| gene transfer and genome plasticity in thermotoga maritima, a model hyperthermophilic species. | the genome sequence of the hyperthermophilic bacterium thermotoga maritima msb8 presents evidence for lateral gene transfer events between bacterial and archaeal species. to estimate the extent of genomic diversity across the order thermotogales, a comparative genomic hybridization study was initiated to compare nine thermotoga strains to the sequenced t. maritima msb8. many differences could be associated with substrate utilization patterns, which are most likely a reflection of the environment ... | 2005 | 15995209 |
| cloning and expression of islandisin, a new thermostable subtilisin from fervidobacterium islandicum, in escherichia coli. | a gene encoding a subtilisin-like protease, designated islandisin, from the extremely thermophilic bacterium fervidobacterium islandicum (dsmz 5733) was cloned and actively expressed in escherichia coli. the gene was identified by pcr using degenerated primers based on conserved regions around two of the three catalytic residues (asp, his, and ser) of subtilisin-like serine protease-encoding genes. using inverse pcr regions flanking the catalytic residues, the gene could be cloned. sequencing re ... | 2005 | 16000809 |
| ethanol feeding enhances age-related deterioration of the rat hepatic mitochondrion. | chronic ethanol feeding damages the hepatic mitochondrion by increasing mitochondrial dna (mtdna) oxidation, lowering mtdna yields and impairing mitochondrial respiration. these effects are also seen during aging. by employing a 21-day chronic feeding regimen, we investigated the effects of ethanol consumption on mtdna content and mitochondrial respiration in 2-, 12-, and 24-mo-old male rats. aging resulted in decreased mtdna content, increased mtdna damage (as indicated by inhibition of taq pol ... | 2005 | 16020655 |
| origin and evolution of the archaeo-eukaryotic primase superfamily and related palm-domain proteins: structural insights and new members. | we report an in-depth computational study of the protein sequences and structures of the superfamily of archaeo-eukaryotic primases (aeps). this analysis greatly expands the range of diversity of the aeps and reveals the unique active site shared by all members of this superfamily. in particular, it is shown that eukaryotic nucleo-cytoplasmic large dna viruses, including poxviruses, asfarviruses, iridoviruses, phycodnaviruses and the mimivirus, encode aeps of a distinct family, which also includ ... | 2005 | 16027112 |
| polyphosphate kinase regulates error-prone replication by dna polymerase iv in escherichia coli. | the ppk gene encodes polyphosphate kinase (ppk), an enzyme that catalyses the polymerization of inorganic phosphate into long chains of polyphosphate (polyp). an insertion mutation in ppk causes a decrease in adaptive mutation in escherichia coli strain fc40. adaptive mutation in fc40 mostly results from error-prone dna polymerase iv (pol iv), encoded by dinb; most of the antimutagenic phenotype of the ppk mutant disappears in a dinb mutant strain. in addition, the ppk mutant causes a decrease i ... | 2005 | 16045619 |
| the involvement of the aspartate triad of the active center in all catalytic activities of multisubunit rna polymerase. | three conserved aspartate residues in the largest subunit of multisubunit rna polymerases (rnaps) coordinate two mg2+ ions involved in the catalysis of phosphodiester bond synthesis. a structural model based on the stereochemistry of nucleotidyl transfer reaction as well as recent crystallographic data predict that these mg2+ ions should also be involved in the reverse reaction of pyrophosphorolysis as well as in the endo- and exonucleolytic cleavage of the nascent rna. here, we check these pred ... | 2005 | 16049026 |
| evidence for a watson-crick hydrogen bonding requirement in dna synthesis by human dna polymerase kappa. | the efficiency and fidelity of nucleotide incorporation by high-fidelity replicative dna polymerases (pols) are governed by the geometric constraints imposed upon the nascent base pair by the active site. consequently, these polymerases can efficiently and accurately replicate through the template bases which are isosteric to natural dna bases but which lack the ability to engage in watson-crick (w-c) hydrogen bonding. dna synthesis by poleta, a low-fidelity polymerase able to replicate through ... | 2005 | 16055723 |
| evolution and molecular phylogeny of listeria monocytogenes isolated from human and animal listeriosis cases and foods. | to probe the evolution and phylogeny of listeria monocytogenes from defined host species and environments, l. monocytogenes isolates from human (n = 60) and animal (n = 30) listeriosis cases and food samples (n = 30) were randomly selected from a larger collection of isolates (n = 354) obtained in new york state between 1999 and 2001. partial sequencing of four housekeeping genes (gap, prs, purm, and ribc), one stress response gene (sigb), and two virulence genes (acta and inla) revealed between ... | 2005 | 16077098 |
| dna sequence-based subtyping and evolutionary analysis of selected salmonella enterica serotypes. | while serotyping and phage typing have been used widely to characterize salmonella isolates, sensitive subtyping methods that allow for evolutionary analyses are essential for examining salmonella transmission, ecology, and evolution. a set of 25 salmonella enterica isolates, representing five clinically relevant serotypes (serotypes agona, heidelberg, schwarzengrund, typhimurium, and typhimurium var. copenhagen) was initially used to develop a multilocus sequence typing (mlst) scheme for salmon ... | 2005 | 16081897 |
| multiplex pcr: use of heat-stable thermus thermophilus reca protein to minimize non-specific pcr products. | in this paper we report that the inclusion of heat-resistant reca protein from a thermophilic bacteria, thermus thermophilus, and its cofactor (atp) in pcr effectively eliminates non-specific pcr products. the effect of reca protein, which catalyzes pairing between homologous dna molecules with great fidelity in genetic recombination, is due to its promotion of precise priming in pcr (i.e. priming at sites where the primer sequence is completely complementary to that of the target sequence). in ... | 2005 | 16087733 |
| a novel plant major intrinsic protein in physcomitrella patens most similar to bacterial glycerol channels. | a gene encoding a novel fifth type of major intrinsic protein (mip) in plants has been identified in the moss physcomitrella patens. phylogenetic analyses show that this protein, glpf-like intrinsic protein (gip1;1), is closely related to a subclass of glycerol transporters in bacteria that in addition to glycerol are highly permeable to water. a likely explanation of the occurrence of this bacterial-like mip in p. patens is horizontal gene transfer. the expressed p. patens gip1;1 gene contains ... | 2005 | 16113222 |
| amylomaltase of pyrobaculum aerophilum im2 produces thermoreversible starch gels. | amylomaltases are 4-alpha-glucanotransferases (ec 2.4.1.25) of glycoside hydrolase family 77 that transfer alpha-1,4-linked glucans to another acceptor, which can be the 4-oh group of an alpha-1,4-linked glucan or glucose. the amylomaltase-encoding gene (pae1209) from the hyperthermophilic archaeon pyrobaculum aerophilum im2 was cloned and expressed in escherichia coli, and the gene product (pyamase) was characterized. pyamase displays optimal activity at ph 6.7 and 95 degrees c and is the most ... | 2005 | 16151092 |
