| global patterns of protein domain gain and loss in superkingdoms. | domains are modules within proteins that can fold and function independently and are evolutionarily conserved. here we compared the usage and distribution of protein domain families in the free-living proteomes of archaea, bacteria and eukarya and reconstructed species phylogenies while tracing the history of domain emergence and loss in proteomes. we show that both gains and losses of domains occurred frequently during proteome evolution. the rate of domain discovery increased approximately lin ... | 2014 | 24499935 |
| discovery and characterization of ionic liquid-tolerant thermophilic cellulases from a switchgrass-adapted microbial community. | the development of advanced biofuels from lignocellulosic biomass will require the use of both efficient pretreatment methods and new biomass-deconstructing enzyme cocktails to generate sugars from lignocellulosic substrates. certain ionic liquids (ils) have emerged as a promising class of compounds for biomass pretreatment and have been demonstrated to reduce the recalcitrance of biomass for enzymatic hydrolysis. however, current commercial cellulase cocktails are strongly inhibited by most of ... | 2014 | 24479406 |
| binding of copper and silver to single-site variants of peptidylglycine monooxygenase reveals the structure and chemistry of the individual metal centers. | peptidylglycine monooxygenase (phm) catalyzes the final step in the biosynthesis of amidated peptides that serve as important signaling molecules in numerous endocrine pathways. the catalytic mechanism has attracted much attention because of a number of unique attributes, including the presence of a pair of uncoupled copper centers separated by 11 å (termed cuh and cum), an unusual cu(i)smet interaction at the oxygen binding m-site, and the postulated cu(ii)-superoxo intermediate. understanding ... | 2014 | 24471980 |
| the omega subunit of the rna polymerase core directs transcription efficiency in cyanobacteria. | the eubacterial rna polymerase core, a transcription machinery performing dna-dependent rna polymerization, consists of two α subunits and β, β' and ω subunits. an additional σ subunit is recruited for promoter recognition and transcription initiation. cyanobacteria, a group of eubacteria characterized by oxygenic photosynthesis, have a unique composition of the rna polymerase (rnap) core due to splitting of the β' subunit to n-terminal γ and c-terminal β' subunits. the physiological roles of th ... | 2014 | 24476911 |
| a bacteriophage transcription regulator inhibits bacterial transcription initiation by σ-factor displacement. | bacteriophages (phages) appropriate essential processes of bacterial hosts to benefit their own development. the multisubunit bacterial rna polymerase (rnap) enzyme, which catalyses dna transcription, is targeted by phage-encoded transcription regulators that selectively modulate its activity. here, we describe the structural and mechanistic basis for the inhibition of bacterial rnap by the transcription regulator p7 encoded by xanthomonas oryzae phage xp10. we reveal that p7 uses a two-step mec ... | 2014 | 24482445 |
| 4'-o-substitutions determine selectivity of aminoglycoside antibiotics. | clinical use of 2-deoxystreptamine aminoglycoside antibiotics, which target the bacterial ribosome, is compromised by adverse effects related to limited drug selectivity. here we present a series of 4',6'-o-acetal and 4'-o-ether modifications on glucopyranosyl ring i of aminoglycosides. chemical modifications were guided by measuring interactions between the compounds synthesized and ribosomes harbouring single point mutations in the drug-binding site, resulting in aminoglycosides that interact ... | 2014 | 24473108 |
| a complex of cas proteins 5, 6, and 7 is required for the biogenesis and stability of clustered regularly interspaced short palindromic repeats (crispr)-derived rnas (crrnas) in haloferax volcanii. | the clustered regularly interspaced short palindromic repeats/crispr-associated (crispr-cas) system is a prokaryotic defense mechanism against foreign genetic elements. a plethora of crispr-cas versions exist, with more than 40 different cas protein families and several different molecular approaches to fight the invading dna. one of the key players in the system is the crispr-derived rna (crrna), which directs the invader-degrading cas protein complex to the invader. the crispr-cas types i and ... | 2014 | 24459147 |
| characterization of cleavage intermediate and star sites of rm.tth111ii. | tth111ii is a thermostable type iigs restriction enzyme that recognizes dna sites caarca (r = a or g) and cleaves downstream at n11/n9. here, the tth111iirm gene was cloned and expressed in e. coli, and tth111ii was purified. the purified enzyme contains internally-bound s-adenosylmethionine (sam). when the internal sam was removed, the endonuclease activity was stimulated by adding sam or its analog sinefungin. the cleavage intermediate is mostly top-strand nicked dna on a single-site plasmid. ... | 2014 | 24452415 |
| subunit positioning and stator filament stiffness in regulation and power transmission in the v1 motor of the manduca sexta v-atpase. | the vacuolar h(+)-atpase (v-atpase) is an atp-driven proton pump essential to the function of eukaryotic cells. its cytoplasmic v1 domain is an atpase, normally coupled to membrane-bound proton pump vo via a rotary mechanism. how these asymmetric motors are coupled remains poorly understood. low energy status can trigger release of v1 from the membrane and curtail atp hydrolysis. to investigate the molecular basis for these processes, we have carried out cryo-electron microscopy three-dimensiona ... | 2014 | 24075871 |
| folding a stable rna pseudoknot through rearrangement of two hairpin structures. | folding messenger rna into specific structures is a common regulatory mechanism involved in translation. in escherichia coli, the operator of the rpso gene transcript folds into a pseudoknot or double-hairpin conformation. s15, the gene product, binds only to the pseudoknot, thereby repressing its own synthesis when it is present in excess in the cell. the two rna conformations have been proposed to exist in equilibrium. however, it remained unclear how structural changes can be achieved between ... | 2014 | 24459133 |
| dynamic protein ligand interactions--insights from ms. | proteins undergo dynamic interactions with carbohydrates, lipids and nucleotides to form catalytic cores, fine-tuned for different cellular actions. the study of dynamic interactions between proteins and their cognate ligands is therefore fundamental to the understanding of biological systems. during the last two decades ms, and its associated techniques, has become accepted as a method for the study of protein-ligand interactions, not only for covalent complexes, where the use of ms is well est ... | 2014 | 24393119 |
