | corynebacterium glutamicum amylomaltase (cgam) catalyzes the formation of large-ring cyclodextrins (lr-cds) with a degree of polymerization of 19 and higher. the cloned cgam gene was ligated into the pet-17b vector and used to transform escherichia coli bl21(de3). site-directed mutagenesis of tyr-172 in cgam to alanine (y172a) was performed to determine its role in the control of lr-cd production. both the recombinant wild-type (wt) and y172a enzymes were purified to apparent homogeneity and cha ... | 2012 | 22865069 |
| basic mechanisms of rna polymerase ii activity and alteration of gene expression in saccharomyces cerevisiae. | transcription by rna polymerase ii (pol ii), and all rna polymerases for that matter, may be understood as comprising two cycles. the first cycle relates to the basic mechanism of the transcription process wherein pol ii must select the appropriate nucleoside triphosphate (ntp) substrate complementary to the dna template, catalyze phosphodiester bond formation, and translocate to the next position on the dna template. performing this cycle in an iterative fashion allows the synthesis of rna chai ... | 2012 | 23022618 |
| basic mechanisms of rna polymerase ii activity and alteration of gene expression in saccharomyces cerevisiae. | transcription by rna polymerase ii (pol ii), and all rna polymerases for that matter, may be understood as comprising two cycles. the first cycle relates to the basic mechanism of the transcription process wherein pol ii must select the appropriate nucleoside triphosphate (ntp) substrate complementary to the dna template, catalyze phosphodiester bond formation, and translocate to the next position on the dna template. performing this cycle in an iterative fashion allows the synthesis of rna chai ... | 2012 | 23022618 |
| dna stabilization at the bacillus subtilis polx core--a binding model to coordinate polymerase, ap-endonuclease and 3'-5' exonuclease activities. | family x dna polymerases (polxs) are involved in dna repair. their binding to gapped dnas relies on two conserved helix-hairpin-helix motifs, one located at the 8-kda domain and the other at the fingers subdomain. bacterial/archaeal polxs have a specifically conserved third helix-hairpin-helix motif (gfgxk) at the fingers subdomain whose putative role in dna binding had not been established. here, mutagenesis at the corresponding residues of bacillus subtilis polx (polxbs), gly130, gly132 and ly ... | 2012 | 22844091 |
| structural basis for translation termination by archaeal rf1 and gtp-bound ef1α complex. | when a stop codon appears at the ribosomal a site, the class i and ii release factors (rfs) terminate translation. in eukaryotes and archaea, the class i and ii rfs form a heterodimeric complex, and complete the overall translation termination process in a gtp-dependent manner. however, the structural mechanism of the translation termination by the class i and ii rf complex remains unresolved. in archaea, archaeal elongation factor 1 alpha (aef1α), a carrier gtpase for trna, acts as a class ii r ... | 2012 | 22772989 |
| draft genome sequence of thermus sp. strain rl, isolated from a hot water spring located atop the himalayan ranges at manikaran, india. | thermus sp. strain rl was isolated from a hot water spring (90°c to 98°c) at manikaran, himachal pradesh, india. here we report the draft genome sequence (20,36,600 bp) of this strain. the draft genome sequence consists of 17 contigs and 1,986 protein-coding sequences and has an average g+c content of 68.77%. | 2012 | 22689228 |
| distinct functions of regions 1.1 and 1.2 of rna polymerase σ subunits from escherichia coli and thermus aquaticus in transcription initiation. | rna polymerase (rnap) from thermophilic thermus aquaticus is characterized by higher temperature of promoter opening, lower promoter complex stability, and higher promoter escape efficiency than rnap from mesophilic escherichia coli. we demonstrate that these differences are in part explained by differences in the structures of the n-terminal regions 1.1 and 1.2 of the e. coli σ(70) and t. aquaticus σ(a) subunits. in particular, region 1.1 and, to a lesser extent, region 1.2 of the e. coli σ(70) ... | 2012 | 22605342 |
| closely related archaeal haloarcula hispanica icosahedral viruses hhiv-2 and sh1 have nonhomologous genes encoding host recognition functions. | studies on viral capsid architectures and coat protein folds have revealed the evolutionary lineages of viruses branching to all three domains of life. a widespread group of icosahedral tailless viruses, the prd1-adenovirus lineage, was the first to be established. a double β-barrel fold for a single major capsid protein is characteristic of these viruses. similar viruses carrying genes coding for two major capsid proteins with a more complex structure, such as thermus phage p23-77 and haloarcha ... | 2012 | 22357274 |