| positive autoregulation of ci is a dispensable feature of the phage lambda gene regulatory circuitry. | complex gene regulatory circuits contain many features that are likely to contribute to their operation. it is unclear, however, whether all these features are necessary for proper circuit behavior or whether certain ones are refinements that make the circuit work better but are dispensable for qualitatively normal behavior. we have addressed this question using the phage lambda regulatory circuit, which can persist in two stable states, the lytic state and the lysogenic state. in the lysogenic ... | 2005 | 16159777 |
| deletion of the gene rpoz, encoding the omega subunit of rna polymerase, in mycobacterium smegmatis results in fragmentation of the beta' subunit in the enzyme assembly. | a deletion mutation in the gene rpoz of mycobacterium smegmatis causes reduced growth rate and a change in colony morphology. during purification of rna polymerase from the mutant strain, the beta' subunit undergoes fragmentation but the fragments remain associated with the enzyme and maintain it in an active state until the whole destabilized assembly breaks down in the final step of purification. complementation of the mutant strain with an integrated copy of the wild-type rpoz brings back the ... | 2005 | 16159791 |
| the muts c terminus is essential for mismatch repair activity in vivo. | an escherichia coli k-12 strain was constructed with a chromosomal deletion (mutsdelta800) in the muts gene that produced the removal of the c-terminal 53 amino acids which are not present in the muts crystal structure. this strain has a muts null phenotype for mutation avoidance, anti-recombination, and sensitivity to cytotoxic agents in a dam mutant background. | 2005 | 16159793 |
| mutational analysis of escherichia coli heat shock transcription factor sigma 32 reveals similarities with sigma 70 in recognition of the -35 promoter element and differences in promoter dna melting and -10 recognition. | upon the exposure of escherichia coli to high temperature (heat shock), cellular levels of the transcription factor sigma32 rise greatly, resulting in the increased formation of the sigma32 holoenzyme, which is capable of transcription initiation at heat shock promoters. higher levels of heat shock proteins render the cell better able to cope with the effects of higher temperatures. to conduct structure-function studies on sigma32 in vivo, we have carried out site-directed mutagenesis and employ ... | 2005 | 16166539 |
| response of rna polymerase to ppgpp: requirement for the omega subunit and relief of this requirement by dksa. | previous studies have come to conflicting conclusions about the requirement for the omega subunit of rna polymerase in bacterial transcription regulation. we demonstrate here that purified rnap lacking omega does not respond in vitro to the effector of the stringent response, ppgpp. dksa, a transcription factor that works in concert with ppgpp to regulate rrna expression in vivo and in vitro, fully rescues the ppgpp-unresponsiveness of rnap lacking omega, likely explaining why strains lacking om ... | 2005 | 16204187 |
| use of random and saturation mutageneses to improve the properties of thermus aquaticus amylomaltase for efficient production of cycloamyloses. | amylomaltase from thermus aquaticus catalyzes intramolecular transglycosylation of alpha-1,4 glucans to produce cyclic alpha-1,4 glucans (cycloamyloses) with degrees of polymerization of 22 and higher. although the amylomaltase mainly catalyzes the transglycosylation reaction, it also has weak hydrolytic activity, which results in a reduction in the yield of the cycloamyloses. in order to obtain amylomaltase with less hydrolytic activity, random mutagenesis was perfromed for the enzyme gene. tyr ... | 2005 | 16204493 |
| polymorphism of variable-number tandem repeats at multiple loci in mycobacterium tuberculosis. | genotyping based on variable-number tandem repeats (vntr) is currently a very promising tool for studying the molecular epidemiology and phylogeny of mycobacterium tuberculosis. here we investigate the polymorphisms of 48 loci of direct or tandem repeats in m. tuberculosis previously identified by our group. thirty-nine loci, including nine novel ones, were polymorphic. ten vntr loci had high allelic diversity (nei's diversity indices >or= 0.6) and subsequently were used as the representative vn ... | 2005 | 16207958 |
| contribution of msh2 and msh6 subunits to the asymmetric atpase and dna mismatch binding activities of saccharomyces cerevisiae msh2-msh6 mismatch repair protein. | previous analyses of both thermus aquaticus muts homodimer and saccharomyces cerevisiae msh2-msh6 heterodimer have revealed that the subunits in these protein complexes bind and hydrolyze atp asymmetrically, emulating their asymmetric dna binding properties. in the muts homodimer, one subunit (s1) binds atp with high affinity and hydrolyzes it rapidly, while the other subunit (s2) binds atp with lower affinity and hydrolyzes it at an apparently slower rate. interaction of muts with mismatched dn ... | 2006 | 16214425 |
| contribution of msh2 and msh6 subunits to the asymmetric atpase and dna mismatch binding activities of saccharomyces cerevisiae msh2-msh6 mismatch repair protein. | previous analyses of both thermus aquaticus muts homodimer and saccharomyces cerevisiae msh2-msh6 heterodimer have revealed that the subunits in these protein complexes bind and hydrolyze atp asymmetrically, emulating their asymmetric dna binding properties. in the muts homodimer, one subunit (s1) binds atp with high affinity and hydrolyzes it rapidly, while the other subunit (s2) binds atp with lower affinity and hydrolyzes it at an apparently slower rate. interaction of muts with mismatched dn ... | 2006 | 16214425 |
| comparative genomics of thermus thermophilus and deinococcus radiodurans: divergent routes of adaptation to thermophily and radiation resistance. | thermus thermophilus and deinococcus radiodurans belong to a distinct bacterial clade but have remarkably different phenotypes. t. thermophilus is a thermophile, which is relatively sensitive to ionizing radiation and desiccation, whereas d. radiodurans is a mesophile, which is highly radiation- and desiccation-resistant. here we present an in-depth comparison of the genomes of these two related but differently adapted bacteria. | 2005 | 16242020 |
| clinical and molecular findings in osteoporosis-pseudoglioma syndrome. | mutations in the low-density lipoprotein receptor-related protein 5 gene (lrp5) cause autosomal recessive osteoporosis-pseudoglioma syndrome (oppg). we sequenced the coding exons of lrp5 in 37 probands suspected of having oppg on the basis of the co-occurrence of severe congenital or childhood-onset visual impairment with bone fragility or osteoporosis recognized by young adulthood. we found two putative mutant alleles in 26 probands, only one mutant allele in 4 probands, and no mutant alleles i ... | 2005 | 16252235 |
| structural basis for transcription inhibition by tagetitoxin. | tagetitoxin (tgt) inhibits transcription by an unknown mechanism. a structure at a resolution of 2.4 a of the thermus thermophilus rna polymerase (rnap)-tgt complex revealed that the tgt-binding site within the rnap secondary channel overlaps that of the stringent control effector ppgpp, which partially protects rnap from tgt inhibition. tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to tgt in vitro. important ... | 2005 | 16273103 |
| the aauaaa motif of bamboo mosaic virus rna is involved in minus-strand rna synthesis and plus-strand rna polyadenylation. | bamboo mosaic virus (bamv) has a single-stranded positive-sense rna genome with a 5'-cap structure and a 3' poly(a) tail. deleting the internal loop that contains the putative polyadenylation signal (aauaaa) in the 3' untranslated region (utr) of bamv genomic rna appeared to diminish coat protein accumulation to 2% (c. p. cheng and c. h. tsai, j. mol. biol. 288:555-565, 1999). to investigate the function of the aauaaa motif, mutations were introduced into an infectious bamv cdna at each residue ... | 2005 | 16282455 |