| distinct functions of the rna polymerase σ subunit region 3.2 in rna priming and promoter escape. | the σ subunit of bacterial rna polymerase (rnap) has been implicated in all steps of transcription initiation, including promoter recognition and opening, priming of rna synthesis, abortive initiation and promoter escape. the post-promoter-recognition σ functions were proposed to depend on its conserved region σ3.2 that directly contacts promoter dna immediately upstream of the rnap active centre and occupies the rna exit path. analysis of the transcription effects of substitutions and deletions ... | 2014 | 24452800 |
| a highly divergent archaeo-eukaryotic primase from the thermococcus nautilus plasmid, ptn2. | we report the characterization of a dna primase/polymerase protein (polptn2) encoded by the ptn2 plasmid from thermococcus nautilus. sequence analysis revealed that this protein corresponds to a fusion between an n-terminal domain homologous to the small catalytic subunit pris of heterodimeric archaeal and eukaryotic primases (aep) and a c-terminal domain related to their large regulatory subunit pril. this unique domain configuration is not found in other virus- and plasmid-encoded primases in ... | 2014 | 24445805 |
| structural and functional analyses of a sterol carrier protein in spodoptera litura. | in insects, cholesterol is one of the membrane components in cells and a precursor of ecdysteroid biosynthesis. because insects lack two key enzymes, squalene synthase and lanosterol synthase, in the cholesterol biosynthesis pathway, they cannot autonomously synthesize cholesterol de novo from simple compounds and therefore have to obtain sterols from their diet. sterol carrier protein (scp) is a cholesterol-binding protein responsible for cholesterol absorption and transport. | 2014 | 24454688 |
| context of action of proline dehydrogenase (prodh) in the hypersensitive response of arabidopsis. | proline (pro) dehydrogenase (prodh) potentiates the oxidative burst and cell death of the plant hypersensitive response (hr) by mechanisms not yet elucidated. prodh converts pro into ∆1 pyrroline-5-carboxylate (p5c) and can act together with p5c dehydrogenase (p5cdh) to produce glu, or with p5c reductase (p5cr) to regenerate pro and thus stimulate the pro/p5c cycle. to better understand the effects of prodh in hr, we studied the enzyme at three stages of the defense response differing in their r ... | 2014 | 24410747 |
| the isolated carboxy-terminal domain of human mitochondrial leucyl-trna synthetase rescues the pathological phenotype of mitochondrial trna mutations in human cells. | mitochondrial (mt) diseases are multisystem disorders due to mutations in nuclear or mtdna genes. among the latter, more than 50% are located in transfer rna (trna) genes and are responsible for a wide range of syndromes, for which no effective treatment is available at present. we show that three human mt aminoacyl-trna syntethases, namely leucyl-, valyl-, and isoleucyl-trna synthetase are able to improve both viability and bioenergetic proficiency of human transmitochondrial cybrid cells carry ... | 2014 | 24413190 |
| crystal structures of ispf from plasmodium falciparum and burkholderia cenocepacia: comparisons inform antimicrobial drug target assessment. | 2c-methyl-d-erythritol-2,4-cyclodiphosphate synthase (ispf) catalyzes the conversion of 4-diphosphocytidyl-2c-methyl-d-erythritol-2-phosphate to 2c-methyl-d-erythritol-2,4-cyclodiphosphate and cytidine monophosphate in production of isoprenoid-precursors via the methylerythritol phosphate biosynthetic pathway. ispf is found in the protozoan plasmodium falciparum, a parasite that causes cerebral malaria, as well as in many gram-negative bacteria such as burkholderia cenocepacia. ispf represents a ... | 2014 | 24410837 |
| mlh1-mlh3, a meiotic crossover and dna mismatch repair factor, is a msh2-msh3-stimulated endonuclease. | crossing over between homologous chromosomes is initiated in meiotic prophase in most sexually reproducing organisms by the appearance of programmed double strand breaks throughout the genome. in saccharomyces cerevisiae the double-strand breaks are resected to form three prime single-strand tails that primarily invade complementary sequences in unbroken homologs. these invasion intermediates are converted into double holliday junctions and then resolved into crossovers that facilitate homolog s ... | 2014 | 24403070 |
| charge segregation and low hydrophobicity are key features of ribosomal proteins from different organisms. | ribosomes are large and highly charged macromolecular complexes consisting of rna and proteins. here, we address the electrostatic and nonpolar properties of ribosomal proteins that are important for ribosome assembly and interaction with other cellular components and may influence protein folding on the ribosome. we examined 50 s ribosomal subunits from 10 species and found a clear distinction between the net charge of ribosomal proteins from halophilic and non-halophilic organisms. we found th ... | 2014 | 24398678 |
| comea is essential for the transfer of external dna into the periplasm in naturally transformable vibrio cholerae cells. | the dna uptake of naturally competent bacteria has been attributed to the action of dna uptake machineries resembling type iv pilus complexes. however, the protein(s) for pulling the dna across the outer membrane of gram-negative bacteria remain speculative. here we show that the competence protein comea binds incoming dna in the periplasm of naturally competent vibrio cholerae cells thereby promoting dna uptake, possibly through ratcheting and entropic forces associated with comea binding. usin ... | 2014 | 24391524 |
| clostridium difficile glutamate dehydrogenase is a secreted enzyme that confers resistance to h2o2. | clostridium difficile produces an nad-specific glutamate dehydrogenase (gdh), which converts l-glutamate into α-ketoglutarate through an irreversible reaction. the enzyme gdh is detected in the stool samples of patients with c. difficile-associated disease and serves as one of the diagnostic tools to detect c. difficile infection (cdi). we demonstrate here that supernatant fluids of c. difficile cultures contain gdh. to understand the role of gdh in the physiology of c. difficile, an isogenic in ... | 2014 | 24145018 |
| ultradeep pyrosequencing and molecular modeling identify key structural features of hepatitis b virus rnase h, a putative target for antiviral intervention. | last-generation nucleoside/nucleotide analogues are potent against hepatitis b virus (hbv) and have a high barrier to resistance. however, delayed responses have been observed in patients previously exposed to other drugs of the same class, long-term resistance is possible, and cure of infection cannot be achieved with these therapies, emphasizing the need for alternative therapeutic approaches. the hbv rnase h represents an interesting target because its enzyme activity is essential to the hbv ... | 2014 | 24173223 |
| iodotyrosine deiodinase: a unique flavoprotein present in organisms of diverse phyla. | iodide is required for thyroid hormone synthesis in mammals and other vertebrates. the role of both iodide and iodinated tyrosine derivatives is currently unknown in lower organisms, yet the presence of a key enzyme in iodide conservation, iodotyrosine deiodinase (iyd), is suggested by genomic data from a wide range of multicellular organisms as well as some bacteria. a representative set of these genes has now been expressed, and the resulting enzymes all catalyze reductive deiodination of diio ... | 2014 | 24153409 |