| characterization of multi-functional properties and conformational analysis of muts2 from thermotoga maritima msb8. | the muts2 homologues have received attention because of their unusual activities that differ from those of muts. in this work, we report on the functional characteristics and conformational diversities of thermotoga maritima muts2 (tmmuts2). various biochemical features of the protein were demonstrated via diverse techniques such as scanning probe microscopy (spm), atpase assays, analytical ultracentrifugation, dna binding assays, size chromatography, and limited proteolytic analysis. dimeric tm ... | 2012 | 22545085 |
| related bifunctional restriction endonuclease-methyltransferase triplets: tspdti, tth111ii/tthhb27i and tsoi with distinct specificities. | we previously defined a family of restriction endonucleases (reases) from thermus sp., which share common biochemical and biophysical features, such as the fusion of both the nuclease and methyltransferase (mtase) activities in a single polypeptide, cleavage at a distance from the recognition site, large molecular size, modulation of activity by s-adenosylmethionine (sam), and incomplete cleavage of the substrate dna. members include related thermophilic reases with five distinct specificities: ... | 2012 | 22489904 |
| a novel phage-encoded transcription antiterminator acts by suppressing bacterial rna polymerase pausing. | gp39, a small protein encoded by thermus thermophilus phage p23-45, specifically binds the host rna polymerase (rnap) and inhibits transcription initiation. here, we demonstrate that gp39 also acts as an antiterminator during transcription through intrinsic terminators. the antitermination activity of gp39 relies on its ability to suppress transcription pausing at poly(u) tracks. gp39 also accelerates transcription elongation by decreasing rnap pausing and backtracking but does not significantly ... | 2012 | 22238378 |
| crystal structures and molecular dynamics simulations of thermophilic malate dehydrogenase reveal critical loop motion for co-substrate binding. | malate dehydrogenase (mdh) catalyzes the conversion of oxaloacetate and malate by using the nad/nadh coenzyme system. the system is used as a conjugate for enzyme immunoassays of a wide variety of compounds, such as illegal drugs, drugs used in therapeutic applications and hormones. we elucidated the biochemical and structural features of mdh from thermus thermophilus (ttmdh) for use in various biotechnological applications. the biochemical characterization of recombinant ttmdh revealed greatly ... | 2013 | 24386145 |
| single molecule analysis of thermus thermophilus ssb protein dynamics on single-stranded dna. | single-stranded (ss) dna binding (ssb) proteins play central roles in dna replication, recombination and repair in all organisms. we previously showed that escherichia coli (eco) ssb, a homotetrameric bacterial ssb, undergoes not only rapid ssdna-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssdna. whereas the majority of bacterial ssb family members function as homotetramers, dimeric ssb proteins were recently discovered in a distinct bacter ... | 2013 | 24371279 |
| single molecule analysis of thermus thermophilus ssb protein dynamics on single-stranded dna. | single-stranded (ss) dna binding (ssb) proteins play central roles in dna replication, recombination and repair in all organisms. we previously showed that escherichia coli (eco) ssb, a homotetrameric bacterial ssb, undergoes not only rapid ssdna-binding mode transitions but also one-dimensional diffusion (or migration) while remaining bound to ssdna. whereas the majority of bacterial ssb family members function as homotetramers, dimeric ssb proteins were recently discovered in a distinct bacter ... | 2013 | 24371279 |
| genetically encoded fluorescent indicator for imaging nad(+)/nadh ratio changes in different cellular compartments. | the ratio of nad(+)/nadh is a key indicator that reflects the overall redox state of the cells. until recently, there were no methods for real time nad(+)/nadh monitoring in living cells. genetically encoded fluorescent probes for nad(+)/nadh are fundamentally new approach for studying the nad(+)/nadh dynamics. | 2013 | 24286672 |
| genetically encoded fluorescent indicator for imaging nad(+)/nadh ratio changes in different cellular compartments. | the ratio of nad(+)/nadh is a key indicator that reflects the overall redox state of the cells. until recently, there were no methods for real time nad(+)/nadh monitoring in living cells. genetically encoded fluorescent probes for nad(+)/nadh are fundamentally new approach for studying the nad(+)/nadh dynamics. | 2013 | 24286672 |
| structure of escherichia coli rna polymerase holoenzyme at last. | | 2013 | 24272941 |
| directed polymerase evolution. | polymerases evolved in nature to synthesize dna and rna, and they underlie the storage and flow of genetic information in all cells. the availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. to circumvent these limit ... | 2013 | 24211837 |
