| crystal structure of human selenocysteine trna. | selenocysteine (sec) is the 21st amino acid in translation. sec trna (trna(sec)) has an anticodon complementary to the uga codon. we solved the crystal structure of human trna(sec). trna(sec) has a 9-bp acceptor stem and a 4-bp t stem, in contrast with the 7-bp acceptor stem and the 5-bp t stem in the canonical trnas. the acceptor stem is kinked between the u6:u67 and g7:c66 base pairs, leading to a bent acceptor-t stem helix. trna(sec) has a 6-bp d stem and a 4-nt d loop. the long d stem includ ... | 2009 | 19692584 |
| mechanism of polymerase collision release from sliding clamps on the lagging strand. | replicative polymerases are tethered to dna by sliding clamps for processive dna synthesis. despite attachment to a sliding clamp, the polymerase on the lagging strand must cycle on and off dna for each okazaki fragment. in the 'collision release' model, the lagging strand polymerase collides with the 5' terminus of an earlier completed fragment, which triggers it to release from dna and from the clamp. this report examines the mechanism of collision release by the escherichia coli pol iii polym ... | 2009 | 19696739 |
| phosphorylated proteins of the mammalian mitochondrial ribosome: implications in protein synthesis. | mitochondria, the powerhouse of eukaryotic cells, have their own translation machinery that is solely responsible for synthesis of 13 mitochondrially encoded protein subunits of oxidative phosphorylation complexes. phosphorylation is a well-known post-translational modification in regulation of many processes in mammalian mitochondria including oxidative phosphorylation. however, there is still very limited knowledge on phosphorylation of mitochondrial ribosomal proteins and their role(s) in rib ... | 2009 | 19702336 |
| the thermus thermophilus dead box helicase hera contains a modified rna recognition motif domain loosely connected to the helicase core. | dead box family helicases consist of a helicase core that is formed by two flexibly linked reca-like domains. the helicase activity can be regulated by n- or c-terminal extensions flanking the core. thermus thermophilus heat resistant rna-dependent atpase (hera) is the first dead box helicase that forms a dimer using a unique dimerization domain. in addition to the dimerization domain, hera contains a c-terminal rna binding domain (rbd) that shares sequence homology only to uncharacterized prote ... | 2009 | 19710183 |
| novel human interleukin-15 agonists. | il-15 is an immunostimulatory cytokine trans-presented with the il-15 receptor alpha-chain to the shared il-2/il-15rbeta and common gamma-chains displayed on the surface of t cells and nk cells. to further define the functionally important regions of this cytokine, activity and binding studies were conducted on human il-15 muteins generated by site-directed mutagenesis. amino acid substitutions of the asparagine residue at position 72, which is located at the end of helix c, were found to provid ... | 2009 | 19710453 |
| the interaction of bacillus subtilis sigmaa with rna polymerase. | rna polymerase (rnap) is an essential and highly conserved enzyme in all organisms. the process of transcription initiation is fundamentally different between prokaryotes and eukaryotes. in prokaryotes, initiation is regulated by sigma factors, making the essential interaction between sigma factors and rnap an attractive target for antimicrobial agents. our objective was to achieve the first step in the process of developing novel antimicrobial agents, namely to prove experimentally that the int ... | 2009 | 19735077 |
| the staphylococcus aureus psk41 plasmid-encoded arta protein is a master regulator of plasmid transmission genes and contains a rhh motif used in alternate dna-binding modes. | plasmids harbored by staphylococcus aureus are a major contributor to the spread of bacterial multi-drug resistance. plasmid conjugation and partition are critical to the dissemination and inheritance of such plasmids. here, we demonstrate that the arta protein encoded by the s. aureus multi-resistance plasmid psk41 is a global transcriptional regulator of psk41 genes, including those involved in conjugation and segregation. arta shows no sequence homology to any structurally characterized dna-b ... | 2009 | 19759211 |
| a trimeric dna polymerase complex increases the native replication processivity. | dna polymerases are essential enzymes in all domains of life for both dna replication and repair. the primary dna replication polymerase from sulfolobus solfataricus (ssodpo1) has been shown previously to provide the necessary polymerization speed and exonuclease activity to replicate the genome accurately. we find that this polymerase is able to physically associate with itself to form a trimer and that this complex is stabilized in the presence of dna. analytical gel filtration and electrophor ... | 2009 | 19773426 |
| adenosine triphosphate stimulates aquifex aeolicus mutl endonuclease activity. | background: human pms2 (hpms2) homologues act to nick 5' and 3' to misincorporated nucleotides during mismatch repair in organisms that lack muth. mn(++) was previously found to stimulate the endonuclease activity of these homologues. atp was required for the nicking activity of hpms2 and ypms1, but was reported to inhibit bacterial mutl proteins from thermus thermophilus and aquifex aeolicus that displayed homology to hpms2. mutational analysis has identified the dqha(x)(2)e(x)(4)e motif presen ... | 2009 | 19777055 |
| evolving a polymerase for hydrophobic base analogues. | hydrophobic base analogues (hbas) have shown great promise for the expansion of the chemical and coding potential of nucleic acids but are generally poor polymerase substrates. while extensive synthetic efforts have yielded examples of hbas with favorable substrate properties, their discovery has remained challenging. here we describe a complementary strategy for improving hba substrate properties by directed evolution of a dedicated polymerase using compartmentalized self-replication (csr) with ... | 2009 | 19778048 |
| mutations in the external loops of bk virus vp1 and urine viral load in renal transplant recipients. | polyomavirus-associated nephropathy (pvan) is a major complication that occurs after renal transplantation and is induced by reactivation of the human polyomavirus bk (bkv). the structure of the viral capsid protein 1 (vp1) is characterized by the presence of external loops, bc, de, ef, gh, and hi, which are involved in receptor binding. the pathogenesis of pvan is not well understood, but viral risk factors are thought to play a crucial role in the onset of this pathology. in an attempt to bett ... | 2010 | 19780025 |
| finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. | chemical cross-linking, followed by identification of the cross-linked residues, is a powerful approach to probe the topologies and interacting surfaces of protein assemblies. in this work, we demonstrate a new bioinformatics approach using multiple program modules within the software package "protein prospector" that greatly facilitates the discovery of cross-linked peptides in chemical cross-linking studies. examples are given for how this approach has been used for defining interfaces in hete ... | 2010 | 19809093 |
| finding chimeras: a bioinformatics strategy for identification of cross-linked peptides. | chemical cross-linking, followed by identification of the cross-linked residues, is a powerful approach to probe the topologies and interacting surfaces of protein assemblies. in this work, we demonstrate a new bioinformatics approach using multiple program modules within the software package "protein prospector" that greatly facilitates the discovery of cross-linked peptides in chemical cross-linking studies. examples are given for how this approach has been used for defining interfaces in hete ... | 2010 | 19809093 |