| detecting conformational differences between rna 3d structures. | a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ... | 2015 | 27330250 |
| detecting conformational differences between rna 3d structures. | a method is described for detecting local conformational differences between two 3d structures of the same rna molecule. these could be distinct 3d structures of the same molecule from the same organism, or homologous molecules from different organisms. in this approach, we detect the variability that exists among the relative translation and rotation operations that are needed to superimpose local neighborhoods after an initial rigid-body global superposition. each translation and rotation is r ... | 2015 | 27330250 |
| short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations. | mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ... | 2015 | 26721932 |
| short peptides from leucyl-trna synthetase rescue disease-causing mitochondrial trna point mutations. | mutations in mitochondrial (mt) genes coding for mt-trnas are responsible for a range of syndromes, for which no effective treatment is available. we recently showed that the carboxy-terminal domain (cterm) of human mt-leucyl trna synthetase rescues the pathologic phenotype associated either with the m.3243a>g mutation in mt-trna(leu(uur)) or with mutations in the mt-trna(ile), both of which are aminoacylated by class i mt-aminoacyl-trna synthetases (mt-aarss). here we show, by using the human t ... | 2015 | 26721932 |
| structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome. | during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ... | 2015 | 26715760 |
| structure of the hypusinylated eukaryotic translation factor eif-5a bound to the ribosome. | during protein synthesis, ribosomes become stalled on polyproline-containing sequences, unless they are rescued in archaea and eukaryotes by the initiation factor 5a (a/eif-5a) and in bacteria by the homologous protein ef-p. while a structure of ef-p bound to the 70s ribosome exists, structural insight into eif-5a on the 80s ribosome has been lacking. here we present a cryo-electron microscopy reconstruction of eif-5a bound to the yeast 80s ribosome at 3.9 å resolution. the structure reveals tha ... | 2015 | 26715760 |
| novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2. | the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ... | 2015 | 26712743 |
| novel insights into guide rna 5'-nucleoside/tide binding by human argonaute 2. | the human argonaute 2 (hago2) protein is a key player of rna interference (rnai). upon complex formation with small non-coding rnas, the protein initially interacts with the 5'-end of a given guide rna through multiple interactions within the mid domain. this interaction has been reported to show a strong bias for u and a over c and g at the 5'-position. performing molecular dynamics simulations of binary hago2/oh-guide-rna complexes, we show that hago2 is a highly flexible protein capable of bi ... | 2015 | 26712743 |
| human holliday junction resolvase gen1 uses a chromodomain for efficient dna recognition and cleavage. | holliday junctions (hjs) are key dna intermediates in homologous recombination. they link homologous dna strands and have to be faithfully removed for proper dna segregation and genome integrity. here, we present the crystal structure of human hj resolvase gen1 complexed with dna at 3.0 å resolution. the gen1 core is similar to other rad2/xpg nucleases. however, unlike other members of the superfamily, gen1 contains a chromodomain as an additional dna interaction site. chromodomains are known fo ... | 2015 | 26682650 |
| resveratrol directly binds to mitochondrial complex i and increases oxidative stress in brain mitochondria of aged mice. | resveratrol is often described as a promising therapeutic molecule for numerous diseases, especially in metabolic and neurodegenerative disorders. while the mechanism of action is still debated, an increasing literature reports that resveratrol regulates the mitochondrial respiratory chain function. in a recent study we have identified mitochondrial complex i as a direct target of this molecule. nevertheless, the mechanisms and consequences of such an interaction still require further investigat ... | 2015 | 26684010 |
| co-evolution of bacterial ribosomal protein s15 with diverse mrna regulatory structures. | rna-protein interactions are critical in many biological processes, yet how such interactions affect the evolution of both partners is still unknown. rna and protein structures are impacted very differently by mechanisms of genomic change. while most protein families are identifiable at the nucleotide level across large phylogenetic distances, rna families display far less nucleotide similarity and are often only shared by closely related bacterial species. ribosomal protein s15 has two rna bind ... | 2015 | 26675164 |
| mechanisms of ribosome stalling by secm at multiple elongation steps. | regulation of translating ribosomes is a major component of gene expression control network. in escherichia coli, ribosome stalling by the c-terminal arrest sequence of secm regulates the seca-dependent secretion pathway. previous studies reported many residues of secm peptide and ribosome exit tunnel are critical for stalling. however, the underlying molecular mechanism is still not clear at the atomic level. here, we present two cryo-em structures of the secm-stalled ribosomes at 3.3-3.7 å res ... | 2015 | 26670735 |
| structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue. | purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ... | 2015 | 26673726 |
| structural and functional insights into trna binding and adenosine n1-methylation by an archaeal trm10 homologue. | purine nucleosides on position 9 of eukaryal and archaeal trnas are frequently modified in vivo by the post-transcriptional addition of a methyl group on their n1 atom. the methyltransferase trm10 is responsible for this modification in both these domains of life. while certain trm10 orthologues specifically methylate either guanosine or adenosine at position 9 of trna, others have a dual specificity. until now structural information about this enzyme family was only available for the catalytic ... | 2015 | 26673726 |
| initiation factor 2 stabilizes the ribosome in a semirotated conformation. | intersubunit rotation and movement of the l1 stalk, a mobile domain of the large ribosomal subunit, have been shown to accompany the elongation cycle of translation. the initiation phase of protein synthesis is crucial for translational control of gene expression; however, in contrast to elongation, little is known about the conformational rearrangements of the ribosome during initiation. bacterial initiation factors (ifs) 1, 2, and 3 mediate the binding of initiator trna and mrna to the small r ... | 2015 | 26668356 |