| efficient isothermal expansion of human telomeric and minisatellite repeats by thermococcus litoralis dna polymerase. | repeating dna sequences, such as telomeres, centromeres, and micro- and mini-satellites, comprise 50% of the genome and play important roles in regulatory and pathogenic mechanisms. in order to study structures and functions of such repeating sequences, it is important to have simple and efficient methods for making them in vitro. here, we describe the efficient and convenient expansion of repetitive telomeric and minisatellite dna sequences starting from small synthetic templates to final produ ... | 2005 | 16284196 |
| coupled protein domain motion in taq polymerase revealed by neutron spin-echo spectroscopy. | long-range conformational changes in proteins are ubiquitous in biology for the transmission and amplification of signals; such conformational changes can be triggered by small-amplitude, nanosecond protein domain motion. understanding how conformational changes are initiated requires the characterization of protein domain motion on these timescales and on length scales comparable to protein dimensions. using neutron spin-echo spectroscopy (nse), normal mode analysis, and a statistical-mechanica ... | 2005 | 16306270 |
| allele-specific amplification in cancer revealed by snp array analysis. | amplification, deletion, and loss of heterozygosity of genomic dna are hallmarks of cancer. in recent years a variety of studies have emerged measuring total chromosomal copy number at increasingly high resolution. similarly, loss-of-heterozygosity events have been finely mapped using high-throughput genotyping technologies. we have developed a probe-level allele-specific quantitation procedure that extracts both copy number and allelotype information from single nucleotide polymorphism (snp) ar ... | 2005 | 16322765 |
| properties of thermus ruber strains isolated from icelandic hot springs and dna:dna homology of thermus ruber and thermus aquaticus. | seventeen pink-pigmented strains of the genus thermus were isolated from samples collected from thermal areas of iceland. the strains were examined by using phenotypic characterization and dna:dna homology and were compared with recognized strains. visually, the strains could be divided into three groups based on their pigmentation; however, spectroscopic studies of the pigments indicated little difference among them. most strains required a vitamin supplement for growth and used fructose, malto ... | 1988 | 16347714 |
| production and extracellular secretion of aqualysin i (a thermophilic subtilisin-type protease) in a host-vector system for thermus thermophilus. | aqualysin i is synthesized as a large precursor, processed, and secreted into the culture medium by thermus aquaticus yt-1. an expression plasmid for the aqualysin i gene in t. thermophilus hb27 was constructed. t. thermophilus cells harboring the recombinant plasmid produced correctly processed aqualysin i, and the mature enzyme was secreted into the culture medium. | 1991 | 16348594 |
| molecular genetic and structural modeling studies of staphylococcus aureus rna polymerase and the fitness of rifampin resistance genotypes in relation to clinical prevalence. | the adaptive and further evolutionary responses of staphylococcus aureus to selection pressure with the antibiotic rifampin have not been explored in detail. we now present a detailed analysis of these systems. the use of rifampin for the chemotherapy of infections caused by s. aureus has resulted in the selection of mutants with alterations within the beta subunit of the target enzyme, rna polymerase. using a new collection of strains, we have identified numerous novel mutations in the beta sub ... | 2006 | 16377701 |
| mutation in the bacillus subtilis rna polymerase beta' subunit confers resistance to lipiarmycin. | | 2006 | 16377724 |
| transcriptomic and proteomic approach for understanding the molecular basis of adaptation of saccharomyces cerevisiae to wine fermentation. | throughout alcoholic fermentation, saccharomyces cerevisiae cells have to cope with several stress conditions that could affect their growth and viability. in addition, the metabolic activity of yeast cells during this process leads to the production of secondary compounds that contribute to the organoleptic properties of the resulting wine. commercial strains have been selected during the last decades for inoculation into the must to carry out the alcoholic fermentation on the basis of physiolo ... | 2006 | 16391125 |
| dual role of muts glutamate 38 in dna mismatch discrimination and in the authorization of repair. | muts plays a critical role in dna mismatch repair in escherichia coli by binding to mismatches and initiating repair in an atp-dependent manner. mutational analysis of a highly conserved glutamate, glu38, has revealed its role in mismatch recognition by enabling muts to discriminate between homoduplex and mismatched dna. crystal structures of muts have shown that glu38 forms a hydrogen bond to one of the mismatched bases. in this study, we have analyzed the crystal structures, dna binding and th ... | 2006 | 16407973 |
| dna polymerase catalysis in the absence of watson-crick hydrogen bonds: analysis by single-turnover kinetics. | we report the first pre-steady-state kinetic studies of dna replication in the absence of hydrogen bonds. we have used nonpolar nucleotide analogues that mimic the shape of a watson-crick base pair to investigate the kinetic consequences of a lack of hydrogen bonds in the polymerase reaction catalyzed by the klenow fragment of dna polymerase i from escherichia coli. with a thymine isostere lacking hydrogen-bonding ability in the nascent pair, the efficiency (k(pol)/kd) of the polymerase reaction ... | 2006 | 16411765 |
| probing the importance of hydrogen bonds in the active site of the subtilisin nattokinase by site-directed mutagenesis and molecular dynamics simulation. | hydrogen bonds occurring in the catalytic triad (asp32, his64 and ser221) and the oxyanion hole (asn155) are very important to the catalysis of peptide bond hydrolysis by serine proteases. for the subtilisin nk (nattokinase), a bacterial serine protease, construction and analysis of a three-dimensional structural model suggested that several hydrogen bonds formed by four residues function to stabilize the transition state of the hydrolysis reaction. these four residues are ser33, asp60, ser62 an ... | 2006 | 16411898 |
| multiplexed detection of anthrax-related toxin genes. | simultaneous analysis of three targets in three colors on any real-time polymerase chain reaction (pcr) instrument would increase the flexibility of real-time pcr. for the detection of bacillus strains that can cause inhalation anthrax-related illness, this ability would be valuable because two plasmids confer virulence, and internal positive controls are needed to monitor the testing in cases lacking target-specific signals. using a real-time pcr platform called multicode-rtx, multiple assays w ... | 2006 | 16436639 |
| mutations in acy1, the gene encoding aminoacylase 1, cause a novel inborn error of metabolism. | n-terminal acetylation of proteins is a widespread and highly conserved process. aminoacylase 1 (acy1; ec 3.5.14) is the most abundant of the aminoacylases, a class of enzymes involved in hydrolysis of n-acetylated proteins. here, we present four children with genetic deficiency of acy1. they were identified through organic acid analyses using gas chromatography-mass spectrometry, revealing increased urinary excretion of several n-acetylated amino acids, including the derivatives of methionine, ... | 2006 | 16465618 |