| directed polymerase evolution. | polymerases evolved in nature to synthesize dna and rna, and they underlie the storage and flow of genetic information in all cells. the availability of these enzymes for use at the bench has driven a revolution in biotechnology and medicinal research; however, polymerases did not evolve to function efficiently under the conditions required for some applications and their high substrate fidelity precludes their use for most applications that involve modified substrates. to circumvent these limit ... | 2013 | 24211837 |
| identification and characterization of a novel trehalose synthase gene derived from saline-alkali soil metagenomes. | a novel trehalose synthase (tres) gene was identified from a metagenomic library of saline-alkali soil by a simple activity-based screening system. sequence analysis revealed that tres encodes a protein of 552 amino acids, with a deduced molecular weight of 63.3 kda. after being overexpressed in escherichia coli and purified, the enzymatic properties of tres were investigated. the recombinant tres displayed its optimal activity at ph 9.0 and 45 °c, and the addition of most common metal ions (1 o ... | 2013 | 24146994 |
| interplay between the trigger loop and the f loop during rna polymerase catalysis. | the trigger loop (tl) in the rna polymerase (rnap) active center plays key roles in the reactions of nucleotide addition and rna cleavage catalyzed by rnap. the adjacent f loop (fl) was proposed to contribute to rnap catalysis by modulating structural changes in the tl. here, we investigate the interplay between these two elements during transcription by bacterial rnap. thermodynamic analysis of catalysis by rnap variants with mutations in the tl and fl suggests that the tl is the key element re ... | 2013 | 24089145 |
| interplay between the trigger loop and the f loop during rna polymerase catalysis. | the trigger loop (tl) in the rna polymerase (rnap) active center plays key roles in the reactions of nucleotide addition and rna cleavage catalyzed by rnap. the adjacent f loop (fl) was proposed to contribute to rnap catalysis by modulating structural changes in the tl. here, we investigate the interplay between these two elements during transcription by bacterial rnap. thermodynamic analysis of catalysis by rnap variants with mutations in the tl and fl suggests that the tl is the key element re ... | 2013 | 24089145 |
| effects of upconversion nanoparticles on polymerase chain reaction. | nanoparticles (nps) are attractive materials owing to their physical and electrochemical properties, which make them extremely useful in diagnostic applications. photon upconversion is the phenomenon where high-energy photons are emitted upon excitation of low-energy photons. nucleic acids detection based on upconversion nanoparticles (ucnps), which display a high signal-to-noise ratio and no photobleaching, has been widely applied. we evaluated whether ucnps can improve polymerase chain reactio ... | 2013 | 24039935 |
| exploration of deinococcus-thermus molecular diversity by novel group-specific pcr primers. | the deeply branching deinococcus-thermus lineage is recognized as one of the most extremophilic phylum of bacteria. in previous studies, the presence of deinococcus-related bacteria in the hot arid tunisian desert of tataouine was demonstrated through combined molecular and culture-based approaches. similarly, thermus-related bacteria have been detected in tunisian geothermal springs. the present work was conducted to explore the molecular diversity within the deinococcus-thermus phylum in these ... | 2013 | 23996915 |
| computational simulation strategies for analysis of multisubunit rna polymerases. | | 2013 | 23987500 |
| incorporation of nucleoside probes opposite o⁶-methylguanine by sulfolobus solfataricus dna polymerase dpo4: importance of hydrogen bonding. | o⁶-methylguanine (o⁶-meg) is a mutagenic dna lesion, arising from the action of methylating agents on guanine (g) in dna. dpo4, an archaeal low-fidelity y-family dna polymerase involved in translesion dna synthesis (tls), is a model for studying how human y-family polymerases bypass dna adducts. previous work showed that dpo4-mediated dttp incorporation is favored opposite o⁶-meg rather than opposite g. however, factors influencing the preference of dpo4 to incorporate dttp opposite o⁶-meg are n ... | 2013 | 23959784 |
| tagetitoxin inhibits transcription by stabilizing pre-translocated state of the elongation complex. | transcription elongation consists of repetition of the nucleotide addition cycle: phosphodiester bond formation, translocation and binding of the next nucleotide. inhibitor of multi-subunit rna polymerase tagetitoxin (tgt) enigmatically slows down addition of nucleotides in a sequence-dependent manner, only at certain positions of the template. here, we show that tgt neither affects chemistry of rna synthesis nor induces backward translocation, nor competes with the nucleoside triphosphate (ntp) ... | 2013 | 23935117 |