| synergistic effect of atp for ruva-ruvb-holliday junction dna complex formation. | the escherichia coli ruvb hexameric ring motor proteins, together with ruvas, promote branch migration of holliday junction dna. zero mode waveguides (zmws) constitute of nanosized holes and enable the visualization of a single fluorescent molecule under micromolar order of the molecules, which is applicable to characterize the formation of ruva-ruvb-holliday junction dna complex. in this study, we used zmws and counted the number of ruvbs binding to ruva-holliday junction dna complex. our data ... | 2015 | 26658024 |
| microbial rhodopsins: wide distribution, rich diversity and great potential. | one of the major topics in biophysics and physicobiology is to understand and utilize biological functions using various advanced techniques. taking advantage of the photoreactivity of the seven-transmembrane rhodopsin protein family has been actively investigated by a variety of methods. rhodopsins serve as models for membrane-embedded proteins, for photoactive proteins and as a fundamental tool for optogenetics, a new technology to control biological activity with light. in this review, we sum ... | 2015 | 27493861 |
| structural basis for specificity and promiscuity in a carrier protein/enzyme system from the sulfur cycle. | the bacterial sox (sulfur oxidation) pathway is an important route for the oxidation of inorganic sulfur compounds. intermediates in the sox pathway are covalently attached to the heterodimeric carrier protein soxyz through conjugation to a cysteine on a protein swinging arm. we have investigated how the carrier protein shuttles intermediates between the enzymes of the sox pathway using the interaction between soxyz and the enzyme soxb as our model. the carrier protein and enzyme interact only w ... | 2015 | 26655737 |
| deciphering the dynamics of non-covalent interactions affecting thermal stability of a protein: molecular dynamics study on point mutant of thermus thermophilus isopropylmalate dehydrogenase. | thermus thermophilius isopropylmalate dehydrogenase catalyzes oxidative decarboxylation and dehydrogenation of isopropylmalate. substitution of leucine to alanine at position 172 enhances the thermal stability among the known point mutants. exploring the dynamic properties of non-covalent interactions such as saltbridges, hydrogen bonds and hydrophobic interactions to explain thermal stability of a protein is interesting in its own right. in this study dynamic changes in the non-covalent interac ... | 2015 | 26657745 |
| atp regulation in bioproduction. | adenosine-5'-triphosphate (atp) is consumed as a biological energy source by many intracellular reactions. thus, the intracellular atp supply is required to maintain cellular homeostasis. the dependence on the intracellular atp supply is a critical factor in bioproduction by cell factories. recent studies have shown that changing the atp supply is critical for improving product yields. in this review, we summarize the recent challenges faced by researchers engaged in the development of engineere ... | 2015 | 26655598 |
| nmr structure and function of helicoverpa armigera sterol carrier protein-2, an important insecticidal target from the cotton bollworm. | the cotton bollworm, helicoverpa armigera, has developed strong resistance to many insecticides. sterol carrier protein-2 (scp-2) is an important non-specific lipid transfer protein in insects and appears to be a potential new target. in order to elucidate the structure and function of helicoverpa armigera scp-2 (hascp-2), nmr spectroscopy, docking simulations, mutagenesis and bioassays were performed. hascp-2 composed of five α-helices and four stranded β-sheets. the folds of α-helices and β-sh ... | 2015 | 26655641 |
| evolutionary limitation and opportunities for developing trna synthetase inhibitors with 5-binding-mode classification. | aminoacyl-trna synthetases (aarss) are enzymes that catalyze the transfer of amino acids to their cognate trnas as building blocks for translation. each of the aars families plays a pivotal role in protein biosynthesis and is indispensable for cell growth and survival. in addition, aarss in higher species have evolved important non-translational functions. these translational and non-translational functions of aars are attractive for developing antibacterial, antifungal, and antiparasitic agents ... | 2015 | 26670257 |
| consistency analysis of genome-scale models of bacterial metabolism: a metamodel approach. | genome-scale metabolic models usually contain inconsistencies that manifest as blocked reactions and gap metabolites. with the purpose to detect recurrent inconsistencies in metabolic models, a large-scale analysis was performed using a previously published dataset of 130 genome-scale models. the results showed that a large number of reactions (~22%) are blocked in all the models where they are present. to unravel the nature of such inconsistencies a metamodel was construed by joining the 130 mo ... | 2015 | 26629901 |
| non-specific blocking of mir-17-5p guide strand in triple negative breast cancer cells by amplifying passenger strand activity. | conventional wisdom holds that only one of the two strands in a micro ribonucleic acid (mirna) precursor duplex is selected as the active mirna guide strand. the complementary mirna passenger strand, however, is thought to be inactive. high levels of the oncogenic mirna (oncomir) guide strand called mir-17-5p is overexpressed in triple negative breast cancer (tnbc) and can inhibit ribosomal translation of tumor suppressor gene mrnas, such as programmed cell death 4 (pdcd4) or phosphatase and ten ... | 2015 | 26629823 |
| engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis. | lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ... | 2015 | 26621798 |
| engineering a thermostable halothermothrix orenii β-glucosidase for improved galacto-oligosaccharide synthesis. | lactose is produced in large amounts as a by-product from the dairy industry. this inexpensive disaccharide can be converted to more useful value-added products such as galacto-oligosaccharides (goss) by transgalactosylation reactions with retaining β-galactosidases (bgals) being normally used for this purpose. hydrolysis is always competing with the transglycosylation reaction, and hence, the yields of goss can be too low for industrial use. we have reported that a β-glucosidase from halothermo ... | 2015 | 26621798 |
| clinical metagenomic identification of balamuthia mandrillaris encephalitis and assembly of the draft genome: the continuing case for reference genome sequencing. | primary amoebic meningoencephalitis (pam) is a rare, often lethal, cause of encephalitis, for which early diagnosis and prompt initiation of combination antimicrobials may improve clinical outcomes. | 2015 | 26620704 |
| activities of the peptidyl transferase center of ribosomes lacking protein l27. | the ribosome is the molecular machine responsible for protein synthesis in all living organisms. its catalytic core, the peptidyl transferase center (ptc), is built of rrna, although several proteins reach close to the inner rrna shell. in the escherichia coli ribosome, the flexible n-terminal tail of the ribosomal protein l27 contacts the a- and p-site trna. based on computer simulations of the ptc and on previous biochemical evidence, the n-terminal α-amino group of l27 was suggested to take p ... | 2015 | 26475831 |
