Publications
| Title | Abstract | Year Filter | PMID(sorted ascending) Filter |
|---|
| proteolysis in hyperthermophilic microorganisms. | proteases are found in every cell, where they recognize and break down unneeded or abnormal polypeptides or peptide-based nutrients within or outside the cell. genome sequence data can be used to compare proteolytic enzyme inventories of different organisms as they relate to physiological needs for protein modification and hydrolysis. in this review, we exploit genome sequence data to compare hyperthermophilic microorganisms from the euryarchaeotal genus pyrococcus, the crenarchaeote sulfolobus ... | 2002 | 15803660 |
| trna m7g methyltransferase trm8p/trm82p: evidence linking activity to a growth phenotype and implicating trm82p in maintaining levels of active trm8p. | we show that saccharomyces cerevisiae strains lacking trm8p/trm82p trna m7g methyltransferase are temperature-sensitive in synthetic media containing glycerol. bacterial trm8 orthologs complement the growth defect of trm8-delta, trm82-delta, and trm8-delta trm82-delta double mutants, suggesting that bacteria employ a single subunit for trm8p/trm82p function. the growth phenotype of trm8 mutants correlates with lack of trna m7g methyltransferase activity in vitro and in vivo, based on analysis of ... | 2005 | 15811913 |
| the affinity of the dynein microtubule-binding domain is modulated by the conformation of its coiled-coil stalk. | the microtubule-binding domain (mtbd) of dynein is separated from the aaa (atpase with any other activity) core of the motor by an approximately 15-nm stalk that is predicted to consist of an antiparallel coiled coil. however, the structure of this coiled coil and the mechanism it uses to mediate communication between the mtbd and atp-binding core are unknown. here, we sought to identify the optimal alignment between the hydrophobic heptad repeats in the two strands of the stalk coiled coil. to ... | 2005 | 15826937 |
| functional characterization of a novel arga from mycobacterium tuberculosis. | the mycobacterium tuberculosis gene rv2747 encodes a novel 19-kda arga that catalyzes the initial step in l-arginine biosynthesis, namely the conversion of l-glutamate to alpha-n-acetyl-l-glutamate. initial velocity studies reveal that rv2747 proceeds through a sequential kinetic mechanism, with k(m) values of 280 mm for l-glutamine and 150 microm for acetyl-coenzyme a and with a k(cat) value of 200 min(-1). initial velocity studies with l-glutamate showed that even at concentrations of 600 mm, ... | 2005 | 15838030 |
| human mitochondrial tyrrs disobeys the tyrosine identity rules. | human tyrosyl-trna synthetase from mitochondria (mt-tyrrs) presents dual sequence features characteristic of eubacterial and archaeal tyrrss, especially in the region containing amino acids recognizing the n1-n72 tyrosine identity pair. this would imply that human mt-tyrrs has lost the capacity to discriminate between the g1-c72 pair typical of eubacterial and mitochondrial trnatyr and the reverse pair c1-g72 present in archaeal and eukaryal trnatyr. this expectation was verified by a functional ... | 2005 | 15840810 |
| crystal structures of apo wild-type m. jannaschii tyrosyl-trna synthetase (tyrrs) and an engineered tyrrs specific for o-methyl-l-tyrosine. | the methanococcus jannaschii trna(tyr)/tyrrs pair has been engineered to incorporate unnatural amino acids into proteins in e. coli. to reveal the structural basis for the altered specificity of mutant tyrrs for o-methyl-l-tyrosine (ometyr), the crystal structures for the apo wild-type and mutant m. jannaschii tyrrs were determined at 2.66 and 3.0 a, respectively, for comparison with the published structure of tyrrs complexed with trna(tyr) and substrate tyrosine. a large conformational change w ... | 2005 | 15840835 |
| inhibition of archaeal growth and dna topoisomerase vi activities by the hsp90 inhibitor radicicol. | type ii dna topoisomerases have been classified into two families, topo iia and topo iib, based on structural and mechanistic dissimilarities. topo iia is the target of many important antibiotics and antitumoural drugs, most of them being inactive on topo iib. the effects and mode of action of topo iia inhibitors in vitro and in vivo have been extensively studied for the last twenty-five years. in contrast, studies of topo iib inhibitors were lacking. to document this field, we have studied two ... | 2005 | 15849317 |
| diagnostic application of padlock probes--multiplex detection of plant pathogens using universal microarrays. | padlock probes (plps) are long oligonucleotides, whose ends are complementary to adjacent target sequences. upon hybridization to the target, the two ends are brought into contact, allowing plp circularization by ligation. plps provide extremely specific target recognition, which is followed by universal amplification and microarray detection. since target recognition is separated from downstream processing, plps enable the development of flexible and extendable diagnostic systems, targeting div ... | 2005 | 15860767 |
| independent binding sites of small protein b onto transfer-messenger rna during trans-translation. | stalled bacterial ribosomes are freed by transfer-messenger rna (tmrna). with the help of small protein b (smpb), protein synthesis restarts and tmrna adds a tag to the stalled protein for destruction. the conformation of a 347 nt long tmrna from a thermophile and its interactions with smpb were monitored using structural probes. the rna is highly folded, including the reading frame, with <30% of unpaired residues. footprints between smpb and tmrna are in the elbow of the trna domain, in some ps ... | 2005 | 15860775 |