| solute probes of conformational changes in open complex (rpo) formation by escherichia coli rna polymerase at the lambdapr promoter: evidence for unmasking of the active site in the isomerization step and for large-scale coupled folding in the subsequent conversion to rpo. | transcription initiation is a multistep process involving a series of requisite conformational changes in rna polymerase (r) and promoter dna (p) that create the open complex (rp(o)). here, we use the small solutes urea and glycine betaine (gb) to probe the extent and type of surface area changes in the formation of rp(o) between esigma(70) rna polymerase and lambdap(r) promoter dna. effects of urea quantitatively reflect changes in amide surface and are particularly well-suited to detect couple ... | 2006 | 16475805 |
| in vitro activity of novel rifamycins against rifamycin-resistant staphylococcus aureus. | we describe novel rifamycin derivatives (new chemical entities [nces]) that retain significant activity against a comprehensive collection of staphylococcus aureus strains that are resistant to rifamycins. this collection of resistant strains contains 21 of the 26 known single-amino-acid alterations in rpob, the target of rifamycins. some nces also demonstrated a lower frequency of resistance development than rifampin and rifalazil in s. aureus as measured in a resistance emergence test. when as ... | 2006 | 16495239 |
| a structural model for the large subunit of the mammalian mitochondrial ribosome. | protein translation is essential for all forms of life and is conducted by a macromolecular complex, the ribosome. evolutionary changes in protein and rna sequences can affect the 3d organization of structural features in ribosomes in different species. the most dramatic changes occur in animal mitochondria, whose genomes have been reduced and altered significantly. the rna component of the mitochondrial ribosome (mitoribosome) is reduced in size, with a compensatory increase in protein content. ... | 2006 | 16510155 |
| mutations in the saccharomyces cerevisiae rpb1 gene conferring hypersensitivity to 6-azauracil. | rna polymerase ii (rnapii) in eukaryotic cells drives transcription of most messenger rnas. rnapii core enzyme is composed of 12 polypeptides where rpb1 is the largest subunit. to further understand the mechanisms of rnapii transcription, we isolated and characterized novel point mutants of rpb1 that are sensitive to the nucleotide-depleting drug 6-azauracil (6au). in this work we reisolated the rpo21-24/rpb1-e1230k allele, which reduces the interaction of rnapii-tfiis, and identified five new p ... | 2006 | 16510790 |
| thermophilic lifestyle for an uncultured archaeon from hydrothermal vents: evidence from environmental genomics. | we present a comparative analysis of two genome fragments isolated from a diverse and widely distributed group of uncultured euryarchaea from deep-sea hydrothermal vents. the optimal activity and thermostability of a dna polymerase predicted in one fragment were close to that of the thermophilic archaeon thermoplasma acidophilum, providing evidence for a thermophilic way of life of this group of uncultured archaea. | 2006 | 16517686 |
| nabp1, a novel rorgamma-regulated gene encoding a single-stranded nucleic-acid-binding protein. | rorgamma2 (retinoid-related orphan receptor gamma2) plays a critical role in the regulation of thymopoiesis. microarray analysis was performed in order to uncover differences in gene expression between thymocytes of wild-type and rorgamma-/- mice. this analysis identified a novel gene encoding a 22 kda protein, referred to as nabp1 (nucleic-acid-binding protein 1). this subsequently led to the identification of an additional protein, closely related to nabp1, designated nabp2. both proteins cont ... | 2006 | 16533169 |
| expression of s100a8 correlates with inflammatory lung disease in congenic mice deficient of the cystic fibrosis transmembrane conductance regulator. | lung disease in cystic fibrosis (cf) patients is dominated by chronic inflammation with an early and inappropriate influx of neutrophils causing airway destruction. congenic c57bl/6 cf mice develop lung inflammatory disease similar to that of patients. in contrast, lungs of congenic balb/c cf mice remain unaffected. the basis of the neutrophil influx to the airways of cf patients and c57bl/6 mice, and its precipitating factor(s) (spontaneous or infection induced) remains unclear. | 2006 | 16571124 |
| a novel processive mechanism for dna synthesis revealed by structure, modeling and mutagenesis of the accessory subunit of human mitochondrial dna polymerase. | mitochondrial dna polymerase (pol gamma) is the sole dna polymerase responsible for replication and repair of animal mitochondrial dna. here, we address the molecular mechanism by which the human holoenzyme achieves high processivity in nucleotide polymerization. we have determined the crystal structure of human pol gamma-beta, the accessory subunit that binds with high affinity to the catalytic core, pol gamma-alpha, to stimulate its activity and enhance holoenzyme processivity. we find that hu ... | 2006 | 16574152 |
| conformational heterogeneity in rna polymerase observed by single-pair fret microscopy. | kinetic, structural, and single-molecule transcription measurements suggest that rna polymerase can adopt many different conformations during elongation. we have measured the geometry of the dna and rna in ternary elongation complexes using single-pair fluorescence resonance energy transfer. six different synthetic transcription elongation complexes were constructed from dna containing an artificial transcription bubble, an rna primer, and core rna polymerase from escherichia coli. two different ... | 2006 | 16581837 |
| operational strategies, monitoring and control of heterologous protein production in the methylotrophic yeast pichia pastoris under different promoters: a review. | the methylotrophic yeast pichia pastoris has been widely reported as a suitable expression system for heterologous protein production. the use of different phenotypes under paox promoter, other alternative promoters, culture medium, and operational strategies with the objective to maximize either yield or productivity of the heterologous protein, but also to obtain a repetitive product batch to batch to get a robust process for the final industrial application have been reported. medium composit ... | 2006 | 16600031 |
| ph-dependent conformational switch activates the inhibitor of transcription elongation. | gfh1, a transcription factor from thermus thermophilus, inhibits all catalytic activities of rna polymerase (rnap). we characterized the gfh1 structure, function and possible mechanism of action and regulation. gfh1 inhibits rnap by competing with ntps for coordinating the active site mg2+ ion. this coordination requires at least two aspartates at the tip of the gfh1 n-terminal coiled-coil domain (ntd). the overall structure of gfh1 is similar to that of the escherichia coli transcript cleavage ... | 2006 | 16628221 |
| differential expression of placental villous angiopoietin-1 and -2 during early, mid and late baboon pregnancy. | although vascular endothelial growth factor (vegf), angiopoietin-1 (ang-1) and ang-2 have important roles in angiogenesis, very little is known about the regulation of these factors in the villous placenta during human pregnancy. in the present study, to investigate whether placental expression of ang-1, ang-2 and vegf was altered in a cell-specific manner with advancing baboon gestation, the mrna levels of these growth factors were determined by rt-pcr in cells isolated by percoll gradient cent ... | 2007 | 16630655 |