| energetic and structural details of the trigger-loop closing transition in rna polymerase ii. | an evolutionarily conserved element in rna polymerase ii, the trigger loop (tl), has been suggested to play an important role in the elongation rate, fidelity of selection of the matched nucleoside triphosphate (ntp), catalysis of transcription elongation, and translocation in both eukaryotes and prokaryotes. in response to ntp binding, the tl undergoes large conformational changes to switch between distinct open and closed states to tighten the active site and avail catalysis. a computational s ... | 2013 | 23931324 |
| by ribosome possessed. | | 2013 | 23814064 |
| x-ray crystal structures of the escherichia coli rna polymerase in complex with benzoxazinorifamycins. | rifampin, a semisynthetic rifamycin, is the cornerstone of current tuberculosis treatment. among many semisynthetic rifamycins, benzoxazinorifamycins have great potential for tb treatment due to their superior affinity for wild-type and rifampin-resistant mycobacterium tuberculosis rna polymerases and their reduced hepatic cyp450 induction activity. in this study, we have determined the crystal structures of the escherichia coli rna polymerase complexes with two benzoxazinorifamycins. the ansa-n ... | 2013 | 23679862 |
| the rna polymerase trigger loop functions in all three phases of the transcription cycle. | the trigger loop (tl) forms a conserved element in the rna polymerase active centre that functions in the elongation phase of transcription. here, we show that the tl also functions in transcription initiation and termination. using recombinant variants of rna polymerase from pyrococcus furiosus and a reconstituted transcription system, we demonstrate that the tl is essential for initial rna synthesis until a complete dna-rna hybrid is formed. the archaeal tl is further important for transcripti ... | 2013 | 23737452 |
| a structural role for the php domain in e. coli dna polymerase iii. | in addition to the core catalytic machinery, bacterial replicative dna polymerases contain a polymerase and histidinol phosphatase (php) domain whose function is not entirely understood. the php domains of some bacterial replicases are active metal-dependent nucleases that may play a role in proofreading. in e. coli dna polymerase iii, however, the php domain has lost several metal-coordinating residues and is likely to be catalytically inactive. | 2013 | 23672456 |
| a rex family transcriptional repressor influences h2o2 accumulation by enterococcus faecalis. | rex factors are bacterial transcription factors thought to respond to the cellular nad(+)/nadh ratio in order to modulate gene expression by differentially binding dna. to date, rex factors have been implicated in regulating genes of central metabolism, oxidative stress response, and biofilm formation. the genome of enterococcus faecalis, a low-gc gram-positive opportunistic pathogen, encodes ef2638, a putative rex factor. to study the role of e. faecalis rex, we purified ef2638 and evaluated it ... | 2013 | 23417491 |
| thermostable mismatch-recognizing protein muts suppresses nonspecific amplification during polymerase chain reaction (pcr). | polymerase chain reaction (pcr)-related technologies are hampered mainly by two types of error: nonspecific amplification and dna polymerase-generated mutations. here, we report that both errors can be suppressed by the addition of a dna mismatch-recognizing protein, muts, from a thermophilic bacterium. although it had been expected that muts has a potential to suppress polymerase-generated mutations, we unexpectedly found that it also reduced nonspecific amplification. on the basis of this find ... | 2013 | 23519109 |
| structure of the poliiiα-τc-dna complex suggests an atomic model of the replisome. | the c-terminal domain (ctd) of the τ subunit of the clamp loader (τc) binds to both the dnab helicase and the dna polymerase iii α subunit (poliiiα), and determines their relative positions and orientations on the leading and lagging strands. here, we present a 3.2 å resolution structure of thermus aquaticus poliiiα in complex with τc and a dna substrate. the structure reveals that the ctd of τc interacts with the ctd of poliiiα through its c-terminal helix and the adjacent loop. additionally, i ... | 2013 | 23478062 |
| x-ray crystal structure of escherichia coli rna polymerase σ70 holoenzyme. | escherichia coli rna polymerase (rnap) is the most studied bacterial rnap and has been used as the model rnap for screening and evaluating potential rnap-targeting antibiotics. however, the x-ray crystal structure of e. coli rnap has been limited to individual domains. here, i report the x-ray structure of the e. coli rnap σ(70) holoenzyme, which shows σ region 1.1 (σ1.1) and the α subunit c-terminal domain for the first time in the context of an intact rnap. σ1.1 is positioned at the rnap dna-b ... | 2013 | 23389035 |