| recurrent structural rna motifs, isostericity matrices and sequence alignments. | the occurrences of two recurrent motifs in ribosomal rna sequences, the kink-turn and the c-loop, are examined in crystal structures and systematically compared with sequence alignments of rrnas from the three kingdoms of life in order to identify the range of the structural and sequence variations. isostericity matrices are used to analyze structurally the sequence variations of the characteristic non-watson-crick base pairs for each motif. we show that isostericity matrices for non-watson-cric ... | 2005 | 15860776 |
| structural and functional divergence of muts2 from bacterial muts1 and eukaryotic msh4-msh5 homologs. | muts homologs, identified in nearly all bacteria and eukaryotes, include the bacterial proteins muts1 and muts2 and the eukaryotic muts homologs 1 to 7, and they often are involved in recognition and repair of mismatched bases and small insertion/deletions, thereby limiting illegitimate recombination and spontaneous mutation. to explore the relationship of muts2 to other muts homologs, we examined conserved protein domains. fundamental differences in structure between muts2 and other muts homolo ... | 2005 | 15866941 |
| severity of the streptomycin resistance and streptomycin dependence phenotypes of ribosomal protein s12 of thermus thermophilus depends on the identity of highly conserved amino acid residues. | the structural basis for the streptomycin dependence phenotype of ribosomal protein s12 mutants is poorly understood. here we describe the application of site-directed mutagenesis and gene replacement of thermus thermophilus rpsl to assess the importance of side chain identity and tertiary interactions as phenotypic determinants of drug-dependent mutants. | 2005 | 15866943 |
| developmental-stage-specific assembly of parb complexes in streptomyces coelicolor hyphae. | in streptomyces coelicolor parb is required for accurate chromosome partitioning during sporulation. using a functional parb-enhanced green fluorescent protein fusion, we observed bright tip-associated foci and other weaker, irregular foci in s. coelicolor vegetative hyphae. in contrast, in aerial hyphae regularly spaced bright foci accompanied sporulation-associated chromosome condensation and septation. | 2005 | 15866947 |
| nebulon: a system for the inference of functional relationships of gene products from the rearrangement of predicted operons. | since operons are unstable across prokaryotes, it has been suggested that perhaps they re-combine in a conservative manner. thus, genes belonging to a given operon in one genome might re-associate in other genomes revealing functional relationships among gene products. we developed a system to build networks of functional relationships of gene products based on their organization into operons in any available genome. the operon predictions are based on inter-genic distances. our system can use d ... | 2005 | 15867197 |
| distribution of genes for synthesis of trehalose and mannosylglycerate in thermus spp. and direct correlation of these genes with halotolerance. | in this study we correlate the presence of genes leading to the synthesis of trehalose and mannosylglycerate (mg) in 17 strains of the genus thermus with the ability of the strains to grow and accumulate these compatible solutes in a defined medium containing nacl. the two sets of genes, namely, otsa/otsb for the synthesis of trehalose and mpgs/mpgp for the synthesis of mg, were necessary for the growth of thermus thermophilus in a defined medium containing up to 6% nacl. strains lacking a compl ... | 2005 | 15870334 |
| a functional relationship between helix 1 and the 900 tetraloop of 16s ribosomal rna within the bacterial ribosome. | the conserved 900 tetraloop that caps helix 27 of 16s ribosomal rna (rrna) interacts with helix 24 of 16s rrna and also with helix 67 of 23s rrna, forming the intersubunit bridge b2c, proximal to the decoding center. in previous studies, we investigated how the interaction between the 900 tetraloop and helix 24 participates in subunit association and translational fidelity. in the present study, we investigated whether the 900 tetraloop is involved in other undetected interactions with different ... | 2005 | 15872184 |
| strain relief at the active site of phosphoserine aminotransferase induced by radiation damage. | the x-ray susceptibility of the lysine-pyridoxal-5'-phosphate schiff base in bacillus alcalophilus phosphoserine aminotransferase has been investigated using crystallographic data collected at 100 k to 1.3 a resolution, complemented by on-line spectroscopic studies. x-rays induce deprotonation of the internal aldimine, changes in the schiff base conformation, displacement of the cofactor molecule, and disruption of the schiff base linkage between pyridoxal-5'-phosphate and the lys residue. analy ... | 2005 | 15883191 |
| predicted highly expressed genes in archaeal genomes. | based primarily on 16s rrna sequence comparisons, life has been broadly divided into the three domains of bacteria, archaea, and eukarya. archaea is further classified into crenarchaea and euryarchaea. archaea generally thrive in extreme environments as assessed by temperature, ph, and salinity. for many prokaryotic organisms, ribosomal proteins (rp), transcription/translation factors, and chaperone genes tend to be highly expressed. a gene is predicted highly expressed (phx) if its codon usage ... | 2005 | 15883368 |