| differential expression of placental villous angiopoietin-1 and -2 during early, mid and late baboon pregnancy. | although vascular endothelial growth factor (vegf), angiopoietin-1 (ang-1) and ang-2 have important roles in angiogenesis, very little is known about the regulation of these factors in the villous placenta during human pregnancy. in the present study, to investigate whether placental expression of ang-1, ang-2 and vegf was altered in a cell-specific manner with advancing baboon gestation, the mrna levels of these growth factors were determined by rt-pcr in cells isolated by percoll gradient cent ... | 2007 | 16630655 |
| the molecular mechanism of dna damage recognition by muts homologs and its consequences for cell death response. | we determined the molecular mechanism of cell death response by muts homologs in distinction to the repair event. key protein-dna contacts differ in the interaction of muts homologs with cisplatinated versus mismatched dna. mutational analyses of protein-dna contacts, which were predicted by molecular dynamics (md) simulations, were performed. mutations in suggested interaction sites can affect repair and cell death response independently, and to different extents. a glutamate residue is identif ... | 2006 | 16648361 |
| localization of the escherichia coli rna polymerase beta' subunit residue phosphorylated by bacteriophage t7 kinase gp0.7. | during bacteriophage t7 infection, the escherichia coli rna polymerase beta' subunit is phosphorylated by the phage-encoded kinase gp0.7. here, we used proteolytic degradation and mutational analysis to localize the phosphorylation site to a single amino acid, thr(1068), in the evolutionarily hypervariable segment of beta'. using a phosphomimetic substitution of thr(1068), we show that phosphorylation of beta' leads to increased rho-dependent transcription termination, which may help to switch f ... | 2006 | 16672600 |
| low-frequency normal modes that describe allosteric transitions in biological nanomachines are robust to sequence variations. | by representing the high-resolution crystal structures of a number of enzymes using the elastic network model, it has been shown that only a few low-frequency normal modes are needed to describe the large-scale domain movements that are triggered by ligand binding. here we explore a link between the nearly invariant nature of the modes that describe functional dynamics at the mesoscopic level and the large evolutionary sequence variations at the residue level. by using a structural perturbation ... | 2006 | 16682636 |
| improvements of rolling circle amplification (rca) efficiency and accuracy using thermus thermophilus ssb mutant protein. | rolling circle amplification (rca) of plasmid or genomic dna using random hexamers and bacteriophage phi29 dna polymerase has become increasingly popular in the amplification of template dna in dna sequencing. we have found that the mutant protein of single-stranded dna binding protein (ssb) from thermus thermophilus (tth) hb8 enhances the efficiency of amplification of dna templates. in addition, the tthssb mutant protein increased the specificity of phi29 dna polymerase. we have overexpressed ... | 2006 | 16707659 |
| ca2+-dependent maturation of subtilisin from a hyperthermophilic archaeon, thermococcus kodakaraensis: the propeptide is a potent inhibitor of the mature domain but is not required for its folding. | subtilisin from the hyperthermophilic archaeon thermococcus kodakaraensis kod1 is a member of the subtilisin family. t. kodakaraensis subtilisin in a proform (t. kodakaraensis pro-subtilisin), as well as its propeptide (t. kodakaraensis propeptide) and mature domain (t. kodakaraensis mat-subtilisin), were independently overproduced in e. coli, purified, and biochemically characterized. t. kodakaraensis pro-subtilisin was inactive in the absence of ca2+ but was activated upon autoprocessing and d ... | 2006 | 16751527 |
| involvement of phi29 dna polymerase thumb subdomain in the proper coordination of synthesis and degradation during dna replication. | phi29 dna polymerase achieves a functional coupling between its 3'-5' exonuclease and polymerization activities by means of important contacts with the dna at both active sites. the placement and orientation of residues lys538, lys555, lys557, gln560, thr571, thr573 and lys575 in a modelled phi29 dna polymerase-dna complex suggest a dna-binding role. in addition, crystal structure of phi29 dna polymerase-oligo (dt)5 complex showed leu567, placed at the tip of the thumb subdomain, lying between t ... | 2006 | 16757576 |
| catalysis by the second class of trna(m1g37) methyl transferase requires a conserved proline. | the enzyme trna(m1g37) methyl transferase catalyzes the transfer of a methyl group from s-adenosyl methionine (adomet) to the n1 position of g37, which is 3' to the anticodon sequence and whose modification is important for maintaining the reading frame fidelity. while the enzyme in bacteria is highly conserved and is encoded by the trmd gene, recent studies show that the counterpart of this enzyme in archaea and eukarya, encoded by the trm5 gene, is unrelated to trmd both in sequence and in str ... | 2006 | 16768442 |
| structure of a gdp:alf4 complex of the srp gtpases ffh and ftsy, and identification of a peripheral nucleotide interaction site. | the signal recognition particle (srp) gtpases ffh and ftsy play a central role in co-translational targeting of proteins, assembling in a gtp-dependent manner to generate the srp targeting complex at the membrane. a suite of residues in ftsy have been identified that are essential for the hydrolysis of gtp that accompanies disengagement. we have argued previously on structural grounds that this region mediates interactions that serve to activate the complex for disengagement and term it the acti ... | 2006 | 16780874 |
| seven different genes encode a diverse mixture of isoforms of bet v 1, the major birch pollen allergen. | pollen of the european white birch (betula pendula, syn. b. verrucosa) is an important cause of hay fever. the main allergen is bet v 1, member of the pathogenesis-related class 10 (pr-10) multigene family. to establish the number of pr-10/bet v 1 genes and the isoform diversity within a single tree, pcr amplification, cloning and sequencing of pr-10 genes was performed on two diploid b. pendula cultivars and one interspecific tetraploid betula hybrid. sequences were attributed to putative genes ... | 2006 | 16820045 |
| identification of single-point mutations in mycobacterial 16s rrna sequences by confocal single-molecule fluorescence spectroscopy. | we demonstrate the specific identification of single nucleotide polymorphism (snp) responsible for rifampicin resistance of mycobacterium tuberculosis applying fluorescently labeled dna-hairpin structures (smart probes) in combination with single-molecule fluorescence spectroscopy. smart probes are singly labeled hairpin-shaped oligonucleotides bearing a fluorescent dye at the 5' end that is quenched by guanosine residues in the complementary stem. upon hybridization to target sequences, a confo ... | 2006 | 16870719 |