| the mechanistic architecture of thermostable pyrococcus furiosus family b dna polymerase motif a and its interaction with the dntp substrate. | thermostable dna polymerases isolated from archaeal organisms have not been completely characterized kinetically and require further study if we are to understand both their dntp binding mechanism and their role within the organism. here, we demonstrate that the thermostable family b dna polymerase from pyrococcus furiosus (pfu pol) contains sensitive determinants of both dntp binding and replicational fidelity within the highly conserved motif a. site-directed mutagenesis of the motif a sylp re ... | 2009 | 19817489 |
| three-dimensional structure of n-terminal domain of dnab helicase and helicase-primase interactions in helicobacter pylori. | replication initiation is a crucial step in genome duplication and homohexameric dnab helicase plays a central role in the replication initiation process by unwinding the duplex dna and interacting with several other proteins during the process of replication. n-terminal domain of dnab is critical for helicase activity and for dnag primase interactions. we present here the crystal structure of the n-terminal domain (ntd) of h. pylori dnab (hpdnab) helicase at 2.2 a resolution and compare the str ... | 2009 | 19841750 |
| reconstitution of gloeobacter violaceus rhodopsin with a light-harvesting carotenoid antenna. | we show that salinixanthin, the light-harvesting carotenoid antenna of xanthorhodopsin, can be reconstituted into the retinal protein from gloeobacter violaceus expressed in escherichia coli. reconstitution of gloeobacter rhodopsin with the carotenoid is accompanied by characteristic absorption changes and the appearance of cd bands similar to those observed for xanthorhodopsin that indicate immobilization and twist of the carotenoid in the binding site. as in xanthorhodopsin, the carotenoid fun ... | 2009 | 19842712 |
| allosteric control of catalysis by the f loop of rna polymerase. | bacterial rna polymerases (rnaps) undergo coordinated conformational changes during catalysis. in particular, concerted folding of the trigger loop and rearrangements of the bridge helix at the rnap active center have been implicated in nucleotide addition and rnap translocation. at moderate temperatures, the rate of catalysis by rnap from thermophilic thermus aquaticus is dramatically reduced compared with its closest mesophilic relative, deinococcus radiodurans. here, we show that a part of th ... | 2009 | 19855007 |
| global conformational dynamics of a y-family dna polymerase during catalysis. | replicative dna polymerases are stalled by damaged dna while the newly discovered y-family dna polymerases are recruited to rescue these stalled replication forks, thereby enhancing cell survival. the y-family dna polymerases, characterized by low fidelity and processivity, are able to bypass different classes of dna lesions. a variety of kinetic and structural studies have established a minimal reaction pathway common to all dna polymerases, although the conformational intermediates are not wel ... | 2009 | 19859523 |
| proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. | deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ... | 2010 | 19875382 |
| proteomics-based refinement of deinococcus deserti genome annotation reveals an unwonted use of non-canonical translation initiation codons. | deinococcaceae are a family of extremely radiation-tolerant bacteria that are currently subjected to numerous studies aimed at understanding the molecular mechanisms for such radiotolerance. to achieve a comprehensive and accurate annotation of the deinococcus deserti genome, we performed an n terminus-oriented characterization of its proteome. for this, we used a labeling reagent, n-tris(2,4,6-trimethoxyphenyl)phosphonium acetyl succinimide, to selectively derivatize protein n termini. the larg ... | 2010 | 19875382 |
| molecular evolution of multisubunit rna polymerases: structural analysis. | comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ... | 2010 | 19895816 |
| molecular evolution of multisubunit rna polymerases: structural analysis. | comprehensive multiple sequence alignments of the multisubunit dna-dependent rna polymerase (rnap) large subunits, including the bacterial beta and beta' subunits and their homologs from archaebacterial rnaps, eukaryotic rnaps i-iii, nuclear-cytoplasmic large double-stranded dna virus rnaps, and plant plastid rnaps, were created [lane, w. j. and darst, s. a. (2009). molecular evolution of multisubunit rna polymerases: sequence analysis. in press]. the alignments were used to delineate sequence r ... | 2010 | 19895816 |
| a two-subunit bacterial sigma-factor activates transcription in bacillus subtilis. | the sigma-like factor yvri and coregulator yvrha activate transcription from a small set of conserved promoters in bacillus subtilis. we report here that these two proteins independently contribute sigma-region 2 and sigma-region 4 functions to a holoenzyme-promoter dna complex. yvri binds rna polymerase (rnap) through a region 4 interaction with the beta-subunit flap domain and mediates specific promoter recognition but cannot initiate dna melting at the -10 promoter element. conversely, yvrha ... | 2009 | 19940246 |
| stereochemical mechanisms of trna methyltransferases. | methylation of trna on the four canonical bases adds structural complexity to the molecule, and improves decoding specificity and efficiency. while many trna methylases are known, detailed insight into the catalytic mechanism is only available in a few cases. of interest among all trna methylases is the structural basis for nucleotide selection, by which the specificity is limited to a single site, or broadened to multiple sites. general themes in catalysis include the basis for rate acceleratio ... | 2010 | 19944101 |
| cohesion group approach for evolutionary analysis of aspartokinase, an enzyme that feeds a branched network of many biochemical pathways. | aspartokinase (ask) exists within a variable network that supports the synthesis of 9 amino acids and a number of other important metabolites. lysine, isoleucine, aromatic amino acids, and dipicolinate may arise from the ask network or from alternative pathways. ask proteins were subjected to cohesion group analysis, a methodology that sorts a given protein assemblage into groups in which evolutionary continuity is assured. two subhomology divisions, ask(alpha) and ask(beta), have been recognize ... | 2009 | 19946135 |
| effect of n2-guanyl modifications on early steps in catalysis of polymerization by sulfolobus solfataricus p2 dna polymerase dpo4 t239w. | translesion dna polymerases are more efficient at bypass of many dna adducts than replicative polymerases. previous work with the translesion polymerase sulfolobus solfataricus dpo4 showed a decrease in catalytic efficiency during bypass of bulky n(2)-alkyl guanine (g) adducts with n(2)-isobutylg showing the largest effect, decreasing approximately 120-fold relative to unmodified deoxyguanosine (zhang, h., eoff, r. l., egli, m., guengerich, f. p. versatility of y-family sulfolobus solfataricus d ... | 2010 | 19969000 |