| the tyra family of aromatic-pathway dehydrogenases in phylogenetic context. | the tyra protein family includes members that catalyze two dehydrogenase reactions in distinct pathways leading to l-tyrosine and a third reaction that is not part of tyrosine biosynthesis. family members share a catalytic core region of about 30 kda, where inhibitors operate competitively by acting as substrate mimics. this protein family typifies many that are challenging for bioinformatic analysis because of relatively modest sequence conservation and small size. | 2005 | 15888209 |
| papillomavirus capsid mutation to escape dendritic cell-dependent innate immunity in cervical cancer. | infection with oncogenic human papillomaviruses (hpvs), typified by hpv type 16 (hpv16), is a necessary cause of cervical cancer. prophylactic vaccination with hpv16 l1 virus-like particles (vlps) provides immunity. hpv16 vlps activate dendritic cells and a potent neutralizing immunoglobulin g (igg) response, yet many cervical cancer patients fail to generate detectable vlp-specific igg. therefore, we examined the role of the innate recognition of hpv16 l1 in vlp-induced immune responses and its ... | 2005 | 15890912 |
| the cryptochromes. | cryptochromes are photoreceptors that regulate entrainment by light of the circadian clock in plants and animals. they also act as integral parts of the central circadian oscillator in animal brains and as receptors controlling photomorphogenesis in response to blue or ultraviolet (uv-a) light in plants. cryptochromes are probably the evolutionary descendents of dna photolyases, which are light-activated dna-repair enzymes, and are classified into three groups -- plant cryptochromes, animal cryp ... | 2005 | 15892880 |
| physics-based protein-structure prediction using a hierarchical protocol based on the unres force field: assessment in two blind tests. | recent improvements in the protein-structure prediction method developed in our laboratory, based on the thermodynamic hypothesis, are described. the conformational space is searched extensively at the united-residue level by using our physics-based unres energy function and the conformational space annealing method of global optimization. the lowest-energy coarse-grained structures are then converted to an all-atom representation and energy-minimized with the ecepp/3 force field. the procedure ... | 2005 | 15894609 |
| structural basis for lysidine formation by atp pyrophosphatase accompanied by a lysine-specific loop and a trna-recognition domain. | lysidine, a lysine-combined modified cytidine, is exclusively located at the anticodon wobble position (position 34) of eubacterial trna(ile)(2) and not only converts the codon specificity from aug to aua, but also converts the aminoacylation specificity from recognition by methionyl-trna synthetase to that by isoleucyl-trna synthetase (ilers). here, we report the crystal structure of lysidine synthetase (tils) from aquifex aeolicus at 2.42-a resolution. tils forms a homodimer, and each subunit ... | 2005 | 15894617 |
| towards understanding the molecular basis of bacterial dna segregation. | bacteria ensure the fidelity of genetic inheritance by the coordinated control of chromosome segregation and cell division. here, we review the molecules and mechanisms that govern the correct subcellular positioning and rapid separation of newly replicated chromosomes and plasmids towards the cell poles and, significantly, the emergence of mitotic-like machineries capable of segregating plasmid dna. we further describe surprising similarities between proteins involved in dna partitioning (para/ ... | 2005 | 15897178 |
| dksa potentiates direct activation of amino acid promoters by ppgpp. | amino acid starvation in escherichia coli results in a spectrum of changes in gene expression, including inhibition of rrna and trna promoters and activation of certain promoters for amino acid biosynthesis and transport. the unusual nucleotide ppgpp plays an important role in both negative and positive regulation. previously, we and others suggested that positive effects of ppgpp might be indirect, resulting from the inhibition of rrna transcription and, thus, liberation of rna polymerase for b ... | 2005 | 15899978 |
| characterization of the atpase activity of topoisomerase ii from leishmania donovani and identification of residues conferring resistance to etoposide. | we have cloned and expressed the 43 kda n-terminal domain of leishmania donovani topoisomerase ii. this protein has an intrinsic atpase activity and obeys michaelis-menten kinetics. cross-linking studies indicate that the n-terminal domain exists as a dimer both in the presence and absence of nucleotides. etoposide, an effective antitumour drug, traps eukaryotic dna topoisomerase ii in a covalent complex with dna. in the present study, we report for the first time that etoposide inhibits the atp ... | 2005 | 15901238 |
| atp-sensitive k+ channel channel/enzyme multimer: metabolic gating in the heart. | cardiac atp-sensitive k(+) (k(atp)) channels, gated by cellular metabolism, are formed by association of the inwardly rectifying potassium channel kir6.2, the potassium conducting subunit, and sur2a, the atp-binding cassette protein that serves as the regulatory subunit. kir6.2 is the principal site of atp-induced channel inhibition, while sur2a regulates k(+) flux through adenine nucleotide binding and catalysis. the atpase-driven conformations within the regulatory sur2a subunit of the k(atp) ... | 2005 | 15910874 |
| genetic analysis reveals a role for the c terminus of the saccharomyces cerevisiae gtpase snu114 during spliceosome activation. | snu114 is the only gtpase required for mrna splicing. as a homolog of elongation factor g, it contains three domains (iii-v) predicted to undergo a large rearrangement following gtp hydrolysis. to assess the functional importance of the domains of snu114, we used random mutagenesis to create conditionally lethal alleles. we identified three main classes: (1) mutations that are predicted to affect gtp binding and hydrolysis, (2) mutations that are clustered in 10- to 20-amino-acid stretches in ea ... | 2005 | 15911574 |