| purification and characterization of a thermostable, haloalkaliphilic extracellular serine protease from the extreme halophilic archaeon halogeometricum borinquense strain tss101. | a novel haloalkaliphilic, thermostable serine protease was purified from the extreme halophilic archaeon, halogeometricum borinquense strain tss101. the protease was isolated from a stationary phase culture, purified 116-fold with 18% yield and characterized biochemically. the molecular mass of the purified enzyme was estimated to be 86 kda. the enzyme showed the highest activity at 60 degrees c and ph 10.0 in 20% nacl. the enzyme had high activity over the ph range from 6.0 to 10.0. enzymatic a ... | 2006 | 16877321 |
| evidence of a genomic biomarker in normal human epithelial mammary cell line, mcf-10a, that is absent in the human breast cancer cell line, mcf-7. | this study investigated the use of dna amplification fingerprinting (daf) to identify biomarkers useful in the elucidating genetic factors that lead to carcinogenesis. the dna amplification fingerprinting (daf) technique was used to generate fingerprint profiles of a normal human mammary epithelial cell line (mcf-10a) and a human breast cancer cell line (mcf-7). when compared with one another, a polymorphic biomarker gene (262 base pairs (bps)) was identified in mcf-10a but was not present in mc ... | 2006 | 16883051 |
| hyperthermophilic dna methyltransferase m.pabi from the archaeon pyrococcus abyssi. | genome sequence comparisons among multiple species of pyrococcus, a hyperthermophilic archaeon, revealed a linkage between a putative restriction-modification gene complex and several large genome polymorphisms/rearrangements. from a region apparently inserted into the pyrococcus abyssi genome, a hyperthermoresistant restriction enzyme [pabi; 5'-(gta/c)] with a novel structure was discovered. in the present work, the neighboring methyltransferase homologue, m.pabi, was characterized. its n-termi ... | 2006 | 16885288 |
| trypanosoma congolense procyclins: unmasking cryptic major surface glycoproteins in procyclic forms. | in the tsetse fly, the protozoan parasite trypanosoma congolense is covered by a dense layer of glycosylphosphatidylinositol (gpi)-anchored molecules. these include a protease-resistant surface molecule (prs), which is expressed by procyclic forms early in infection, and a glutamic acid- and alanine-rich protein (garp), which appears at later stages. since neither of these surface antigens is expressed at intermediate stages, we investigated whether a gpi-anchored protein of 50 to 58 kda, previo ... | 2006 | 16896226 |
| the structural basis for promoter -35 element recognition by the group iv sigma factors. | the control of bacterial transcription initiation depends on a primary sigma factor for housekeeping functions, as well as alternative sigma factors that control regulons in response to environmental stresses. the largest and most diverse subgroup of alternative sigma factors, the group iv extracytoplasmic function sigma factors, directs the transcription of genes that regulate a wide variety of responses, including envelope stress and pathogenesis. we determined the 2.3-a resolution crystal str ... | 2006 | 16903784 |
| elongation complexes of thermus thermophilus rna polymerase that possess distinct translocation conformations. | we have characterized elongation complexes (ecs) of rna polymerase from the extremely thermophilic bacterium, thermus thermophilus. we found that complexes assembled on nucleic acid scaffolds are transcriptionally competent at high temperature (50-80 degrees c) and, depending upon the organization of the scaffold, possess distinct translocation conformations. ecs assembled on scaffolds with a 9 bp rna:dna hybrid are highly stable, resistant to pyrophosphorolysis, and are in the posttranslocated ... | 2006 | 16914440 |
| unique classes of mutations in the saccharomyces cerevisiae g-protein translation elongation factor 1a suppress the requirement for guanine nucleotide exchange. | g-proteins play critical roles in many cellular processes and are regulated by accessory proteins that modulate the nucleotide-bound state. such proteins, including eukaryotic translation elongation factor 1a (eef1a), are frequently reactivated by guanine nucleotide exchange factors (gefs). in the yeast saccharomyces cerevisiae, only the catalytic subunit of the gef complex, eef1balpha, is essential for viability. the requirement for the tef5 gene encoding eef1balpha can be suppressed by the pre ... | 2006 | 16951075 |
| easi--enrichment of alternatively spliced isoforms. | alternative splicing produces more than one protein from the majority of genes and the rarer forms can have dominant functions. instability of alternative transcripts can also hinder the study of regulation of gene expression by alternative splicing. to investigate the true extent of alternative splicing we have developed a simple method of enriching alternatively spliced isoforms (easi) from pcrs using beads charged with thermus aquaticus single-stranded dna-binding protein (t.aq ssb). this dir ... | 2006 | 16951290 |
| two metallocarboxypeptidases from the protozoan trypanosoma cruzi belong to the m32 family, found so far only in prokaryotes. | mcps (metallocarboxypeptidases) of the m32 family of peptidases have been identified in a number of prokaryotic organisms, and only a few of them have been characterized biochemically. members of this family are absent from eukaryotic genomes, with the remarkable exception of those of trypanosomatids. the genome of the cl brener clone of trypanosoma cruzi, the causative agent of chagas' disease, encodes two such mcps, with 64% identity between them: tcmcp-1 and tcmcp-2. both genes, which are pre ... | 2007 | 17007610 |
| two metallocarboxypeptidases from the protozoan trypanosoma cruzi belong to the m32 family, found so far only in prokaryotes. | mcps (metallocarboxypeptidases) of the m32 family of peptidases have been identified in a number of prokaryotic organisms, and only a few of them have been characterized biochemically. members of this family are absent from eukaryotic genomes, with the remarkable exception of those of trypanosomatids. the genome of the cl brener clone of trypanosoma cruzi, the causative agent of chagas' disease, encodes two such mcps, with 64% identity between them: tcmcp-1 and tcmcp-2. both genes, which are pre ... | 2007 | 17007610 |
| a novel endonuclease iv post-pcr genotyping system. | here we describe a novel endonuclease iv (endo iv) based assay utilizing a substrate that mimics the abasic lesions that normally occur in double-stranded dna. the three component substrate is characterized by single-stranded dna target, an oligonucleotide probe, separated from a helper oligonucleotide by a one base gap. the oligonucleotide probe contains a non-fluorescent quencher at the 5' end and fluorophore attached to the 3' end through a special rigid linker. fluorescence of the oligonucle ... | 2006 | 17012270 |
| structural and functional analysis of the muts c-terminal tetramerization domain. | the escherichia coli dna mismatch repair (mmr) protein muts is essential for the correction of dna replication errors. in vitro, muts exists in a dimer/tetramer equilibrium that is converted into a monomer/dimer equilibrium upon deletion of the c-terminal 53 amino acids. in vivo and in vitro data have shown that this c-terminal domain (ctd, residues 801-853) is critical for tetramerization and the function of muts in mmr and anti-recombination. we report the expression, purification and analysis ... | 2006 | 17012287 |
| regulatory loop between redox sensing of the nadh/nad(+) ratio by rex (ydih) and oxidation of nadh by nadh dehydrogenase ndh in bacillus subtilis. | nadh dehydrogenase is a key component of the respiratory chain. it catalyzes the oxidation of nadh by transferring electrons to ubiquinone and establishes a proton motive force across the cell membrane. the yjld (renamed ndh) gene of bacillus subtilis is predicted to encode an enzyme similar to the nadh dehydrogenase ii of escherichia coli, encoded by the ndh gene. we have shown that the yjlc-ndh operon is negatively regulated by ydih (renamed rex), a homolog of rex in streptomyces coelicolor, a ... | 2006 | 17015645 |