| structural basis of transcriptional pausing in bacteria. | transcriptional pausing by multisubunit rna polymerases (rnaps) is a key mechanism for regulating gene expression in both prokaryotes and eukaryotes and is a prerequisite for transcription termination. pausing and termination states are thought to arise through a common, elemental pause state that is inhibitory for nucleotide addition. we report three crystal structures of thermus rnap elemental paused elongation complexes (epecs). the structures reveal the same relaxed, open-clamp rnap conforma ... | 2013 | 23374340 |
| whole genome sequencing of thermus oshimai jl-2 and thermus thermophilus jl-18, incomplete denitrifiers from the united states great basin. | the strains thermus oshimai jl-2 and thermus thermophilus jl-18 each have a circular chromosome, 2.07 mb and 1.9 mb in size, respectively, and each has two plasmids ranging from 0.27 mb to 57.2 kb. the megaplasmid of each strain contains a gene cluster for the reduction of nitrate to nitrous oxide, consistent with their incomplete denitrification phenotypes. | 2013 | 23405355 |
| five checkpoints maintaining the fidelity of transcription by rna polymerases in structural and energetic details. | transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in rna, is essential for life. results from molecular dynamics (md) simulations of eukaryotic rna polymerase (rnap) ii and bacterial rnap with experimental data suggest that fidelity may involve as many as five checkpoints. using md simulations, the effects of different active site ntps in both open and closed trigger loop (tl) structures of rnaps are compared. unfavorable initial binding of mism ... | 2014 | 25550432 |
| five checkpoints maintaining the fidelity of transcription by rna polymerases in structural and energetic details. | transcriptional fidelity, which prevents the misincorporation of incorrect nucleoside monophosphates in rna, is essential for life. results from molecular dynamics (md) simulations of eukaryotic rna polymerase (rnap) ii and bacterial rnap with experimental data suggest that fidelity may involve as many as five checkpoints. using md simulations, the effects of different active site ntps in both open and closed trigger loop (tl) structures of rnaps are compared. unfavorable initial binding of mism ... | 2014 | 25550432 |
| the tfe-induced transient native-like structure of the intrinsically disordered σ₄⁷⁰ domain of escherichia coli rna polymerase. | the transient folding of domain 4 of an e. coli rna polymerase σ⁷⁰ subunit (recσ₄⁷⁰) induced by an increasing concentration of 2,2,2-trifluoroethanol (tfe) in an aqueous solution was monitored by means of cd and heteronuclear nmr spectroscopy. nmr data, collected at a 30% tfe, allowed the estimation of the population of a locally folded recσ₄⁷⁰ structure (csi descriptors) and of local backbone dynamics ((15)n relaxation). the spontaneous organization of the helical regions of the initially unfol ... | 2014 | 25261014 |
| dna polymerases as useful reagents for biotechnology - the history of developmental research in the field. | dna polymerase is a ubiquitous enzyme that synthesizes complementary dna strands according to the template dna in living cells. multiple enzymes have been identified from each organism, and the shared functions of these enzymes have been investigated. in addition to their fundamental role in maintaining genome integrity during replication and repair, dna polymerases are widely used for dna manipulation in vitro, including dna cloning, sequencing, labeling, mutagenesis, and other purposes. the fu ... | 2014 | 25221550 |
| replication slippage of the thermophilic dna polymerases b and d from the euryarchaeota pyrococcus abyssi. | replication slippage or slipped-strand mispairing involves the misalignment of dna strands during the replication of repeated dna sequences, and can lead to genetic rearrangements such as microsatellite instability. here, we show that polb and pold replicative dna polymerases from the archaeal model pyrococcus abyssi (pab) slip in vitro during replication of a single-stranded dna template carrying a hairpin structure and short direct repeats. we find that this occurs in both their wild-type (exo ... | 2014 | 25177316 |
| from metagenomics to pure culture: isolation and characterization of the moderately halophilic bacterium spiribacter salinus gen. nov., sp. nov. | recent metagenomic studies on saltern ponds with intermediate salinities have determined that their microbial communities are dominated by both euryarchaeota and halophilic bacteria, with a gammaproteobacterium closely related to the genera alkalilimnicola and arhodomonas being one of the most predominant microorganisms, making up to 15% of the total prokaryotic population. here we used several strategies and culture media in order to isolate this organism in pure culture. we report the isolatio ... | 2014 | 24747894 |