| new mutations and horizontal transfer of rpob among rifampin-resistant streptococcus pneumoniae from four spanish hospitals. | a total of 103 (0.7%) of 14,236 streptococcus pneumoniae isolates collected in four spanish hospitals from 1989 to 2003 were resistant to rifampin (mics, 4 to 512 microg/ml). only sixty-one (59.2%) of these isolates were available for molecular characterization. resistance was mostly related to human immunodeficiency virus (hiv) infection in adult patients and to conjunctivitis in children. thirty-six different pulsed-field gel electrophoresis patterns were identified among resistant isolates, f ... | 2005 | 15917517 |
| heptameric (l12)6/l10 rather than canonical pentameric complexes are found by tandem ms of intact ribosomes from thermophilic bacteria. | ribosomes are universal translators of the genetic code into protein and represent macromolecular structures that are asymmetric, often heterogeneous, and contain dynamic regions. these properties pose considerable challenges for modern-day structural biology. despite these obstacles, high-resolution x-ray structures of the 30s and 50s subunits have revealed the rna architecture and its interactions with proteins for ribosomes from thermus thermophilus, deinococcus radiodurans, and haloarcula ma ... | 2005 | 15923259 |
| the pseudouridine synthase rlud is required for normal ribosome assembly and function in escherichia coli. | rlud is the pseudouridine synthase responsible for the formation of psi1911, psi1915, and psi1917 in escherichia coli 23s rrna. previous work from our laboratory demonstrated that disruption of the rlud gene and/or loss of the pseudouridine residues for which it is responsible resulted in a severe growth phenotype. in the current work we have examined further the effect of the loss of the rlud protein and its product pseudouridine residues in a deletion strain lacking the rlud gene. this strain ... | 2005 | 15928344 |
| sacb-5-fluoroorotic acid-pyre-based bidirectional selection for integration of unmarked alleles into the chromosome of rhodobacter capsulatus. | the gram-negative, purple nonsulfur, facultative photosynthetic bacterium rhodobacter capsulatus is a widely used model organism and has well-developed molecular genetics. in particular, interposon mutagenesis using selectable gene cartridges is frequently employed for construction of a variety of chromosomal knockout mutants. however, as the gene cartridges are often derived from antibiotic resistance-conferring genes, their numbers are limited, which restricts the construction of multiple knoc ... | 2005 | 15932997 |
| increase in xylanase production by streptomyces lividans through simultaneous use of the sec- and tat-dependent protein export systems. | xylanase b1 (xlnb1) from streptomyces lividans is a protein consisting of two discrete structural and functional units, an n-terminal catalytic domain and a c-terminal substrate binding domain. in the culture medium, two forms of xylanase b are present, namely, xlnb1 and xlnb2, the latter of which corresponds to the catalytic domain of xlnb1 deprived of the substrate binding domain. both forms of the xylanase have the same activity on xylan. the enzyme is secreted through the sec-dependent pathw ... | 2005 | 15933005 |
| membrane-associated maturation of the heterotetrameric nitrate reductase of thermus thermophilus. | the nar operon, coding for the respiratory nitrate reductase of thermus thermophilus (nrt), encodes a di-heme b-type (narj) and a di-heme c-type (narc) cytochrome. the role of both cytochromes and that of a putative chaperone (narj) in the synthesis and maturation of nrt was studied. mutants of t. thermophilus lacking either nari or narc synthesized a soluble form of narg, suggesting that a putative narci complex constitutes the attachment site for the enzyme. interestingly, the narg protein syn ... | 2005 | 15937161 |
| nmr structure and mg2+ binding of an rna segment that underlies the l7/l12 stalk in the e.coli 50s ribosomal subunit. | helix 42 of domain ii of escherichia coli 23s ribosomal rna underlies the l7/l12 stalk in the ribosome and may be significant in positioning this feature relative to the rest of the 50s ribosomal subunit. unlike the haloarcula marismortui and deinococcus radiodurans examples, the lower portion of helix 42 in e.coli contains two consecutive g*a oppositions with both adenines on the same side of the stem. herein, the structure of an analog of positions 1037-1043 and 1112-1118 in the helix 42 regio ... | 2005 | 15939932 |
| the tetr family of transcriptional repressors. | we have developed a general profile for the proteins of the tetr family of repressors. the stretch that best defines the profile of this family is made up of 47 amino acid residues that correspond to the helix-turn-helix dna binding motif and adjacent regions in the three-dimensional structures of tetr, qacr, cprb, and ethr, four family members for which the function and three-dimensional structure are known. we have detected a set of 2,353 nonredundant proteins belonging to this family by scree ... | 2005 | 15944459 |
| a census of membrane-bound and intracellular signal transduction proteins in bacteria: bacterial iq, extroverts and introverts. | analysis of complete microbial genomes showed that intracellular parasites and other microorganisms that inhabit stable ecological niches encode relatively primitive signaling systems, whereas environmental microorganisms typically have sophisticated systems of environmental sensing and signal transduction. | 2005 | 15955239 |