| effect of n2-guanyl modifications on early steps in catalysis of polymerization by sulfolobus solfataricus p2 dna polymerase dpo4 t239w. | translesion dna polymerases are more efficient at bypass of many dna adducts than replicative polymerases. previous work with the translesion polymerase sulfolobus solfataricus dpo4 showed a decrease in catalytic efficiency during bypass of bulky n(2)-alkyl guanine (g) adducts with n(2)-isobutylg showing the largest effect, decreasing approximately 120-fold relative to unmodified deoxyguanosine (zhang, h., eoff, r. l., egli, m., guengerich, f. p. versatility of y-family sulfolobus solfataricus d ... | 2010 | 19969000 |
| new approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of forster resonance energy transfer probes in 5'-nuclease assays. | the article describes a new technology for real-time polymerase chain reaction (pcr) detection of nucleic acids. similar to taqman, this new method, named snake, utilizes the 5'-nuclease activity of thermus aquaticus (taq) dna polymerase that cleaves dual-labeled förster resonance energy transfer (fret) probes and generates a fluorescent signal during pcr. however, the mechanism of the probe cleavage in snake is different. in this assay, pcr amplicons fold into stem-loop secondary structures. hy ... | 2010 | 19969535 |
| new approach to real-time nucleic acids detection: folding polymerase chain reaction amplicons into a secondary structure to improve cleavage of forster resonance energy transfer probes in 5'-nuclease assays. | the article describes a new technology for real-time polymerase chain reaction (pcr) detection of nucleic acids. similar to taqman, this new method, named snake, utilizes the 5'-nuclease activity of thermus aquaticus (taq) dna polymerase that cleaves dual-labeled förster resonance energy transfer (fret) probes and generates a fluorescent signal during pcr. however, the mechanism of the probe cleavage in snake is different. in this assay, pcr amplicons fold into stem-loop secondary structures. hy ... | 2010 | 19969535 |
| mobilization studies in complement-deficient mice reveal that optimal amd3100 mobilization of hematopoietic stem cells depends on complement cascade activation by amd3100-stimulated granulocytes. | we reported that complement cascade (cc) becomes activated in bone marrow (bm) during mobilization of hematopoietic stem/progenitor cells (hspcs) induced by granulocyte colony-stimulating factor (g-csf) and c5 cleavage has an important function in optimal egress of hspcs. in this work, we explored whether cc is involved in mobilization of hspcs induced by the cxcr4 antagonist, amd3100. to address this question, we performed mobilization studies in mice that display a defect in the activation of ... | 2010 | 20033053 |
| mobilization studies in complement-deficient mice reveal that optimal amd3100 mobilization of hematopoietic stem cells depends on complement cascade activation by amd3100-stimulated granulocytes. | we reported that complement cascade (cc) becomes activated in bone marrow (bm) during mobilization of hematopoietic stem/progenitor cells (hspcs) induced by granulocyte colony-stimulating factor (g-csf) and c5 cleavage has an important function in optimal egress of hspcs. in this work, we explored whether cc is involved in mobilization of hspcs induced by the cxcr4 antagonist, amd3100. to address this question, we performed mobilization studies in mice that display a defect in the activation of ... | 2010 | 20033053 |
| characterization of nucleotide misincorporation patterns in the iceman's mitochondrial dna. | the degradation of dna represents one of the main issues in the genetic analysis of archeological specimens. in the recent years, a particular kind of post-mortem dna modification giving rise to nucleotide misincorporation ("miscoding lesions") has been the object of extensive investigations. | 2010 | 20072618 |
| saccharomyces cerevisiae msh2-msh6 dna binding kinetics reveal a mechanism of targeting sites for dna mismatch repair. | the dna mismatch repair system (mmr) identifies replication errors and damaged bases in dna and functions to preserve genomic integrity. muts performs the task of locating mismatched base pairs, loops and lesions and initiating mmr, and the fundamental question of how this protein targets specific sites in dna is unresolved. to address this question, we examined the interactions between saccharomyces cerevisiae msh2-msh6, a eukaryotic muts homolog, and dna in real time. the reaction kinetics rev ... | 2010 | 20080735 |
| saccharomyces cerevisiae msh2-msh6 dna binding kinetics reveal a mechanism of targeting sites for dna mismatch repair. | the dna mismatch repair system (mmr) identifies replication errors and damaged bases in dna and functions to preserve genomic integrity. muts performs the task of locating mismatched base pairs, loops and lesions and initiating mmr, and the fundamental question of how this protein targets specific sites in dna is unresolved. to address this question, we examined the interactions between saccharomyces cerevisiae msh2-msh6, a eukaryotic muts homolog, and dna in real time. the reaction kinetics rev ... | 2010 | 20080735 |
| a mechanistic view of human mitochondrial dna polymerase gamma: providing insight into drug toxicity and mitochondrial disease. | mitochondrial dna polymerase gamma (pol gamma) is the sole polymerase responsible for replication of the mitochondrial genome. the study of human pol gamma is of key importance to clinically relevant issues such as nucleoside analog toxicity and mitochondrial disorders such as progressive external ophthalmoplegia. the development of a recombinant form of the human pol gamma holoenzyme provided an essential tool in understanding the mechanism of these clinically relevant phenomena using kinetic m ... | 2010 | 20083238 |
| evaluation of localized and systemic immune responses in cutaneous leishmaniasis caused by leishmania tropica: interleukin-8, monocyte chemotactic protein-1 and nitric oxide are major regulatory factors. | we have established leishmania tropica as the causative agent of cutaneous leishmaniasis (cl) in the region of india where the disease is endemic. the association between localized and circulating levels of immune-determinants in cl patients was evaluated. reverse transcription-polymerase chain reaction analysis revealed up-regulation of interferon-gamma (ifn-gamma), interleukin (il)-1beta, il-8, tumour necrosis factor-alpha (tnf-alpha), il-10 and il-4 in dermal lesions at the pretreatment stage ... | 2010 | 20102417 |
| primase directs the release of dnac from dnab. | an aaa+ atpase, dnac, delivers dnab helicase at the e. coli chromosomal origin by a poorly understood process. this report shows that mutant proteins bearing alanine substitutions for two conserved arginines in a motif named box vii are defective in dna replication, but this deficiency does not arise from impaired interactions with atp, dnab, or single-stranded dna. despite their ability to deliver dnab to the chromosomal origin to form the prepriming complex, this intermediate is inactive. quan ... | 2010 | 20129058 |
| t7 phage protein gp2 inhibits the escherichia coli rna polymerase by antagonizing stable dna strand separation near the transcription start site. | infection of escherichia coli by the t7 phage leads to rapid and selective inhibition of the host rna polymerase (rnap)--a multi-subunit enzyme responsible for gene transcription--by a small ( approximately 7 kda) phage-encoded protein called gp2. gp2 is also a potent inhibitor of e. coli rnap in vitro. here we describe the first atomic resolution structure of gp2, which reveals a distinct run of surface-exposed negatively charged amino acid residues on one side of the molecule. our comprehensiv ... | 2010 | 20133868 |