| an s6:s18 complex inhibits translation of e. coli rpsf. | more than half of the ribosomal protein operons in escherichia coli are regulated by structures within the mrna transcripts that interact with specific ribosomal proteins to inhibit further protein expression. this regulation is accomplished using a variety of mechanisms and the rna structures responsible for regulation are often not conserved across bacterial phyla. a widely conserved mrna structure preceding the ribosomal protein operon containing rpsf and rpsr (encoding s6 and s18) was recent ... | 2015 | 26447183 |
| concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii. | we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ... | 2015 | 26619013 |
| concentric-flow electrokinetic injector enables serial crystallography of ribosome and photosystem ii. | we describe a concentric-flow electrokinetic injector for efficiently delivering microcrystals for serial femtosecond x-ray crystallography analysis that enables studies of challenging biological systems in their unadulterated mother liquor. we used the injector to analyze microcrystals of geobacillus stearothermophilus thermolysin (2.2-å structure), thermosynechococcus elongatus photosystem ii (<3-å diffraction) and thermus thermophilus small ribosomal subunit bound to the antibiotic paromomyci ... | 2015 | 26619013 |
| clpb n-terminal domain plays a regulatory role in protein disaggregation. | clpb/hsp100 is an atp-dependent disaggregase that solubilizes and reactivates protein aggregates in cooperation with the dnak/hsp70 chaperone system. the clpb-substrate interaction is mediated by conserved tyrosine residues located in flexible loops in nucleotide-binding domain-1 that extend into the clpb central pore. in addition to the tyrosines, the clpb n-terminal domain (ntd) was suggested to provide a second substrate-binding site; however, the manner in which the ntd recognizes and binds ... | 2015 | 26621746 |
| dancing through life: molecular dynamics simulations and network-centric modeling of allosteric mechanisms in hsp70 and hsp110 chaperone proteins. | hsp70 and hsp110 chaperones play an important role in regulating cellular processes that involve protein folding and stabilization, which are essential for the integrity of signaling networks. although many aspects of allosteric regulatory mechanisms in hsp70 and hsp110 chaperones have been extensively studied and significantly advanced in recent experimental studies, the atomistic picture of signal propagation and energetics of dynamics-based communication still remain unresolved. in this work, ... | 2015 | 26619280 |
| characterization of aspartate kinase from corynebacterium pekinense and the critical site of arg169. | aspartate kinase (ak) is the key enzyme in the biosynthesis of aspartate-derived amino acids. recombinant ak was efficiently purified and systematically characterized through analysis under optimal conditions combined with steady-state kinetics study. homogeneous ak was predicted as a decamer with a molecular weight of ~48 kda and a half-life of 4.5 h. the enzymatic activity was enhanced by ethanol and ni(2+). moreover, steady-state kinetic study confirmed that ak is an allosteric enzyme, and it ... | 2015 | 26633359 |
| active site coupling in plasmodium falciparum gmp synthetase is triggered by domain rotation. | gmp synthetase (gmps), a key enzyme in the purine biosynthetic pathway performs catalysis through a coordinated process across two catalytic pockets for which the mechanism remains unclear. crystal structures of plasmodium falciparum gmps in conjunction with mutational and enzyme kinetic studies reported here provide evidence that an 85° rotation of the gatase domain is required for ammonia channelling and thus for the catalytic activity of this two-domain enzyme. we suggest that conformational ... | 2015 | 26592566 |
| identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna. | the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ... | 2015 | 26590840 |
| identification of the methyltransferase targeting c2499 in deinococcus radiodurans 23s ribosomal rna. | the bacterium deinococcus radiodurans-like all other organisms-introduces nucleotide modifications into its ribosomal rna. we have previously found that the bacterium contains a carbon-5 methylation on cytidine 2499 of its 23s ribosomal rna, which is so far the only modified version of cytidine 2499 reported. using homology search, we identified the open reading frame dr_0049 as the primary candidate gene for the methyltransferase that modifies cytidine 2499. mass spectrometric analysis demonstr ... | 2015 | 26590840 |
| metagenomics of an alkaline hot spring in galicia (spain): microbial diversity analysis and screening for novel lipolytic enzymes. | a fosmid library was constructed with the metagenomic dna from the water of the lobios hot spring (76°c, ph = 8.2) located in ourense (spain). metagenomic sequencing of the fosmid library allowed the assembly of 9722 contigs ranging in size from 500 to 56,677 bp and spanning ~18 mbp. 23,207 orfs (open reading frames) were predicted from the assembly. biodiversity was explored by taxonomic classification and it revealed that bacteria were predominant, while the archaea were less abundant. the six ... | 2015 | 26635759 |
| metagenomics: retrospect and prospects in high throughput age. | in recent years, metagenomics has emerged as a powerful tool for mining of hidden microbial treasure in a culture independent manner. in the last two decades, metagenomics has been applied extensively to exploit concealed potential of microbial communities from almost all sorts of habitats. a brief historic progress made over the period is discussed in terms of origin of metagenomics to its current state and also the discovery of novel biological functions of commercial importance from metagenom ... | 2015 | 26664751 |
| natural guided genome engineering reveals transcriptional regulators controlling quorum-sensing signal degradation. | quorum-quenching (qq) are natural or engineered processes disrupting the quorum-sensing (qs) signalling which controls virulence and persistence (e.g. biofilm) in numerous bacteria. qq involves different enzymes including lactonases, amidases, oxidases and reductases which degrade the qs molecules such as n-acylhomoserine lactones (nahl). rhodococcus erythropolis known to efficiently degrade nahl is proposed as a biocontrol agent and a reservoir of qq-enzymes for biotechnology. in r. erythropoli ... | 2015 | 26554837 |
| spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha. | we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ... | 2015 | 26553877 |