| physiological analysis of the stringent response elicited in an extreme thermophilic bacterium, thermus thermophilus. | guanosine tetraphosphate (ppgpp) is a key mediator of stringent control, an adaptive response of bacteria to amino acid starvation, and has thus been termed a bacterial alarmone. previous x-ray crystallographic analysis has provided a structural basis for the transcriptional regulation of rna polymerase activity by ppgpp in the thermophilic bacterium thermus thermophilus. here we investigated the physiological basis of the stringent response by comparing the changes in intracellular ppgpp levels ... | 2006 | 17015650 |
| a mechanism of nucleotide misincorporation during transcription due to template-strand misalignment. | transcription errors by t7 rna polymerase (rnap) may occur as the result of a mechanism in which the template base two positions downstream of the 3' end of the rna (the tsn+1 base) is utilized during two consecutive nucleotide-addition cycles. in the first cycle, misalignment of the template strand leads to incorporation of a nucleotide that is complementary to the tsn+1 base. in the second cycle, the template is realigned and the mismatched primer is efficiently extended, resulting in a substi ... | 2006 | 17052458 |
| structures of the pin domains of smg6 and smg5 reveal a nuclease within the mrna surveillance complex. | smg6 and smg5 are essential factors in nonsense-mediated mrna decay, a conserved pathway that degrades mrnas with premature translation termination codons. both smg5 and smg6 have been predicted to contain a c-terminal pin (pilt n-terminus) domain, present in proteins with ribonuclease activity. we have determined the structures of human smg5 and smg6 pin domains. although they share a similar overall fold related to ribonucleases of the rnase h family, they have local differences at the putativ ... | 2006 | 17053788 |
| site-directed mutagenesis in the fingers subdomain of hiv-1 reverse transcriptase reveals a specific role for the beta3-beta4 hairpin loop in dntp selection. | hiv-1 reverse transcriptase shares the key features of high fidelity polymerases, such as a closed architecture of the active site, but displays a level of fidelity that is intermediate to that of high fidelity, replicative polymerases and low fidelity translesion synthesis (tls) polymerases. the beta3-beta4 loop of the hiv-1 rt fingers subdomain makes transient contacts with the dntp and template base. to investigate the role of active site architecture in hiv-1 rt fidelity, we truncated the be ... | 2007 | 17055529 |
| site-directed mutagenesis in the fingers subdomain of hiv-1 reverse transcriptase reveals a specific role for the beta3-beta4 hairpin loop in dntp selection. | hiv-1 reverse transcriptase shares the key features of high fidelity polymerases, such as a closed architecture of the active site, but displays a level of fidelity that is intermediate to that of high fidelity, replicative polymerases and low fidelity translesion synthesis (tls) polymerases. the beta3-beta4 loop of the hiv-1 rt fingers subdomain makes transient contacts with the dntp and template base. to investigate the role of active site architecture in hiv-1 rt fidelity, we truncated the be ... | 2007 | 17055529 |
| mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase. | numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ... | 2007 | 17095011 |
| mechanism of template-independent nucleotide incorporation catalyzed by a template-dependent dna polymerase. | numerous template-dependent dna polymerases are capable of catalyzing template-independent nucleotide additions onto blunt-end dna. such non-canonical activity has been hypothesized to increase the genomic hypermutability of retroviruses including human immunodeficiency viruses. here, we employed pre-steady state kinetics and x-ray crystallography to establish a mechanism for blunt-end additions catalyzed by sulfolobus solfataricus dpo4. our kinetic studies indicated that the first blunt-end dat ... | 2007 | 17095011 |
| characterization of specific donor binding to alpha1,4-n-acetylhexosaminyltransferase extl2 using isothermal titration calorimetry. | glycosyltransferases encompass one of the largest families of enzymes found in nature. their principle function is to catalyze the transfer of activated donor-sugar molecules to various acceptor substrates. the molecular basis that governs this specific transfer reaction, such as how a given transferase determines donor-sugar specificity, remains to be elucidated. human alpha1,4-n-acetylhexosaminyltransferase (extl2) transfers n-acetylglucosamine and n-acetylgalactosamine but does not transfer g ... | 2006 | 17113856 |
| essential bacterial functions encoded by gene pairs. | to address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. in this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. we identified 135 putative protein pairs in bacillus subtilis and attempted to disrupt the gene ... | 2007 | 17114254 |
| essential bacterial functions encoded by gene pairs. | to address the need for new antibacterials, a number of bacterial genomes have been systematically disrupted to identify essential genes. such programs have focused on the disruption of single genes and may have missed functions encoded by gene pairs or multiple genes. in this work, we hypothesized that we could predict the identity of pairs of proteins within one organism that have the same function. we identified 135 putative protein pairs in bacillus subtilis and attempted to disrupt the gene ... | 2007 | 17114254 |
| a unique error signature for human dna polymerase nu. | human dna polymerase nu (pol nu) is one of three a family polymerases conserved in vertebrates. although its biological functions are unknown, pol nu has been implicated in dna repair and in translesion dna synthesis (tls). pol nu lacks intrinsic exonucleolytic proofreading activity and discriminates poorly against misinsertion of dntp opposite template thymine or guanine, implying that it should copy dna with low base substitution fidelity. to test this prediction and to comprehensively examine ... | 2007 | 17118716 |
| a unique error signature for human dna polymerase nu. | human dna polymerase nu (pol nu) is one of three a family polymerases conserved in vertebrates. although its biological functions are unknown, pol nu has been implicated in dna repair and in translesion dna synthesis (tls). pol nu lacks intrinsic exonucleolytic proofreading activity and discriminates poorly against misinsertion of dntp opposite template thymine or guanine, implying that it should copy dna with low base substitution fidelity. to test this prediction and to comprehensively examine ... | 2007 | 17118716 |
| acta is required for crossing of the fetoplacental barrier by listeria monocytogenes. | the facultative intracellular bacterial pathogen listeria monocytogenes induces severe fetal infection during pregnancy. little is known about the molecular mechanisms allowing the maternofetal transmission of bacteria. in this work, we studied fetoplacental invasion by infecting mice with various mutants lacking virulence factors involved in the intracellular life cycle of l. monocytogenes. we found that the placenta was highly susceptible to bacteria, including avirulent bacteria, such as an l ... | 2007 | 17118980 |