| muts and mutl are dispensable for maintenance of the genomic mutation rate in the halophilic archaeon halobacterium salinarum nrc-1. | the genome of the halophilic archaeon halobacterium salinarum nrc-1 encodes for homologs of muts and mutl, which are key proteins of a dna mismatch repair pathway conserved in bacteria and eukarya. mismatch repair is essential for retaining the fidelity of genetic information and defects in this pathway result in the deleterious accumulation of mutations and in hereditary diseases in humans. | 2010 | 20140215 |
| mutagenic potential of dna glycation: miscoding by (r)- and (s)-n2-(1-carboxyethyl)-2'-deoxyguanosine. | elevated circulating glucose resulting from complications of obesity and metabolic disease can result in the accumulation of advanced glycation end products (ages) of proteins, lipids, and dna. the formation of dna-ages assumes particular importance as these adducts may contribute to genetic instability and elevated cancer risk associated with metabolic disease. the principal dna-age, n(2)-(1-carboxyethyl)-2'-deoxyguanosine (cedg), is formed as a mixture of r and s isomers at both the polymer an ... | 2010 | 20143879 |
| evolutionary conservation of residues in vertebrate dna polymerase n conferring low fidelity and bypass activity. | poln is a nuclear a-family dna polymerase encoded in vertebrate genomes. poln has unusual fidelity and dna lesion bypass properties, including strong strand displacement activity, low fidelity favoring incorporation of t for template g and accurate translesion synthesis past a 5s-thymine glycol (5s-tg). we searched for conserved features of the polymerase domain that distinguish it from prokaryotic pol i-type dna polymerases. a lys residue (679 in human poln) of particular interest was identifie ... | 2010 | 20144948 |
| characterization of endott, a novel single-stranded dna-specific endonuclease from thermoanaerobacter tengcongensis. | endott encoded by tte0829 of thermoanaerobacter tengcongensis binds and cleaves single-stranded (ss) and damaged double-stranded (ds) dna in vitro as well as binding dsdna. in the presence of a low concentration of nacl, endott cleaved ss regions of damaged dsdna efficiently but did not cleave dna that was entirely ss or ds. at high concentrations of nacl or mgcl(2) or atp, there was also specific cleavage of ssdna. this suggested a preference for ss/ds junctions to stimulate cleavage of the dna ... | 2010 | 20172959 |
| involvement of the beta subunit of rna polymerase in resistance to streptolydigin and streptovaricin in the producer organisms streptomyces lydicus and streptomyces spectabilis. | streptomyces lydicus nrrl2433 and s. spectabilis nrrl2494 produce two inhibitors of bacterial rna polymerase: the 3-acyltetramic acid streptolydigin and the naphthalenic ansamycin streptovaricin, respectively. both strains are highly resistant to their own antibiotics. independent expression of the s. lydicus and s. spectabilis rpob and rpoc genes, encoding the beta- and beta'-subunits of rna polymerase, respectively, in s. albus showed that resistance is mediated by rpob, with no effect of rpoc ... | 2010 | 20176899 |
| probing dna- and atp-mediated conformational changes in the muts family of mispair recognition proteins using deuterium exchange mass spectrometry. | we have performed deuterium exchange mass spectrometry (dxms) to probe the conformational changes that the bacterial muts homodimer and the homologous eukaryotic heterodimer msh2-msh6 undergo when binding to atp or dna. the dxms data support the view that high affinity binding to mispair-containing dna and low affinity binding to fully base-paired dna both involve forming rings by muts protein family dimers around the dna; however, mispair binding protects additional regions from deuterium excha ... | 2010 | 20181951 |
| recognition of a signal peptide by the signal recognition particle. | targeting of proteins to appropriate subcellular compartments is a crucial process in all living cells. secretory and membrane proteins usually contain an amino-terminal signal peptide, which is recognized by the signal recognition particle (srp) when nascent polypeptide chains emerge from the ribosome. the srp-ribosome nascent chain complex is then targeted through its gtp-dependent interaction with srp receptor to the protein-conducting channel on endoplasmic reticulum membrane in eukaryotes o ... | 2010 | 20364120 |
| redox sensing by a rex-family repressor is involved in the regulation of anaerobic gene expression in staphylococcus aureus. | an alignment of upstream regions of anaerobically induced genes in staphylococcus aureus revealed the presence of an inverted repeat, corresponding to rex binding sites in streptomyces coelicolor. gel shift experiments of selected upstream regions demonstrated that the redox-sensing regulator rex of s. aureus binds to this inverted repeat. the binding sequence--ttgtgaaw(4)ttcacaa--is highly conserved in s. aureus. rex binding to this sequence leads to the repression of genes located downstream. ... | 2010 | 20374494 |
| structural aspects of drug resistance and inhibition of hiv-1 reverse transcriptase. | hiv-1 reverse transcriptase (hiv-1 rt) has been the target of numerous approved anti-aids drugs that are key components of highly active anti-retroviral therapies (haart). it remains the target of extensive structural studies that continue unabated for almost twenty years. the crystal structures of wild-type or drug-resistant mutant hiv rts in the unliganded form or in complex with substrates and/or drugs have offered valuable glimpses into the enzyme's folding and its interactions with dna and ... | 2010 | 20376302 |
| transient tether between the srp rna and srp receptor ensures efficient cargo delivery during cotranslational protein targeting. | kinetic control of macromolecular interactions plays key roles in biological regulation. an example of such control occurs in cotranslational protein targeting by the signal recognition particle (srp), during which the srp rna and the cargo both accelerate complex assembly between the srp and srp receptor ftsy 10(2)-fold. the molecular mechanism underlying these rate accelerations was unclear. here we show that a highly conserved basic residue, lys399, on the lateral surface of ftsy provides a n ... | 2010 | 20385832 |
| pyrosequencing-based comparative genome analysis of the nosocomial pathogen enterococcus faecium and identification of a large transferable pathogenicity island. | the gram-positive bacterium enterococcus faecium is an important cause of nosocomial infections in immunocompromized patients. | 2010 | 20398277 |
| a unique group of virus-related, genome-integrating elements found solely in the bacterial family thermaceae and the archaeal family halobacteriaceae. | viruses sh1 and p23-77, infecting archaeal haloarcula species and bacterial thermus species, respectively, were recently designated to form a novel viral lineage. in this study, the lineage is expanded to archaeal halomicrobium and bacterial meiothermus species by analysis of five genome-integrated elements that share the core genes with these viruses. | 2010 | 20400546 |
| replication through an abasic dna lesion: structural basis for adenine selectivity. | abasic sites represent the most frequent dna lesions in the genome that have high mutagenic potential and lead to mutations commonly found in human cancers. although these lesions are devoid of the genetic information, adenine is most efficiently inserted when abasic sites are bypassed by dna polymerases, a phenomenon termed a-rule. in this study, we present x-ray structures of a dna polymerase caught while incorporating a nucleotide opposite an abasic site. we found that a functionally importan ... | 2010 | 20400942 |