| inteins as indicators of gene flow in the halobacteria. | this research uses inteins, a type of mobile genetic element, to infer patterns of gene transfer within the halobacteria. we surveyed 118 genomes representing 26 genera of halobacteria for intein sequences. we then used the presence-absence profile, sequence similarity and phylogenies from the inteins recovered to explore how intein distribution can provide insight on the dynamics of gene flow between closely related and divergent organisms. we identified 24 proteins in the halobacteria that hav ... | 2014 | 25018750 |
| transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27. | thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ... | 2014 | 24948436 |
| transposon mutagenesis of the extremely thermophilic bacterium thermus thermophilus hb27. | thermus thermophilus is an extremely thermophilic bacterium that grows between 50 and 80 °c and is an excellent model organism not only for understanding life at high temperature but also for its biotechnological and industrial applications. multiple molecular capabilities are available including targeted gene inactivation and the use of shuttle plasmids that replicate in t. thermophilus and escherichia coli; however, the ability to disrupt gene function randomly by transposon insertion has not ... | 2014 | 24948436 |
| modification of rifamycin polyketide backbone leads to improved drug activity against rifampicin-resistant mycobacterium tuberculosis. | rifamycin b, a product of amycolatopsis mediterranei s699, is the precursor of clinically used antibiotics that are effective against tuberculosis, leprosy, and aids-related mycobacterial infections. however, prolonged usage of these antibiotics has resulted in the emergence of rifamycin-resistant strains of mycobacterium tuberculosis. as part of our effort to generate better analogs of rifamycin, we substituted the acyltransferase domain of module 6 of rifamycin polyketide synthase with that of ... | 2014 | 24923585 |
| molecular basis of rna polymerase promoter specificity switch revealed through studies of thermus bacteriophage transcription regulator. | transcription initiation is the central point of gene expression regulation. understanding of molecular mechanism of transcription regulation requires, ultimately, the structural understanding of consequences of transcription factors binding to dna-dependent rna polymerase (rnap), the enzyme of transcription. we recently determined a structure of a complex between transcription factor gp39 encoded by a thermus bacteriophage and thermus rnap holoenzyme. in this addendum to the original publicatio ... | 2014 | 25105059 |
| pcr performance of a thermostable heterodimeric archaeal dna polymerase. | dna polymerases are versatile tools used in numerous important molecular biological core technologies like the ubiquitous polymerase chain reaction (pcr), cdna cloning, genome sequencing, and nucleic acid based diagnostics. taking into account the multiple dna amplification techniques in use, different dna polymerases must be optimized for each type of application. one of the current tendencies is to reengineer or to discover new dna polymerases with increased performance and broadened substrate ... | 2014 | 24847315 |
| mycobacterial rna polymerase requires a u-tract at intrinsic terminators and is aided by nusg at suboptimal terminators. | intrinsic terminators, which encode gc-rich rna hairpins followed immediately by a 7-to-9-nucleotide (nt) u-rich "u-tract," play principal roles of punctuating and regulating transcription in most bacteria. however, canonical intrinsic terminators with strong u-tracts are underrepresented in some bacterial lineages, notably mycobacteria, leading to proposals that their rna polymerases stop at noncanonical intrinsic terminators encoding various rna structures lacking u-tracts. we generated recomb ... | 2014 | 24713321 |
| the impact of drug resistance on mycobacterium tuberculosis physiology: what can we learn from rifampicin? | the emergence of drug-resistant pathogens poses a major threat to public health. although influenced by multiple factors, high-level resistance is often associated with mutations in target-encoding or related genes. the fitness cost of these mutations is, in turn, a key determinant of the spread of drug-resistant strains. rifampicin (rif) is a frontline anti-tuberculosis agent that targets the rpob-encoded β subunit of the dna-dependent rna polymerase (rnap). in mycobacterium tuberculosis (mtb), ... | 2014 | 26038512 |
| antibiotic streptolydigin requires noncatalytic mg2+ for binding to rna polymerase. | multisubunit rna polymerase, an enzyme that accomplishes transcription in all living organisms, is a potent target for antibiotics. the antibiotic streptolydigin inhibits rna polymerase by sequestering the active center in a catalytically inactive conformation. here, we show that binding of streptolydigin to rna polymerase strictly depends on a noncatalytic magnesium ion which is likely chelated by the aspartate of the bridge helix of the active center. substitutions of this aspartate may explai ... | 2014 | 24342645 |