| characterization of a thermostable uvrd helicase and its participation in helicase-dependent amplification. | helicase-dependent amplification (hda) is an isothermal in vitro dna amplification method based upon the coordinated actions of helicases to separate double-stranded dna and dna polymerases to synthesize dna. previously, a mesophilic form of hda (mhda) utilizing the escherichia coli uvrd helicase, dna polymerase i klenow fragment, two accessory proteins, mutl and single-stranded dna-binding protein (ssb), was developed (1). in an effort to improve the specificity and performance of hda, we have ... | 2005 | 15955821 |
| comparison of qualitative (cobas amplicor hcv 2.0 versus versant hcv rna) and quantitative (cobas amplicor hcv monitor 2.0 versus versant hcv rna 3.0) assays for hepatitis c virus (hcv) rna detection and quantification: impact on diagnosis and treatment of hcv infections. | quantitative measurements of serum hepatitis c virus (hcv) rna are becoming increasingly important in the management of hcv-infected patients. here we compared two quantitative assays, the cobas amplicor hcv monitor 2.0 assay (roche diagnostics) and the branched dna-based versant hcv rna 3.0 assay (bayer diagnostics) for hcv rna measurement in 344 samples derived from 120 patients with chronic genotype 1 hcv infection. the overall concordance between the results of the two tests was 95%, and the ... | 2005 | 15956369 |
| engineering and functional evaluation of a single-chain antibody against hiv-1 external glycoprotein gp120. | the hiv-1 envelope glycoprotein surface subunit gp120 is an attractive target for molecular intervention. this is because anti-hiv-1 gp120 neutralizing antibodies display the potential ability to inhibit hiv-1 infection. the present investigation describes the construction of a genetically engineered single chain antibody (scfv102) against hiv-1 gp120, its expression and functional evaluation. the parental hybridoma cell line (102) produces an immunoglobulin directed against the conserved cd4-bi ... | 2005 | 15958072 |
| comparative 3-d modeling of tmrna. | trans-translation releases stalled ribosomes from truncated mrnas and tags defective proteins for proteolytic degradation using transfer-messenger rna (tmrna). this small stable rna represents a hybrid of trna- and mrna-like domains connected by a variable number of pseudoknots. comparative sequence analysis of tmrnas found in bacteria, plastids, and mitochondria provides considerable insights into their secondary structures. progress toward understanding the molecular mechanism of template swit ... | 2005 | 15958166 |
| mapping the interaction of smpb with ribosomes by footprinting of ribosomal rna. | in trans-translation transfer messenger rna (tmrna) and small protein b (smpb) rescue ribosomes stalled on truncated or in other ways problematic mrnas. smpb promotes the binding of tmrna to the ribosome but there is uncertainty about the number of participating smpb molecules as well as their ribosomal location. here, the interaction of smpb with ribosomal subunits and ribosomes was studied by isolation of smpb containing complexes followed by chemical modification of ribosomal rna with dimethy ... | 2005 | 15972795 |
| identification of novel restriction endonuclease-like fold families among hypothetical proteins. | restriction endonucleases and other nucleic acid cleaving enzymes form a large and extremely diverse superfamily that display little sequence similarity despite retaining a common core fold responsible for cleavage. the lack of significant sequence similarity between protein families makes homology inference a challenging task and hinders new family identification with traditional sequence-based approaches. using the consensus fold recognition method meta-basic that combines sequence profiles wi ... | 2005 | 15972856 |
| popscomp: an automated interaction analysis of biomolecular complexes. | large-scale analysis of biomolecular complexes reveals the functional network within the cell. computational methods are required to extract the essential information from the available data. the popscomp server is designed to calculate the interaction surface between all components of a given complex structure consisting of proteins, dna or rna molecules. the server returns matrices and graphs of surface area burial that can be used to automatically annotate components and residues that are inv ... | 2005 | 15980485 |
| profunc: a server for predicting protein function from 3d structure. | profunc (http://www.ebi.ac.uk/thornton-srv/databases/profunc) is a web server for predicting the likely function of proteins whose 3d structure is known but whose function is not. users submit the coordinates of their structure to the server in pdb format. profunc makes use of both existing and novel methods to analyse the protein's sequence and structure identifying functional motifs or close relationships to functionally characterized proteins. a summary of the analyses provides an at-a-glance ... | 2005 | 15980588 |
| guanine-nucleotide exchange on ribosome-bound elongation factor g initiates the translocation of trnas. | during the translation of mrna into polypeptide, elongation factor g (ef-g) catalyzes the translocation of peptidyl-trna from the a site to the p site of the ribosome. according to the 'classical' model, ef-g in the gtp-bound form promotes translocation, while hydrolysis of the bound gtp promotes dissociation of the factor from the post-translocation ribosome. according to a more recent model, ef-g operates like a 'motor protein' and drives translocation of the peptidyl-trna after gtp hydrolysis ... | 2005 | 15985150 |