| two novel families of plasmids from hyperthermophilic archaea encoding new families of replication proteins. | thermococcales (phylum euryarchaeota) are model organisms for physiological and molecular studies of hyperthermophiles. here we describe three new plasmids from thermococcales that could provide new tools and model systems for genetic and molecular studies in archaea. the plasmids ptn2 from thermococcus nautilus sp. 30-1 and pp12-1 from pyrococcus sp. 12-1 belong to the same family. they have similar size (approximately 12 kb) and share six genes, including homologues of genes encoded by the vir ... | 2010 | 20403814 |
| functional studies and homology modeling of msh2-msh3 predict that mispair recognition involves dna bending and strand separation. | the msh2-msh3 heterodimer recognizes various dna mispairs, including loops of dna ranging from 1 to 14 nucleotides and some base-base mispairs. homology modeling of the mispair-binding domain (mbd) of msh3 using the related msh6 mbd revealed that mismatch recognition must be different, even though the mbd folds must be similar. model-based point mutation alleles of saccharomyces cerevisiae msh3 designed to disrupt mispair recognition fell into two classes. one class caused defects in repair of b ... | 2010 | 20421420 |
| solution structure of rv2377c-founding member of the mbth-like protein family. | the mycobacterium tuberculosis protein rv2377c (71 residues, mw=8.4kda) has been characterized using nuclear magnetic resonance (nmr) and circular dichroism (cd) spectroscopy. rv2377c was the first identified member of the mbth-like family of proteins. mbth-like proteins have been implicated in siderophore biosynthesis, however, their precise biochemical function remain unknown. size exclusion chromatography and nmr spectroscopy show that rv2377c is a monomer in solution. circular dichroism spec ... | 2010 | 20434955 |
| thrombin regulates the metastatic potential of human rhabdomyosarcoma cells: distinct role of par1 and par3 signaling. | we observed that human rhabdomyosarcoma (rms) cells highly express a tissue factor that promotes thrombin formation, which indirectly and directly affects rms progression. first, we found that thrombin activates platelets to generate microvesicles (pmv), which transfer to rms cells' alpha2beta3 integrin and increase their adhesiveness to endothelial cells. accordingly, rms cells covered with pmvs showed higher metastatic potential after i.v. injection into immunodeficient mice. furthermore, pmvs ... | 2010 | 20442298 |
| testing computational prediction of missense mutation phenotypes: functional characterization of 204 mutations of human cystathionine beta synthase. | predicting the phenotypes of missense mutations uncovered by large-scale sequencing projects is an important goal in computational biology. high-confidence predictions can be an aid in focusing experimental and association studies on those mutations most likely to be associated with causative relationships between mutation and disease. as an aid in developing these methods further, we have derived a set of random mutations of the enzymatic domains of human cystathionine beta synthase. this enzym ... | 2010 | 20455263 |
| multiple roles of the rna polymerase {beta}' sw2 region in transcription initiation, promoter escape, and rna elongation. | interactions of rna polymerase (rnap) with nucleic acids must be tightly controlled to ensure precise and processive rna synthesis. the rnap β'-subunit switch-2 (sw2) region is part of a protein network that connects the clamp domain with the rnap body and mediates opening and closing of the active center cleft. sw2 interacts with the template dna near the rnap active center and is a target for antibiotics that block dna melting during initiation. here, we show that substitutions of a conserved ... | 2010 | 20457751 |
| mass spectrometry defines the stoichiometry of ribosomal stalk complexes across the phylogenetic tree. | the ribosomal stalk complex plays a crucial role in delivering translation factors to the catalytic site of the ribosome. it has a very similar architecture in all cells, although the protein components in bacteria are unrelated to those in archaea and eukaryotes. here we used mass spectrometry to investigate ribosomal stalk complexes from bacteria, eukaryotes, and archaea in situ on the ribosome. specifically we targeted ribosomes with different optimal growth temperatures. our results showed t ... | 2010 | 20467040 |
| discrimination of thermophilic and mesophilic proteins. | there is a considerable literature on the source of the thermostability of proteins from thermophilic organisms. understanding the mechanisms for this thermostability would provide insights into proteins generally and permit the design of synthetic hyperstable biocatalysts. | 2010 | 20487512 |
| essential biological processes of an emerging pathogen: dna replication, transcription, and cell division in acinetobacter spp. | within the last 15 years, members of the bacterial genus acinetobacter have risen from relative obscurity to be among the most important sources of hospital-acquired infections. the driving force for this has been the remarkable ability of these organisms to acquire antibiotic resistance determinants, with some strains now showing resistance to every antibiotic in clinical use. there is an urgent need for new antibacterial compounds to combat the threat imposed by acinetobacter spp. and other in ... | 2010 | 20508250 |
| central role of the rna polymerase trigger loop in intrinsic rna hydrolysis. | the active center of rna polymerase can hydrolyze phosphodiester bonds in nascent rna, a reaction thought to be important for proofreading of transcription. the reaction proceeds via a general two mg(2+) mechanism and is assisted by the 3' end nucleotide of the transcript. here, by using thermus aquaticus rna polymerase, we show that the reaction also requires the flexible domain of the active center, the trigger loop (tl). we show that the invariant histidine (beta' his1242) of the tl is essent ... | 2010 | 20534498 |
| thermodynamics of the dna structural selectivity of the pol i dna polymerases from escherichia coli and thermus aquaticus. | understanding the thermodynamics of substrate selection by dna polymerase i is important for characterizing the balance between replication and repair for this enzyme in vivo. due to their sequence and structural similarities, klenow and klentaq, the large fragments of the pol i dna polymerases from escherichia coli and thermus aquaticus, are considered functional homologs. klentaq, however, does not have a functional proofreading site. examination of the dna binding thermodynamics of klenow and ... | 2010 | 20550914 |
| dmso and betaine greatly improve amplification of gc-rich constructs in de novo synthesis. | in synthetic biology, de novo synthesis of gc-rich constructs poses a major challenge because of secondary structure formation and mispriming. while there are many web-based tools for codon optimizing difficult regions, no method currently exists that allows for potentially phenotypically important sequence conservation. therefore, to overcome these limitations in researching gc-rich genes and their non-coding elements, we explored the use of dmso and betaine in two conventional methods of assem ... | 2010 | 20552011 |