| spectroscopic and kinetic properties of the molybdenum-containing, nad+-dependent formate dehydrogenase from ralstonia eutropha. | we have examined the rapid reaction kinetics and spectroscopic properties of the molybdenum-containing, nad(+)-dependent fdsabg formate dehydrogenase from ralstonia eutropha. we confirm previous steady-state studies of the enzyme and extend its characterization to a rapid kinetic study of the reductive half-reaction (the reaction of formate with oxidized enzyme). we have also characterized the electron paramagnetic resonance signal of the molybdenum center in its mo(v) state and demonstrated the ... | 2015 | 26553877 |
| extremely thermophilic microorganisms as metabolic engineering platforms for production of fuels and industrial chemicals. | enzymes from extremely thermophilic microorganisms have been of technological interest for some time because of their ability to catalyze reactions of industrial significance at elevated temperatures. thermophilic enzymes are now routinely produced in recombinant mesophilic hosts for use as discrete biocatalysts. genome and metagenome sequence data for extreme thermophiles provide useful information for putative biocatalysts for a wide range of biotransformations, albeit involving at most a few ... | 2015 | 26594201 |
| thermus thermophilus as a source of thermostable lipolytic enzymes. | lipolytic enzymes, esterases (ec 3.1.1.1) and lipases (ec 3.1.1.3), catalyze the hydrolysis of ester bonds between alcohols and carboxylic acids, and its formation in organic media. at present, they represent about 20% of commercialized enzymes for industrial use. lipolytic enzymes from thermophilic microorganisms are preferred for industrial use to their mesophilic counterparts, mainly due to higher thermostability and resistance to several denaturing agents. however, the production at an indus ... | 2015 | 27682117 |
| structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism. | paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ... | 2015 | 26538563 |
| structural and functional characterization of the paai thioesterase from streptococcus pneumoniae reveals a dual specificity for phenylacetyl-coa and medium-chain fatty acyl-coas and a novel coa-induced fit mechanism. | paai thioesterases are members of the te13 thioesterase family that catalyze the hydrolysis of thioester bonds between coenzyme a and phenylacetyl-coa. in this study we characterize the paai thioesterase from streptococcus pneumoniae (sppaai), including structural analysis based on crystal diffraction data to 1.8-å resolution, to reveal two double hotdog domains arranged in a back to back configuration. consistent with the crystallography data, both size exclusion chromatography and small angle ... | 2015 | 26538563 |
| the presence of highly disruptive 16s rrna mutations in clinical samples indicates a wider role for mutations of the mitochondrial ribosome in human disease. | mitochondrial dna mutations are well recognized as an important cause of disease, with over two hundred variants in the protein encoding and mt-trna genes associated with human disorders. in contrast, the two genes encoding the mitochondrial rrnas (mt-rrnas) have been studied in far less detail. this is because establishing the pathogenicity of mt-rrna mutations is a major diagnostic challenge. only two disease causing mutations have been identified at these loci, both mapping to the small subun ... | 2015 | 26349026 |
| coevolution of rtcb and archease created a multiple-turnover rna ligase. | rtcb is a noncanonical rna ligase that joins either 2',3'-cyclic phosphate or 3'-phosphate termini to 5'-hydroxyl termini. the genes encoding rtcb and archease constitute a trna splicing operon in many organisms. archease is a cofactor of rtcb that accelerates rna ligation and alters the ntp specificity of the ligase from pyrococcus horikoshii. yet, not all organisms that encode rtcb also encode archease. here we sought to understand the differences between archease-dependent and archease-indepe ... | 2015 | 26385509 |
| structure and function of mitochondrial membrane protein complexes. | biological energy conversion in mitochondria is carried out by the membrane protein complexes of the respiratory chain and the mitochondrial atp synthase in the inner membrane cristae. recent advances in electron cryomicroscopy have made possible new insights into the structural and functional arrangement of these complexes in the membrane, and how they change with age. this review places these advances in the context of what is already known, and discusses the fundamental questions that remain ... | 2015 | 26515107 |
| current and future resources for functional metagenomics. | functional metagenomics is a powerful experimental approach for studying gene function, starting from the extracted dna of mixed microbial populations. a functional approach relies on the construction and screening of metagenomic libraries-physical libraries that contain dna cloned from environmental metagenomes. the information obtained from functional metagenomics can help in future annotations of gene function and serve as a complement to sequence-based metagenomics. in this perspective, we b ... | 2015 | 26579102 |
| structure and two-metal mechanism of a eukaryal nick-sealing rna ligase. | atp-dependent rna ligases are agents of rna repair that join 3'-oh and 5'-po4 rna ends. naegleria gruberi rna ligase (ngrrnl) exemplifies a family of rna nick-sealing enzymes found in bacteria, viruses, and eukarya. crystal structures of ngrrnl at three discrete steps along the reaction pathway-covalent ligase-(lysyl-nζ)-amp•mn(2+) intermediate; ligase•atp•(mn(2+))2 michaelis complex; and ligase•mn(2+) complex-highlight a two-metal mechanism of nucleotidyl transfer, whereby (i) an enzyme-bound " ... | 2015 | 26512110 |
| enzyme-modified particles for selective biocatalytic hydrogenation by hydrogen-driven nadh recycling. | we describe a new approach to selective h2-driven hydrogenation that exploits a sequence of enzymes immobilised on carbon particles. we used a catalyst system that comprised alcohol dehydrogenase, hydrogenase and an nad(+) reductase on carbon black to demonstrate a greater than 98 % conversion of acetophenone to phenylethanol. oxidation of h2 by the hydrogenase provides electrons through the carbon for nad(+) reduction to recycle the nadh cofactor required by the alcohol dehydrogenase. this bioc ... | 2015 | 26613009 |
| defining the mrna recognition signature of a bacterial toxin protein. | bacteria contain multiple type ii toxins that selectively degrade mrnas bound to the ribosome to regulate translation and growth and facilitate survival during the stringent response. ribosome-dependent toxins recognize a variety of three-nucleotide codons within the aminoacyl (a) site, but how these endonucleases achieve substrate specificity remains poorly understood. here, we identify the critical features for how the host inhibition of growth b (higb) toxin recognizes each of the three a-sit ... | 2015 | 26508639 |
| thermodynamics of protein denaturation at temperatures over 100 °c: cuta1 mutant proteins substituted with hydrophobic and charged residues. | although the thermodynamics of protein denaturation at temperatures over 100 °c is essential for the rational design of highly stable proteins, it is not understood well because of the associated technical difficulties. we designed certain hydrophobic mutant proteins of cuta1 from escherichia coli, which have denaturation temperatures (td) ranging from 101 to 113 °c and show a reversible heat denaturation. using a hydrophobic mutant as a template, we successfully designed a hyperthermostable mut ... | 2015 | 26497062 |