| the cm56 trna modification in archaea is catalyzed either by a specific 2'-o-methylase, or a c/d srnp. | we identified the first archaeal trna ribose 2'-o-methylase, atrm56, belonging to the cluster of orthologous groups (cog) 1303 that contains archaeal genes only. the corresponding protein exhibits a spout s-adenosylmethionine (adomet)-dependent methyltransferase domain found in bacterial and yeast g18 trna 2'-o-methylases (spou, trm3). we cloned the pyrococcus abyssi pab1040 gene belonging to this cog, expressed and purified the corresponding protein, and showed that in vitro, it specifically ca ... | 2005 | 15987815 |
| not all j domains are created equal: implications for the specificity of hsp40-hsp70 interactions. | heat shock protein 40s (hsp40s) and heat shock protein 70s (hsp70s) form chaperone partnerships that are key components of cellular chaperone networks involved in facilitating the correct folding of a broad range of client proteins. while the hsp40 family of proteins is highly diverse with multiple forms occurring in any particular cell or compartment, all its members are characterized by a j domain that directs their interaction with a partner hsp70. specific hsp40-hsp70 chaperone partnerships ... | 2005 | 15987899 |
| mutational analysis of 16s and 23s rrna genes of thermus thermophilus. | structural studies of the ribosome have benefited greatly from the use of organisms adapted to extreme environments. however, little is known about the mechanisms by which ribosomes or other ribonucleoprotein complexes have adapted to functioning under extreme conditions, and it is unclear to what degree mutant phenotypes of extremophiles will resemble those of their counterparts adapted to more moderate environments. it is conceivable that phenotypes of mutations affecting thermophilic ribosome ... | 2005 | 15995195 |
| systematic characterization of the adp-ribose pyrophosphatase family in the cyanobacterium synechocystis sp. strain pcc 6803. | we have characterized four putative adp-ribose pyrophosphatases sll1054, slr0920, slr1134, and slr1690 in the cyanobacterium synechocystis sp. strain pcc 6803. each of the recombinant proteins was overexpressed in escherichia coli and purified. sll1054 and slr0920 hydrolyzed adp-ribose specifically, while slr1134 hydrolyzed not only adp-ribose but also nadh and flavin adenine dinucleotide. by contrast, slr1690 showed very low activity for adp-ribose and had four substitutions of amino acids in t ... | 2005 | 15995214 |
| the pd-(d/e)xk superfamily revisited: identification of new members among proteins involved in dna metabolism and functional predictions for domains of (hitherto) unknown function. | the pd-(d/e)xk nuclease superfamily, initially identified in type ii restriction endonucleases and later in many enzymes involved in dna recombination and repair, is one of the most challenging targets for protein sequence analysis and structure prediction. typically, the sequence similarity between these proteins is so low, that most of the relationships between known members of the pd-(d/e)xk superfamily were identified only after the corresponding structures were determined experimentally. th ... | 2005 | 16011798 |
| kinetics of substrate recognition and cleavage by human 8-oxoguanine-dna glycosylase. | human 8-oxoguanine-dna glycosylase (hogg1) excises 8-oxo-7,8-dihydroguanine (8-oxog) from damaged dna. we report a pre-steady-state kinetic analysis of hogg1 mechanism using stopped-flow and enzyme fluorescence monitoring. the kinetic scheme for hogg1 processing an 8-oxog:c-containing substrate was found to include at least three fast equilibrium steps followed by two slow, irreversible steps and another equilibrium step. the second irreversible step was rate-limiting overall. by comparing data ... | 2005 | 16024742 |
| 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 |
| identification of a novel gene encoding a flavin-dependent trna:m5u methyltransferase in bacteria--evolutionary implications. | formation of 5-methyluridine (ribothymidine) at position 54 of the t-psi loop of trna is catalyzed by site-specific trna methyltransferases (trna:m(5)u-54 mtase). in all eukarya and many gram-negative bacteria, the methyl donor for this reaction is s-adenosyl-l-methionine (s-adomet), while in several gram-positive bacteria, the source of carbon is n(5), n(10)-methylenetetrahydrofolate (ch(2)h(4)folate). we have identified the gene for bacillus subtilis trna:m(5)u-54 mtase. the encoded recombinan ... | 2005 | 16027442 |
| temperature differentially affects adenosine triphosphatase activity in hsc70 orthologs from antarctic and new zealand notothenioid fishes. | to test the temperature sensitivity of molecular chaperones in poikilothermic animals, we purified the molecular chaperone hsc70 from 2 closely related notothenioid fishes--the antarctic species trematomus bernacchii and the temperate new zealand species notothenia angustata--and characterized the effect of temperature on hsc70 adenosine triphosphatase (atpase) activity. hsc70 atpase activity was measured using [alpha-32p]-adenosine triphosphate (atp)-based in vitro assays followed by separation ... | 2005 | 16038407 |
| protein content of minimal and ancestral ribosome. | minimal genome approaches seek to define the smallest gene complement compatible with modern-type cellular life on earth. a consensus of computational and experimental approaches indicates that a minimal genome is close to 300 protein-coding genes, if a rich medium is provided for cell growth. i relate ribosomal gene content in completely sequenced genomes to ribosomal subunit structure and approximate the protein components of the putative minimal ribosome and the ribosome of the last universal ... | 2005 | 16043494 |