| multi-site-specific 16s rrna methyltransferase rsmf from thermus thermophilus. | cells devote a significant effort toward the production of multiple modified nucleotides in rrnas, which fine tune the ribosome function. here, we report that two methyltransferases, rsmb and rsmf, are responsible for all four 5-methylcytidine (m(5)c) modifications in 16s rrna of thermus thermophilus. like escherichia coli rsmb, t. thermophilus rsmb produces m(5)c967. in contrast to e. coli rsmf, which introduces a single m(5)c1407 modification, t. thermophilus rsmf modifies three positions, gen ... | 2010 | 20558545 |
| structural basis for the suppression of skin cancers by dna polymerase eta. | dna polymerase eta (poleta) is unique among eukaryotic polymerases in its proficient ability for error-free replication through ultraviolet-induced cyclobutane pyrimidine dimers, and inactivation of poleta (also known as polh) in humans causes the variant form of xeroderma pigmentosum (xpv). we present the crystal structures of saccharomyces cerevisiae poleta (also known as rad30) in ternary complex with a cis-syn thymine-thymine (t-t) dimer and with undamaged dna. the structures reveal that the ... | 2010 | 20577207 |
| protein-protein interactions between sigma(70) region 4 of rna polymerase and escherichia coli soxs, a transcription activator that functions by the prerecruitment mechanism: evidence for "off-dna" and "on-dna" interactions. | according to the prerecruitment hypothesis, escherichia coli soxs activates the transcription of the genes of the soxrs regulon by forming binary complexes with rna polymerase (rnap) that scan the chromosome for class i and class ii soxs-dependent promoters. we showed previously that the alpha subunit's c-terminal domain plays a role in activating both classes of promoter by making protein-protein contacts with soxs; some of these contacts are made in solution in the absence of promoter dna, a c ... | 2010 | 20595001 |
| promoter melting triggered by bacterial rna polymerase occurs in three steps. | rna synthesis, carried out by dna-dependent rna polymerase (rnap) in a process called transcription, involves several stages. in bacteria, transcription initiation starts with promoter recognition and binding of rnap holoenzyme, resulting in the formation of the closed (r.p(c)) rnap-promoter dna complex. subsequently, a transition to the open r.p(o) complex occurs, characterized by separation of the promoter dna strands in an approximately 12 base-pair region to form the transcription bubble. us ... | 2010 | 20615963 |
| a novel heme a insertion factor gene cotranscribes with the thermus thermophilus cytochrome ba3 oxidase locus. | studying the biogenesis of the thermus thermophilus cytochrome ba(3) oxidase, we analyze heme a cofactor insertion into this membrane protein complex. only three proteins linked to oxidase maturation have been described for this extreme thermophile, and in particular, no evidence for a canonical surf1 homologue, required for heme a insertion, is available from genome sequence data. here, we characterize the product of an open reading frame, cbax, in the operon encoding subunits of the ba(3)-type ... | 2010 | 20622059 |
| part i: characterization of the extracellular proteome of the extreme thermophile caldicellulosiruptor saccharolyticus by gelc-ms2. | the proteome of extremely thermophilic microorganisms affords a glimpse into the dynamics of microbial ecology of high temperature environments. the secretome, or extracellular proteome of these microorganisms, no doubt harbors technologically important enzymes and other thermostable biomolecules that, to date, have been characterized only to a limited extent. in the first of a two-part study on selected thermophiles, defining the secretome requires a sample preparation method that has no negati ... | 2010 | 20623222 |
| active site mutations in mammalian dna polymerase delta alter accuracy and replication fork progression. | dna polymerase δ (pol δ) is one of the two main replicative polymerases in eukaryotes; it synthesizes the lagging dna strand and also functions in dna repair. in previous work, we demonstrated that heterozygous expression of the pol δ l604g variant in mice results in normal life span and no apparent phenotype, whereas a different substitution at the same position, l604k, is associated with shortened life span and accelerated carcinogenesis. here, we report in vitro analysis of the homologous mut ... | 2010 | 20628184 |
| functional analysis of the cucumisin propeptide as a potent inhibitor of its mature enzyme. | cucumisin is a subtilisin-like serine protease (subtilase) that is found in the juice of melon fruits (cucumis melo l.). it is synthesized as a preproprotein consisting of a signal peptide, nh(2)-terminal propeptide, and 67-kda protease domain. we investigated the role of this propeptide (88 residues) in the cucumisin precursor. complementary dnas encoding the propeptides of cucumisin, two other plant subtilases (arabidopsis ara12 and rice rsp1), and bacterial subtilisin e were expressed in esch ... | 2010 | 20639575 |
| conformational dynamics of bacteriophage t7 dna polymerase and its processivity factor, escherichia coli thioredoxin. | gene 5 of bacteriophage t7 encodes a dna polymerase (gp5) responsible for the replication of the phage dna. gp5 polymerizes nucleotides with low processivity, dissociating after the incorporation of 1 to 50 nucleotides. thioredoxin (trx) of escherichia coli binds tightly (kd = 5 nm) to a unique segment in the thumb subdomain of gp5 and increases processivity. we have probed the molecular basis for the increase in processivity. a single-molecule experiment reveals differences in rates of enzymati ... | 2010 | 20696935 |
| a nuclear family a dna polymerase from entamoeba histolytica bypasses thymine glycol. | eukaryotic family a dna polymerases are involved in mitochondrial dna replication or translesion dna synthesis. here, we present evidence that the sole family a dna polymerase from the parasite protozoan e. histolytica (ehdnapola) localizes to the nucleus and that its biochemical properties indicate that this dna polymerase may be involved in translesion dna synthesis. | 2010 | 20706627 |
| dna mismatch repair in eukaryotes and bacteria. | dna mismatch repair (mmr) corrects mismatched base pairs mainly caused by dna replication errors. the fundamental mechanisms and proteins involved in the early reactions of mmr are highly conserved in almost all organisms ranging from bacteria to human. the significance of this repair system is also indicated by the fact that defects in mmr cause human hereditary nonpolyposis colon cancers as well as sporadic tumors. to date, 2 types of mmrs are known: the human type and escherichia coli type. t ... | 2010 | 20725617 |
| a mutation within the β subunit of escherichia coli rna polymerase impairs transcription from bacteriophage t4 middle promoters. | during infection of escherichia coli, bacteriophage t4 usurps the host transcriptional machinery, redirecting it to the expression of early, middle, and late phage genes. middle genes, whose expression begins about 1 min postinfection, are transcribed both from the extension of early rna into middle genes and by the activation of t4 middle promoters. middle-promoter activation requires the t4 transcriptional activator mota and coactivator asia, which are known to interact with σ(70), the specifi ... | 2010 | 20729353 |
| binding of the dimeric deinococcus radiodurans single-stranded dna binding protein to single-stranded dna. | deinococcus radiodurans single-stranded (ss) dna binding protein (drssb) originates from a radiation-resistant bacterium and participates in dna recombination, replication, and repair. although it functions as a homodimer, it contains four dna binding domains (ob-folds) and thus is structurally similar to the escherichia coli ssb (ecossb) homotetramer. we examined the equilibrium binding of drssb to ssdna for comparison with that of ecossb. we find that the occluded site size of drssb on poly(dt ... | 2010 | 20795631 |