| saxs fingerprints of aldehyde dehydrogenase oligomers. | enzymes of the aldehyde dehydrogenase (aldh) superfamily catalyze the nicotinamide adenine dinucleotide-dependent oxidation of aldehydes to carboxylic acids. aldhs are important in detoxification of aldehydes, amino acid metabolism, embryogenesis and development, neurotransmission, oxidative stress, and cancer. mutations in genes encoding aldhs cause metabolic disorders, including alcohol flush reaction (aldh2), sjögren-larsson syndrome (aldh3a2), hyperprolinemia type ii (aldh4a1), γ-hydroxybuty ... | 2015 | 26693506 |
| crystal structure of the human trna m(1)a58 methyltransferase-trna(3)(lys) complex: refolding of substrate trna allows access to the methylation target. | human trna3(lys) is the primer for reverse transcription of hiv; the 3' end is complementary to the primer-binding site on hiv rna. the complementarity ends at the 18th base, a58, which in trna3(lys) is modified to remove watson-crick pairing. motivated to test the role of the modification in terminating the primer-binding sequence and thus limiting run-on transcription, we asked how the modification of rna could be accomplished. trna m(1)a58 methyltransferase (m(1)a58 mtase) methylates n1 of a5 ... | 2015 | 26470919 |
| discovery and functional characterization of diverse class 2 crispr-cas systems. | microbial crispr-cas systems are divided into class 1, with multisubunit effector complexes, and class 2, with single protein effectors. currently, only two class 2 effectors, cas9 and cpf1, are known. we describe here three distinct class 2 crispr-cas systems. the effectors of two of the identified systems, c2c1 and c2c3, contain ruvc-like endonuclease domains distantly related to cpf1. the third system, c2c2, contains an effector with two predicted hepn rnase domains. whereas production of mat ... | 2015 | 26593719 |
| how to show the real microbial biodiversity? a comparison of seven dna extraction methods for bacterial population analyses in matrices containing highly charged natural nanoparticles. | a dna extraction that comprises the dna of all available taxa in an ecosystem is an essential step in population analysis, especially for next generation sequencing applications. many nanoparticles as well as naturally occurring clay minerals contain charged surfaces or edges that capture negatively charged dna molecules after cell lysis within dna extraction. depending on the methodology of dna extraction, this phenomenon causes a shift in detection of microbial taxa in ecosystems and a possibl ... | 2015 | 27682112 |
| a non-canonical multisubunit rna polymerase encoded by a giant bacteriophage. | the infection of pseudomonas aeruginosa by the giant bacteriophage phikz is resistant to host rna polymerase (rnap) inhibitor rifampicin. phikz encodes two sets of polypeptides that are distantly related to fragments of the two largest subunits of cellular multisubunit rnaps. polypeptides of one set are encoded by middle phage genes and are found in the phikz virions. polypeptides of the second set are encoded by early phage genes and are absent from virions. here, we report isolation of a five- ... | 2015 | 26490960 |
| mechanism of eif6 release from the nascent 60s ribosomal subunit. | sbds protein (deficient in the inherited leukemia-predisposition disorder shwachman-diamond syndrome) and the gtpase efl1 (an ef-g homolog) activate nascent 60s ribosomal subunits for translation by catalyzing eviction of the antiassociation factor eif6 from nascent 60s ribosomal subunits. however, the mechanism is completely unknown. here, we present cryo-em structures of human sbds and sbds-efl1 bound to dictyostelium discoideum 60s ribosomal subunits with and without endogenous eif6. sbds ass ... | 2015 | 26479198 |
| computational analysis of candidate prion-like proteins in bacteria and their role. | prion proteins were initially associated with diseases such as creutzfeldt jakob and transmissible spongiform encephalopathies. however, deeper research revealed them as versatile tools, exploited by the cells to execute fascinating functions, acting as epigenetic elements or building membrane free compartments in eukaryotes. one of the most intriguing properties of prion proteins is their ability to propagate a conformational assembly, even across species. in this context, it has been observed ... | 2015 | 26528269 |
| structural insights into species-specific features of the ribosome from the pathogen staphylococcus aureus. | the emergence of bacterial multidrug resistance to antibiotics threatens to cause regression to the preantibiotic era. here we present the crystal structure of the large ribosomal subunit from staphylococcus aureus, a versatile gram-positive aggressive pathogen, and its complexes with the known antibiotics linezolid and telithromycin, as well as with a new, highly potent pleuromutilin derivative, bc-3205. these crystal structures shed light on specific structural motifs of the s. aureus ribosome ... | 2015 | 26464510 |
| ribosome hibernation facilitates tolerance of stationary-phase bacteria to aminoglycosides. | upon entry into stationary phase, bacteria dimerize 70s ribosomes into translationally inactive 100s particles by a process called ribosome hibernation. previously, we reported that the hibernation-promoting factor (hpf) of listeria monocytogenes is required for 100s particle formation and facilitates adaptation to a number of stresses. here, we demonstrate that hpf is required for the high tolerance of stationary-phase cultures to aminoglycosides but not to beta-lactam or quinolone antibiotics. ... | 2015 | 26324267 |
| fr171456 is a specific inhibitor of mammalian nsdhl and yeast erg26p. | fr171456 is a natural product with cholesterol-lowering properties in animal models, but its molecular target is unknown, which hinders further drug development. here we show that fr171456 specifically targets the sterol-4-alpha-carboxylate-3-dehydrogenase (saccharomyces cerevisiae--erg26p, homo sapiens--nsdhl (nad(p) dependent steroid dehydrogenase-like)), an essential enzyme in the ergosterol/cholesterol biosynthesis pathway. fr171456 significantly alters the levels of cholesterol pathway inte ... | 2015 | 26456460 |
| structural analysis of nucleosomal barrier to transcription. | thousands of human and drosophila genes are regulated at the level of transcript elongation and nucleosomes are likely targets for this regulation. however, the molecular mechanisms of formation of the nucleosomal barrier to transcribing rna polymerase ii (pol ii) and nucleosome survival during/after transcription remain unknown. here we show that both dna-histone interactions and pol ii backtracking contribute to formation of the barrier and that nucleosome survival during transcription likely ... | 2015 | 26460019 |