| lead(ii) cleavage analysis of rnase p rna in vivo. | the overall conformation of m1 rna, the catalytic rna subunit of rnase p in escherichia coli, was analyzed in vivo and, in the presence of the c5 protein subunit, in vitro by lead(ii) acetate probing. the partial cleavage patterns obtained are congruent with previous structure mapping performed in vitro. most of the known major and minor cleavages in m1 rna were supported and could be mapped onto a secondary structure model. the data obtained indicate that c5 has only minor effects on the overal ... | 2005 | 16043496 |
| conformation of 4.5s rna in the signal recognition particle and on the 30s ribosomal subunit. | the signal recognition particle (srp) from escherichia coli consists of 4.5s rna and protein ffh. it is essential for targeting ribosomes that are translating integral membrane proteins to the translocation pore in the plasma membrane. independently of ffh, 4.5s rna also interacts with elongation factor g (ef-g) and the 30s ribosomal subunit. here we use a cross-linking approach to probe the conformation of 4.5s rna in srp and in the complex with the 30s ribosomal subunit and to map the binding ... | 2005 | 16043501 |
| rna secondary structure prediction by centroids in a boltzmann weighted ensemble. | prediction of rna secondary structure by free energy minimization has been the standard for over two decades. here we describe a novel method that forsakes this paradigm for predictions based on boltzmann-weighted structure ensemble. we introduce the notion of a centroid structure as a representative for a set of structures and describe a procedure for its identification. in comparison with the minimum free energy (mfe) structure using diverse types of structural rnas, the centroid of the ensemb ... | 2005 | 16043502 |
| molecular mimicry: quantitative methods to study structural similarity between protein and rna. | with rapidly increasing availability of three-dimensional structures, one major challenge for the post-genome era is to infer the functions of biological molecules based on their structural similarity. while quantitative studies of structural similarity between the same type of biological molecules (e.g., protein vs. protein) have been carried out intensively, the comparable study of structural similarity between different types of biological molecules (e.g., protein vs. rna) remains unexplored. ... | 2005 | 16043503 |
| remodeling protein complexes: insights from the aaa+ unfoldase clpx and mu transposase. | multiprotein complexes in the cell are dynamic entities that are constantly undergoing changes in subunit composition and conformation to carry out their functions. the protein-dna complex that promotes recombination of the bacteriophage mu is a prime example of a complex that must undergo specific changes to carry out its function. the clp/hsp100 family of aaa+ atpases plays a critical role in mediating such changes. the clp/hsp100 unfolding enzymes have been extensively studied for the roles t ... | 2005 | 16046622 |
| three-dimensional structure of the aah26994.1 protein from mus musculus, a putative eukaryotic urm1. | we have used nmr spectroscopy to determine the solution structure of protein aah26994.1 from mus musculus and propose that it represents the first three-dimensional structure of a ubiquitin-related modifier 1 (urm1) protein. amino acid sequence comparisons indicate that aah26994.1 belongs to the urm1 family of ubiquitin-like modifier proteins. the best characterized member of this family has been shown to be involved in nutrient sensing, invasive growth, and budding in yeast. proteins in this fa ... | 2005 | 16046629 |
| structural and functional analysis of 5s rrna in saccharomyces cerevisiae. | 5s rrna extends from the central protuberance of the large ribosomal subunit, through the a-site finger, and down to the gtpase-associated center. here, we present a structure-function analysis of seven 5s rrna alleles which are sufficient for viability in the yeast saccharomyces cerevisiae when expressed in the absence of wild-type 5s rrnas, and extend this analysis using a large bank of mutant alleles that show semi-dominant phenotypes in the presence of wild-type 5s rrna. this analysis suppor ... | 2005 | 16047201 |
| analysis of the function of e. coli 23s rrna helix-loop 69 by mutagenesis. | the ribosome is a two-subunit enzyme known to exhibit structural dynamism during protein synthesis. the intersubunit bridges have been proposed to play important roles in decoding, translocation, and the peptidyl transferase reaction; yet the physical nature of their contributions is ill understood. an intriguing intersubunit bridge, b2a, which contains 23s rrna helix 69 as a major component, has been implicated by proximity in a number of catalytically important regions. in addition to contacti ... | 2005 | 16053518 |
| exploring the flexibility of ribosome recycling factor using molecular dynamics. | ribosome recycling factor is proposed to be flexible, and that flexibility is believed to be important to its function. here we use molecular dynamics to test the flexibility of escherichia coli rrf (ecrrf) with and without decanoic acid bound to a hydrophobic pocket between domains 1 and 2, and thermus thermophilus rrf (ttrrf) with and without a mutation in the hinge between domains 1 and 2. our simulations show that the structure of ecrrf rapidly goes from having an interdomain angle of 124 de ... | 2005 | 16055531 |