| unique dna repair gene variations and potential associations with the primary antibody deficiency syndromes igad and cvid. | despite considerable effort, the genetic factors responsible for >90% of the antibody deficiency syndromes igad and cvid remain elusive. to produce a functionally diverse antibody repertoire b lymphocytes undergo class switch recombination. this process is initiated by aid-catalyzed deamination of cytidine to uridine in switch region dna. subsequently, these residues are recognized by the uracil excision enzyme ung2 or the mismatch repair proteins mutsalpha (msh2/msh6) and mutlalpha (pms2/mlh1). ... | 2010 | 20805886 |
| twenty-eight divergent polysaccharide loci specifying within- and amongst-strain capsule diversity in three strains of bacteroides fragilis. | comparison of the complete genome sequence of bacteroides fragilis 638r, originally isolated in the usa, was made with two previously sequenced strains isolated in the uk (nctc 9343) and japan (ych46). the presence of 10 loci containing genes associated with polysaccharide (ps) biosynthesis, each including a putative wzx flippase and wzy polymerase, was confirmed in all three strains, despite a lack of cross-reactivity between nctc 9343 and 638r surface ps-specific antibodies by immunolabelling ... | 2010 | 20829291 |
| dna polymerase: structural homology, conformational dynamics, and the effects of carcinogenic dna adducts. | dna replication is vital for an organism to proliferate and lying at the heart of this process is the enzyme dna polymerase. most dna polymerases have a similar three dimensional fold, akin to a human right hand, despite differences in sequence homology. this structural homology would predict a relatively unvarying mechanism for dna synthesis yet various polymerases exhibit markedly different properties on similar substrates, indicative of each type of polymerase being prescribed to a specific r ... | 2010 | 20847947 |
| identification of critical residues for the tight binding of both correct and incorrect nucleotides to human dna polymerase λ. | dna polymerase λ (pol λ) is a novel x-family dna polymerase that shares 34% sequence identity with dna polymerase β. pre-steady-state kinetic studies have shown that the pol λ-dna complex binds both correct and incorrect nucleotides 130-fold tighter, on average, than the dna polymerase β-dna complex, although the base substitution fidelity of both polymerases is 10(-)(4) to 10(-5). to better understand pol λ's tight nucleotide binding affinity, we created single-substitution and double-substitut ... | 2010 | 20851705 |
| strong in vitro activities of two new rifabutin analogs against multidrug-resistant mycobacterium tuberculosis. | two new rifabutin analogs, rfa-1 and rfa-2, show high in vitro antimycobacterial activities against mycobacterium tuberculosis. mic values of rfa-1 and rfa-2 were ≤0.02 μg/ml against rifamycin-susceptible strains and 0.5 μg/ml against a wide selection of multidrug-resistant strains, compared to ≥50 μg/ml for rifampin and 10 μg/ml for rifabutin. molecular dynamic studies indicate that the compounds may exert tighter binding to mutants of rna polymerase that have adapted to the rifamycins. | 2010 | 20855731 |
| complete structural model of escherichia coli rna polymerase from a hybrid approach. | the escherichia coli transcription system is the best characterized from a biochemical and genetic point of view and has served as a model system. nevertheless, a molecular understanding of the details of e. coli transcription and its regulation, and therefore its full exploitation as a model system, has been hampered by the absence of high-resolution structural information on e. coli rna polymerase (rnap). we use a combination of approaches, including high-resolution x-ray crystallography, ab i ... | 2010 | 20856905 |
| molecular mechanisms underlying ca2+-mediated motility of human pancreatic duct cells. | we recently reported that transforming growth factor-β (tgf-β) induces an increase in cytosolic ca(2+) ([ca(2+)](cyt)) in pancreatic cancer cells, but the mechanisms by which tgf-β mediates [ca(2+)](cyt) homeostasis in these cells are currently unknown. transient receptor potential (trp) channels and na(+)/ca(2+) exchangers (ncx) are plasma membrane proteins that play prominent roles in controlling [ca(2+)](cyt) homeostasis in normal mammalian cells, but little is known regarding their roles in ... | 2010 | 20861471 |
| novel application of locked nucleic acid chemistry for a taqman assay for measuring diverse human immunodeficiency virus type 1 subtypes. | there remains a need for sensitive and cost-effective assays to monitor therapy in human immunodeficiency virus type-1 (hiv-1) infection. however, the genetic diversity of hiv poses difficulties for traditional real-time pcr assays that require long oligonucleotides probes. lna™ probes may be useful in overcoming these limits to traditional probe design. a new application of lna™ chemistry in a taqman assay applicable to a wide range of hiv-1 subtypes is described. this assay, based on a 13-mer ... | 2010 | 20863855 |
| a one-step method for quantitative determination of uracil in dna by real-time pcr. | uracil may occur in dna due to either cytosine deamination or thymine replacing incorporation. its quantitative characterization is important in assessing dna damages in cells with perturbed thymidylate metabolism or within different dna segments involved in immunoglobulin gene diversification. the archaeal dna polymerase from pyrococcus furiosus binds strongly to the deaminated base uracil and stalls on uracil-containing templates. here, we present a straightforward method for quantitative asse ... | 2010 | 20864450 |
| genetic analysis of baker's yeast msh4-msh5 reveals a threshold crossover level for meiotic viability. | during meiosis, the msh4-msh5 complex is thought to stabilize single-end invasion intermediates that form during early stages of recombination and subsequently bind to holliday junctions to facilitate crossover formation. to analyze msh4-msh5 function, we mutagenized 57 residues in saccharomyces cerevisiae msh4 and msh5 that are either conserved across all msh4/5 family members or are specific to msh4 and msh5. the msh5 subunit appeared more sensitive to mutagenesis. we identified msh4 and msh5 ... | 2010 | 20865162 |
| varied molecular interactions at the active sites of several dna polymerases: nonpolar nucleoside isosteres as probes. | we describe a survey of protein-dna interactions with seven different dna polymerases and reverse transcriptases, carried out with nonpolar nucleoside isosteres f (a thymidine analog) and z and q (deoxyadenosine analogues). previous results have shown that z and f can be efficiently replicated opposite each other by the exonuclease-free klenow fragment of dna polymerase i from escherichia coli (kf(-)), although both of them lack watson-crick h-bonding ability. we find that exonuclease-inactive t ... | 2000 | 20882113 |
| an adenylyl cyclase signaling pathway predicts direct dopaminergic input to vestibular hair cells. | adenylyl cyclase (ac) signaling pathways have been identified in a model hair cell preparation from the trout saccule, for which the hair cell is the only intact cell type. the use of degenerate primers targeting cdna sequence conserved across ac isoforms, and reverse transcription-polymerase chain reaction (rt-pcr), coupled with cloning of amplification products, indicated expression of ac9, ac7 and ac5/6, with cloning efficiencies of 11:5:2. ac9 and ac5/6 are inhibited by ca(2+), the former in ... | 2010 | 20883745 |