| structural basis for promoter specificity switching of rna polymerase by a phage factor. | transcription of dna to rna by dna-dependent rna polymerase (rnap) is the first step of gene expression and a major regulation point. bacteriophages hijack their host's transcription machinery and direct it to serve their needs. the gp39 protein encoded by thermus thermophilus phage p23-45 binds the host's rnap and inhibits transcription initiation from its major "-10/-35" class promoters. phage promoters belonging to the minor "extended -10" class are minimally inhibited. we report the crystal ... | 2014 | 24589779 |
| novel highly thermostable endolysin from thermus scotoductus mat2119 bacteriophage ph2119 with amino acid sequence similarity to eukaryotic peptidoglycan recognition proteins. | in this study, we present the discovery and characterization of a highly thermostable endolysin from bacteriophage ph2119 infecting thermus strain mat2119 isolated from geothermal areas in iceland. nucleotide sequence analysis of the 16s rrna gene affiliated the strain with the species thermus scotoductus. bioinformatics analysis has allowed identification in the genome of phage 2119 of an open reading frame (468 bp in length) coding for a 155-amino-acid basic protein with an mr of 17,555. ph211 ... | 2014 | 24271162 |
| structure of the carboxy-terminal domain of mycobacterium tuberculosis card protein: an essential rrna transcriptional regulator. | the card protein is highly expressed in mycobacterial strains under basal conditions and is transcriptionally induced during multiple types of genotoxic stress and starvation. the card protein binds the β subunit of rna polymerase and influences gene expression. the disruption of interactions between card and the β subunit of rna polymerase has a significant effect on mycobacterial survival, resistance to stress and pathogenesis. to understand the structure of card and its interaction with the β ... | 2014 | 24637748 |
| aminopeptidase t of m29 family acts as a novel intracellular virulence factor for listeria monocytogenes infection. | the foodborne pathogen listeria monocytogenes employs a number of virulence determinants including metalloproteases to infect hosts. here for the first time, we identified an m29 family aminopeptidase t (encoded by lmo1603) from l. monocytogenes that possesses a typical feature to catalyze the cleavage of amino acids from peptide substrates, with a preference for arginine. the purified recombinant lmo1603 was activated by fe(3+), zn(2+) and mn(2+), but strongly stimulated by co(2+), indicating t ... | 2015 | 26610705 |
| adaptation of the autotrophic acetogen sporomusa ovata to methanol accelerates the conversion of co2 to organic products. | acetogens are efficient microbial catalysts for bioprocesses converting c1 compounds into organic products. here, an adaptive laboratory evolution approach was implemented to adapt sporomusa ovata for faster autotrophic metabolism and co2 conversion to organic chemicals. s. ovata was first adapted to grow quicker autotrophically with methanol, a toxic c1 compound, as the sole substrate. better growth on different concentrations of methanol and with h2-co2 indicated the adapted strain had a more ... | 2015 | 26530351 |
| structural dissection of the maltodextrin disproportionation cycle of the arabidopsis plastidial disproportionating enzyme 1 (dpe1). | the degradation of transitory starch in the chloroplast to provide fuel for the plant during the night requires a suite of enzymes that generate a series of short chain linear glucans. however, glucans of less than four glucose units are no longer substrates for these enzymes, whereas export from the plastid is only possible in the form of either maltose or glucose. in order to make use of maltotriose, which would otherwise accumulate, disproportionating enzyme 1 (dpe1; a 4-α-glucanotransferase) ... | 2015 | 26504082 |
| complete genome sequence of thermus aquaticus y51mc23. | thermus aquaticus y51mc23 was isolated from a boiling spring in the lower geyser basin of yellowstone national park. remarkably, this t. aquaticus strain is able to grow anaerobically and produces multiple morphological forms. y51mc23 is a gram-negative, rod-shaped organism that grows well between 50°c and 80°c with maximum growth rate at 65°c to 70°c. growth studies suggest that y51mc23 primarily scavenges protein from the environment, supported by the high number of secreted and intracellular ... | 2015 | 26465632 |
| complete genome sequence of the thermophilic thermus sp. ccb_us3_uf1 from a hot spring in malaysia. | thermus sp. strain ccb_us3_uf1 is a thermophilic bacterium of the genus thermus, a member of the family thermaceae. members of the genus thermus have been widely used as a biological model for structural biology studies and to understand the mechanism of microbial adaptation under thermal environments. here, we present the complete genome sequence of thermus sp. ccb_us3_uf1 isolated from a hot spring in malaysia, which is the fifth member of the genus thermus with a completely sequenced and publ ... | 2015 | 26457128 |