| structural comparison between the open and closed forms of citrate synthase from thermus thermophilus hb8. | the crystal structures of citrate synthase from the thermophilic eubacteria thermus thermophilus hb8 (ttcs) were determined for an open form at 1.5 å resolution and for closed form at 2.3 å resolution, respectively. in the absence of ligands ttcs in the open form was crystalized into a tetragonal form with a single subunit in the asymmetric unit. ttcs was also co-crystallized with citrate and coenzyme-a to form an orthorhombic crystal with two homodimers in the asymmetric unit. citrate and coa a ... | 2015 | 27493854 |
| caenorhabditis elegans glp-4 encodes a valyl aminoacyl trna synthetase. | germline stem cell proliferation is necessary to populate the germline with sufficient numbers of cells for gametogenesis and for signaling the soma to control organismal properties such as aging. the caenorhabditis elegans gene glp-4 was identified by the temperature-sensitive allele bn2 where mutants raised at the restrictive temperature produce adults that are essentially germ cell deficient, containing only a small number of stem cells arrested in the mitotic cycle but otherwise have a morph ... | 2015 | 26464357 |
| structure of a human translation termination complex. | in contrast to bacteria that have two release factors, rf1 and rf2, eukaryotes only possess one unrelated release factor erf1, which recognizes all three stop codons of the mrna and hydrolyses the peptidyl-trna bond. while the molecular basis for bacterial termination has been elucidated, high-resolution structures of eukaryotic termination complexes have been lacking. here we present a 3.8 å structure of a human translation termination complex with erf1 decoding a uaa(a) stop codon. the complex ... | 2015 | 26384426 |
| structural insight into fungal cell wall recognition by a cvnh protein with a single lysm domain. | mgg_03307 is a lectin isolated from magnaporte oryzae, a fungus that causes devastating rice blast disease. its function is associated with protecting m. oryzae from the host immune response in plants. to provide the structural basis of how mgg_03307 protects the fungus, crystal structures of its cvnh-lysm module were determined in the absence and presence of glcnac-containing cell wall chitin constituents, which can act as pathogen-associated molecular patterns. our structures revealed that gly ... | 2015 | 26455798 |
| a particular silent codon exchange in a recombinant gene greatly influences host cell metabolic activity. | recombinant protein production using escherichia coli as expression host is highly efficient, however, it also induces strong host cell metabolic burden. energy and biomass precursors are withdrawn from the host's metabolism as they are required for plasmid replication, heterologous gene expression and protein production. rare codons in a heterologous gene may be a further drawback. this study aims to investigate the influence of particular silent codon exchanges within a heterologous gene on ho ... | 2015 | 26438243 |
| an extended dsrbd is required for post-transcriptional modification in human trnas. | in trna, dihydrouridine is a conserved modified base generated by the post-transcriptional reduction of uridine. formation of dihydrouridine 20, located in the d-loop, is catalyzed by dihydrouridine synthase 2 (dus2). human dus2 (hsdus2) expression is upregulated in lung cancers, offering a growth advantage throughout its ability to interact with components of the translation apparatus and inhibit apoptosis. here, we report the crystal structure of the individual domains of hsdus2 and their func ... | 2015 | 26429968 |
| effect of monovalent cations on the kinetics of hypoxic conformational change of mitochondrial complex i. | mitochondrial complex i is a large, membrane-bound enzyme central to energy metabolism, and its dysfunction is implicated in cardiovascular and neurodegenerative diseases. an interesting feature of mammalian complex i is the so-called a/d transition, when the idle enzyme spontaneously converts from the active (a) to the de-active, dormant (d) form. the a/d transition plays an important role in tissue response to ischemia and rate of the conversion can be a crucial factor determining outcome of i ... | 2015 | 26009015 |
| recent insights into the structure, regulation, and function of the v-atpases. | the vacuolar (h(+))-atpases (v-atpases) are atp-dependent proton pumps that acidify intracellular compartments and are also present at the plasma membrane. they function in such processes as membrane traffic, protein degradation, virus and toxin entry, bone resorption, ph homeostasis, and tumor cell invasion. v-atpases are large multisubunit complexes, composed of an atp-hydrolytic domain (v1) and a proton translocation domain (v0), and operate by a rotary mechanism. this review focuses on recen ... | 2015 | 26410601 |
| variation in the ribosome interacting loop of the sec61α from giardia lamblia. | the interaction between the ribosome and the endoplasmic reticulum-located sec61 protein translocon is mediated through an arginine residue of sec61α, which is conserved in all prokaryotic and eukaryotic orthologues characterized to date. using in silico approaches we report that instead of arginine, this ribosome-interaction function is most likely discharged by a lysine residue in the protist giardia lamblia. this functional substitution of the r with a k in glsec61α may have taken place to ac ... | 2015 | 26424409 |
| choosing a suitable method for the identification of replication origins in microbial genomes. | as the replication of genomic dna is arguably the most important task performed by a cell and given that it is controlled at the initiation stage, the events that occur at the replication origin play a central role in the cell cycle. making sense of dna replication origins is important for improving our capacity to study cellular processes and functions in the regulation of gene expression, genome integrity in much finer detail. thus, clearly comprehending the positions and sequences of replicat ... | 2015 | 26483774 |
| affinity purification and structural features of the yeast vacuolar atpase vo membrane sector. | the membrane sector (vo) of the proton pumping vacuolar atpase (v-atpase, v1vo-atpase) from saccharomyces cerevisiae was purified to homogeneity, and its structure was characterized by em of single molecules and two-dimensional crystals. projection images of negatively stained vo two-dimensional crystals showed a ring-like structure with a large asymmetric mass at the periphery of the ring. a cryo-em reconstruction of vo from single-particle images showed subunits a and d in close contact on the ... | 2015 | 26416888 |
| acoustic vibrations contribute to the diffuse scatter produced by ribosome crystals. | the diffuse scattering pattern produced by frozen crystals of the 70s ribosome from thermus thermophilus is as highly structured as it would be if it resulted entirely from domain-scale motions within these particles. however, the qualitative properties of the scattering pattern suggest that acoustic displacements of the crystal lattice make a major contribution to it. | 2015 | 26457426 |