| rational design, synthesis, and evaluation of new selective inhibitors of microbial class ii (zinc dependent) fructose bis-phosphate aldolases. | we report the synthesis and biochemical evaluation of several selective inhibitors of class ii (zinc dependent) fructose bis-phosphate aldolases (fba). the products were designed as transition-state analogues of the catalyzed reaction, structurally related to the substrate fructose bis-phosphate (or sedoheptulose bis-phosphate) and based on an n-substituted hydroxamic acid, as a chelator of the zinc ion present in active site. the compounds synthesized were tested on class ii fbas from various p ... | 2010 | 20929256 |
| the core-independent promoter-specific interaction of primary sigma factor. | previous studies have led to a model in which the promoter-specific recognition of prokaryotic transcription initiation factor, sigma (σ), is core dependent. most σ functions were studied on the basis of this tenet. here, we provide in vitro evidence demonstrating that the intact bacillus subtilis primary sigma, σ(a), by itself, is able to interact specifically with promoter deoxyribonucleic acid (dna), albeit with low sequence selectivity. the core-independent promoter-specific interaction of t ... | 2010 | 20935043 |
| the core-independent promoter-specific interaction of primary sigma factor. | previous studies have led to a model in which the promoter-specific recognition of prokaryotic transcription initiation factor, sigma (σ), is core dependent. most σ functions were studied on the basis of this tenet. here, we provide in vitro evidence demonstrating that the intact bacillus subtilis primary sigma, σ(a), by itself, is able to interact specifically with promoter deoxyribonucleic acid (dna), albeit with low sequence selectivity. the core-independent promoter-specific interaction of t ... | 2010 | 20935043 |
| reversal of a mutator activity by a nearby fidelity-neutral substitution in the rb69 dna polymerase binding pocket. | phage rb69 b-family dna polymerase is responsible for the overall high fidelity of rb69 dna synthesis. fidelity is compromised when conserved tyr567, one of the residues that form the nascent polymerase base-pair binding pocket, is replaced by alanine. the y567a mutator mutant has an enlarged binding pocket and can incorporate and extend mispairs efficiently. ser565 is a nearby conserved residue that also contributes to the binding pocket, but a s565g replacement has only a small impact on dna r ... | 2010 | 20950625 |
| structures of a key interaction protein from the trypanosoma brucei editosome in complex with single domain antibodies. | several major global diseases are caused by single-cell parasites called trypanosomatids. these organisms exhibit many unusual features including a unique and essential u-insertion/deletion rna editing process in their single mitochondrion. many key rna editing steps occur in ∼20s editosomes, which have a core of 12 proteins. among these, the "interaction protein" krepa6 performs a central role in maintaining the integrity of the editosome core and also binds to ssrna. the use of llama single do ... | 2010 | 20969962 |
| structures of a key interaction protein from the trypanosoma brucei editosome in complex with single domain antibodies. | several major global diseases are caused by single-cell parasites called trypanosomatids. these organisms exhibit many unusual features including a unique and essential u-insertion/deletion rna editing process in their single mitochondrion. many key rna editing steps occur in ∼20s editosomes, which have a core of 12 proteins. among these, the "interaction protein" krepa6 performs a central role in maintaining the integrity of the editosome core and also binds to ssrna. the use of llama single do ... | 2010 | 20969962 |
| site-directed mutagenesis of the χ subunit of dna polymerase iii and single-stranded dna-binding protein of e. coli reveals key residues for their interaction. | during dna replication in escherichia coli, single-stranded dna-binding protein (ssb) protects single-stranded dna from nuclease action and hairpin formation. it is known that the highly conserved c-terminus of ssb contacts the χ subunit of dna polymerase iii. however, there only exists a theoretical model in which the 11 c-terminal amino acids of ssb have been docked onto the surface of χ. in order to refine this model of ssb/χ interaction, we exchanged amino acids in χ and ssb by site-directed ... | 2010 | 20972214 |
| site-directed mutagenesis of the χ subunit of dna polymerase iii and single-stranded dna-binding protein of e. coli reveals key residues for their interaction. | during dna replication in escherichia coli, single-stranded dna-binding protein (ssb) protects single-stranded dna from nuclease action and hairpin formation. it is known that the highly conserved c-terminus of ssb contacts the χ subunit of dna polymerase iii. however, there only exists a theoretical model in which the 11 c-terminal amino acids of ssb have been docked onto the surface of χ. in order to refine this model of ssb/χ interaction, we exchanged amino acids in χ and ssb by site-directed ... | 2010 | 20972214 |
| omnipotent role of archaeal elongation factor 1 alpha (ef1α in translational elongation and termination, and quality control of protein synthesis. | the molecular mechanisms of translation termination and mrna surveillance in archaea remain unclear. in eukaryotes, erf3 and hbs1, which are homologous to the trna carrier gtpase ef1α, respectively bind erf1 and pelota to decipher stop codons or to facilitate mrna surveillance. however, genome-wide searches of archaea have failed to detect any orthologs to both gtpases. here, we report the crystal structure of arf1 from an archaeon, aeropyrum pernix, and present strong evidence that the authenti ... | 2010 | 20974926 |
| molecular mechanisms of the whole dna repair system: a comparison of bacterial and eukaryotic systems. | dna is subjected to many endogenous and exogenous damages. all organisms have developed a complex network of dna repair mechanisms. a variety of different dna repair pathways have been reported: direct reversal, base excision repair, nucleotide excision repair, mismatch repair, and recombination repair pathways. recent studies of the fundamental mechanisms for dna repair processes have revealed a complexity beyond that initially expected, with inter- and intrapathway complementation as well as f ... | 2010 | 20981145 |
| transcription of the t4 late genes. | this article reviews the current state of understanding of the regulated transcription of the bacteriophage t4 late genes, with a focus on the underlying biochemical mechanisms, which turn out to be unique to the t4-related family of phages or significantly different from other bacterial systems. the activator of t4 late transcription is the gene 45 protein (gp45), the sliding clamp of the t4 replisome. gp45 becomes topologically linked to dna through the action of its clamp-loader, but it is no ... | 2010 | 21029432 |
| temporal regulation of gene expression of the thermus thermophilus bacteriophage p23-45. | regulation of gene expression during infection of the thermophilic bacterium thermus thermophilus hb8 with the bacteriophage p23-45 was investigated. macroarray analysis revealed host transcription shut-off and identified three temporal classes of phage genes; early, middle and late. primer extension experiments revealed that the 5' ends of p23-45 early transcripts are preceded by a common sequence motif that likely defines early viral promoters. t. thermophilus hb8 rna polymerase (rnap) recogni ... | 2010 | 21050864 |