| from structure-function analyses to protein engineering for practical applications of dna ligase. | dna ligases are indispensable in all living cells and ubiquitous in all organs. dna ligases are broadly utilized in molecular biology research fields, such as genetic engineering and dna sequencing technologies. here we review the utilization of dna ligases in a variety of in vitro gene manipulations, developed over the past several decades. during this period, fewer protein engineering attempts for dna ligases have been made, as compared to those for dna polymerases. we summarize the recent pro ... | 2015 | 26508902 |
| mismatch repair. | highly conserved muts homologs (msh) and mutl homologs (mlh/pms) are the fundamental components of mismatch repair (mmr). after decades of debate, it appears clear that the msh proteins initiate mmr by recognizing a mismatch and forming multiple extremely stable atp-bound sliding clamps that diffuse without hydrolysis along the adjacent dna. the function(s) of mlh/pms proteins is less clear, although they too bind atp and are targeted to mmr by msh sliding clamps. structural analysis combined wi ... | 2015 | 26354434 |
| cbr antimicrobials inhibit rna polymerase via at least two bridge-helix cap-mediated effects on nucleotide addition. | rna polymerase inhibitors like the cbr class that target the enzyme's complex catalytic center are attractive leads for new antimicrobials. catalysis by rna polymerase involves multiple rearrangements of bridge helix, trigger loop, and active-center side chains that isomerize the triphosphate of bound ntp and two mg(2+) ions from a preinsertion state to a reactive configuration. cbr inhibitors target a crevice between the n-terminal portion of the bridge helix and a surrounding cap region within ... | 2015 | 26195788 |
| structural basis for the interconversion of maltodextrins by malq, the amylomaltase of escherichia coli. | amylomaltase malq is essential for the metabolism of maltose and maltodextrins in escherichia coli. it catalyzes transglycosylation/disproportionation reactions in which glycosyl or dextrinyl units are transferred among linear maltodextrins of various lengths. to elucidate the molecular basis of transglycosylation by malq, we have determined three crystal structures of this enzyme, i.e. the apo-form, its complex with maltose, and an inhibitor complex with the transition state analog acarviosine- ... | 2015 | 26139606 |
| thermus parvatiensis rl(t) sp. nov., isolated from a hot water spring, located atop the himalayan ranges at manikaran, india. | a gram negative, yellow pigmented, rod shaped bacterium designated as rl(t) was isolated from a hot water spring (90-98 °c) located at manikaran in northern india. the isolate grows at 60-80 °c (optimum, 70 °c) and at ph 7.0-9.0 (optimum ph 7.2). phylogenetic analysis of 16s rrna gene sequences and levels of dna-dna relatedness together indicate that the new isolate represents a novel species of the genus thermus with closest affinity to thermus thermophilus hb8(t) (99.5 %) followed by thermus a ... | 2015 | 26543260 |
| protein synthesis during cellular quiescence is inhibited by phosphorylation of a translational elongation factor. | in nature, most organisms experience conditions that are suboptimal for growth. to survive, cells must fine-tune energy-demanding metabolic processes in response to nutrient availability. here, we describe a novel mechanism by which protein synthesis in starved cells is down-regulated by phosphorylation of the universally conserved elongation factor tu (ef-tu). phosphorylation impairs the essential gtpase activity of ef-tu, thereby preventing its release from the ribosome. as a consequence, phos ... | 2015 | 26056311 |
| first glycoside hydrolase family 2 enzymes from thermus antranikianii and thermus brockianus with β-glucosidase activity. | two glycoside hydrolase encoding genes (tagh2 and tbgh2) were identified from different thermus species using functional screening. based on amino acid similarities, the enzymes were predicted to belong to glycoside hydrolase (gh) family 2. surprisingly, both enzymes (tagh2 and tbgh2) showed twofold higher activities for the hydrolysis of nitrophenol-linked β-d-glucopyranoside than of -galactopyranoside. specific activities of 3,966 u/mg for tagh2 and 660 u/mg for tbgh2 were observed. in accorda ... | 2015 | 26090361 |
| draft genome sequence of the thermophile thermus filiformis atcc 43280, producer of carotenoid-(di)glucoside-branched fatty acid (di)esters and source of hyperthermostable enzymes of biotechnological interest. | here, we present the draft genome sequence of thermus filiformis strain atcc 43280, a thermophile bacterium capable of producing glycosylated carotenoids acylated with branched fatty acids and enzymes of biotechnological potential. | 2015 | 25977443 |