| acta is required for crossing of the fetoplacental barrier by listeria monocytogenes. | the facultative intracellular bacterial pathogen listeria monocytogenes induces severe fetal infection during pregnancy. little is known about the molecular mechanisms allowing the maternofetal transmission of bacteria. in this work, we studied fetoplacental invasion by infecting mice with various mutants lacking virulence factors involved in the intracellular life cycle of l. monocytogenes. we found that the placenta was highly susceptible to bacteria, including avirulent bacteria, such as an l ... | 2007 | 17118980 |
| biochemical characterisation of lign, an nad+-dependent dna ligase from the halophilic euryarchaeon haloferax volcanii that displays maximal in vitro activity at high salt concentrations. | dna ligases are required for dna strand joining in all forms of cellular life. nad+-dependent dna ligases are found primarily in eubacteria but also in some eukaryotic viruses, bacteriophage and archaea. among the archaeal nad+-dependent dna ligases is the lign enzyme of the halophilic euryarchaeon haloferax volcanii, the gene for which was apparently acquired by hfx. volcanii through lateral gene transfer (lgt) from a halophilic eubacterium. genetic studies show that the lgt-acquired lign enzym ... | 2006 | 17132163 |
| asfv dna polymerse x is extremely error-prone under diverse assay conditions and within multiple dna sequence contexts. | we previously demonstrated that the dna repair system encoded by the african swine fever virus (asfv) is both extremely error-prone during the single-nucleotide gap-filling step (catalyzed by asfv dna polymerase x) and extremely error-tolerant during the nick-sealing step (catalyzed by asfv dna ligase). on the basis of these findings we have suggested that at least some of the diversity known to exist among asfv isolates may be a consequence of mutagenic dna repair, wherein damaged nucleotides a ... | 2006 | 17144676 |
| structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(c) from mycobacterium tuberculosis. | sigma factors are transcriptional regulatory proteins that bind to the rna polymerase and dictate gene expression. the extracytoplasmic function (ecf) sigma factors govern the environment dependent regulation of transcription. ecf sigma factors have two domains sigma(2) and sigma(4) that recognize the -10 and -35 promoter elements. however, unlike the primary sigma factor sigma(a), the ecf sigma factors lack sigma(3), a region that helps in the recognition of the extended -10 element and sigma(1 ... | 2007 | 17145760 |
| structural and biophysical studies on two promoter recognition domains of the extra-cytoplasmic function sigma factor sigma(c) from mycobacterium tuberculosis. | sigma factors are transcriptional regulatory proteins that bind to the rna polymerase and dictate gene expression. the extracytoplasmic function (ecf) sigma factors govern the environment dependent regulation of transcription. ecf sigma factors have two domains sigma(2) and sigma(4) that recognize the -10 and -35 promoter elements. however, unlike the primary sigma factor sigma(a), the ecf sigma factors lack sigma(3), a region that helps in the recognition of the extended -10 element and sigma(1 ... | 2007 | 17145760 |
| infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu. | mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ... | 2007 | 17160893 |
| infantile encephalopathy and defective mitochondrial dna translation in patients with mutations of mitochondrial elongation factors efg1 and eftu. | mitochondrial protein translation is a complex process performed within mitochondria by an apparatus composed of mitochondrial dna (mtdna)-encoded rnas and nuclear dna-encoded proteins. although the latter by far outnumber the former, the vast majority of mitochondrial translation defects in humans have been associated with mutations in rna-encoding mtdna genes, whereas mutations in protein-encoding nuclear genes have been identified in a handful of cases. genetic investigation involving patient ... | 2007 | 17160893 |
| srp rna provides the physiologically essential gtpase activation function in cotranslational protein targeting. | the signal recognition particle (srp) cotranslationally targets proteins to cell membranes by coordinated binding and release of ribosome-associated nascent polypeptides and a membrane-associated srp receptor. gtp uptake and hydrolysis by the srp-receptor complex govern this targeting cycle. because no gtpase-activating proteins (gaps) are known for the srp and srp receptor gtpases, however, it has been unclear whether and how gtp hydrolysis is stimulated during protein trafficking in vivo. usin ... | 2007 | 17164479 |
| unusual phyletic distribution of peptidases as a tool for identifying potential drug targets. | eukaryote homologues of carboxypeptidases taq have been discovered by niemirowicz et al. in the protozoan trypanosoma cruzi, the causative agent of chagas' disease. this is surprising, because the peptidase family was thought to be restricted to bacteria and archaea. in this issue of the biochemical journal, the authors propose that the trypanosoma carboxypeptidases are potential drug targets for treatment of the disease. the authors also propose that the presence of the genes in the zooflagella ... | 2007 | 17173540 |
| unusual phyletic distribution of peptidases as a tool for identifying potential drug targets. | eukaryote homologues of carboxypeptidases taq have been discovered by niemirowicz et al. in the protozoan trypanosoma cruzi, the causative agent of chagas' disease. this is surprising, because the peptidase family was thought to be restricted to bacteria and archaea. in this issue of the biochemical journal, the authors propose that the trypanosoma carboxypeptidases are potential drug targets for treatment of the disease. the authors also propose that the presence of the genes in the zooflagella ... | 2007 | 17173540 |
| functional organization of the rpb5 subunit shared by the three yeast rna polymerases. | rpb5, a subunit shared by the three yeast rna polymerases, combines a eukaryotic n-terminal module with a globular c-end conserved in all non-bacterial enzymes. conditional and lethal mutants of the moderately conserved eukaryotic module showed that its large n-terminal helix and a short motif at the end of the module are critical in vivo. lethal or conditional mutants of the c-terminal globe altered the binding of rpb5 to rpb1-beta25/26 (prolonging the bridge helix) and rpb1-alpha44/47 (ahead o ... | 2007 | 17179178 |
| functional organization of the rpb5 subunit shared by the three yeast rna polymerases. | rpb5, a subunit shared by the three yeast rna polymerases, combines a eukaryotic n-terminal module with a globular c-end conserved in all non-bacterial enzymes. conditional and lethal mutants of the moderately conserved eukaryotic module showed that its large n-terminal helix and a short motif at the end of the module are critical in vivo. lethal or conditional mutants of the c-terminal globe altered the binding of rpb5 to rpb1-beta25/26 (prolonging the bridge helix) and rpb1-alpha44/47 (ahead o ... | 2007 | 17179178 |
| structure of the gmppnp-stabilized ng domain complex of the srp gtpases ffh and ftsy. | ffh and ftsy are gtpase components of the signal recognition particle co-translational targeting complex that assemble during the srp cycle to form a gtp-dependent and pseudo twofold symmetric heterodimer. previously the srp gtpase heterodimer has been stabilized and purified for crystallographic studies using both the non-hydrolysable gtp analog gmppcp and the pseudo-transition state analog gdp:alf4, revealing in both cases a buried nucleotide pair that bridges and forms a key element of the he ... | 2007 | 17184999 |