| stationary-phase expression and aminoacylation of a transfer-rna-like small rna. | genome-scale analyses have shown numerous functional duplications in the canonical translational machinery. one of the most striking examples is the occurrence of unrelated class i and class ii lysyl-transfer rna synthetases (lysrs), which together may aminoacylate non-canonical trnas. we show that, in bacillus cereus, the two lysrss together aminoacylate a small rna of unknown function named trna(other), and that the aminoacylated product stably binds translation elongation factor tu. in vitro ... | 2005 | 16065067 |
| simultaneous detection of microsatellite repeats and snps in the macrophage migration inhibitory factor (mif) gene by thin-film biosensor chips and application to rural field studies. | microsatellite repeat and single nucleotide polymorphisms (snps) are abundant sources of genetic variation, but existing methodologies cannot simultaneously detect these variants in a facile or inexpensive way. we describe herein a thin-film biosensor chip based on an allele-discriminating oligonucleotide array that enables genotyping for both microsatellite repeats and snps in a single analysis. we validated this methodology for the functionally polymorphic -794 catt(5-8) repeat and -173 g/c sn ... | 2005 | 16077028 |
| structure and topology of microbial communities in the major gut compartments of melolontha melolontha larvae (coleoptera: scarabaeidae). | physicochemical gut conditions and the composition and topology of the intestinal microbiota in the major gut compartments of the root-feeding larva of the european cockchafer (melolontha melolontha) were studied. axial and radial profiles of ph, o2, h2, and redox potential were measured with microsensors. terminal restriction fragment length polymorphism (t-rflp) analysis of bacterial 16s rrna genes in midgut samples of individual larvae revealed a simple but variable and probably nonspecific c ... | 2005 | 16085849 |
| 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 |
| dissecting homo-heptamer thermodynamics by isothermal titration calorimetry: entropy-driven assembly of co-chaperonin protein 10. | normally, isothermal titration calorimetry (itc) is used to study binding reactions between two different biomolecules. self-association processes leading to homo-oligomeric complexes have usually not been studied by itc; instead, methods such as spectroscopy and analytical ultracentrifugation, which only provide affinity and gibbs-free energy (i.e., k(d) and deltag), are employed. we here demonstrate that complete thermodynamic descriptions (i.e., k(d), deltag, deltah, and deltas) for self-asso ... | 2005 | 16100270 |
| e1 enzyme of the pyruvate dehydrogenase complex in corynebacterium glutamicum: molecular analysis of the gene and phylogenetic aspects. | the e1p enzyme is an essential part of the pyruvate dehydrogenase complex (pdhc) and catalyzes the oxidative decarboxylation of pyruvate with concomitant acetylation of the e2p enzyme within the complex. we analyzed the corynebacterium glutamicum acee gene, encoding the e1p enzyme, and constructed and characterized an e1p-deficient mutant. sequence analysis of the c. glutamicum acee gene and adjacent regions revealed that acee is not flanked by genes encoding other enzymes of the pdhc. transcrip ... | 2005 | 16109942 |
| the genomics of disulfide bonding and protein stabilization in thermophiles. | thermophilic organisms flourish in varied high-temperature environmental niches that are deadly to other organisms. recently, genomic evidence has implicated a critical role for disulfide bonds in the structural stabilization of intracellular proteins from certain of these organisms, contrary to the conventional view that structural disulfide bonds are exclusively extracellular. here both computational and structural data are presented to explore the occurrence of disulfide bonds as a protein-st ... | 2005 | 16111437 |
| comparison of trna motions in the free and ribosomal bound structures. | a general method is presented that allows the separation of the rigid body motions from the nonrigid body motions of structural subunits when bound in a complex. the application presented considers the motions of the trnas: free, bound to the ribosome and to a synthase. we observe that both the rigid body and nonrigid body motions of the structural subunits are highly controlled by the large ribosomal assembly and are important for the functional motions of the assembly. for the intact ribosome, ... | 2005 | 16113113 |
| a unique trna recognition mechanism of caenorhabditis elegans mitochondrial ef-tu2. | nematode mitochondria expresses two types of extremely truncated trnas that are specifically recognized by two distinct elongation factor tu (ef-tu) species named ef-tu1 and ef-tu2. this is unlike the canonical ef-tu molecule that participates in the standard protein biosynthesis systems, which basically recognizes all elongator trnas. ef-tu2 specifically recognizes ser-trna(ser) that lacks a d arm but has a short t arm. our previous study led us to speculate the lack of the d arm may be essenti ... | 2005 | 16113240 |
| inhibition of bacterial rna polymerase by streptolydigin: stabilization of a straight-bridge-helix active-center conformation. | we define the target, mechanism, and structural basis of inhibition of bacterial rna polymerase (rnap) by the tetramic acid antibiotic streptolydigin (stl). stl binds to a site adjacent to but not overlapping the rnap active center and stabilizes an rnap-active-center conformational state with a straight-bridge helix. the results provide direct support for the proposals that alternative straight-bridge-helix and bent-bridge-helix rnap-active-center conformations exist and that cycling between st ... | 2005 | 16122422 |
| structure of the uncomplexed dna repair enzyme endonuclease viii indicates significant interdomain flexibility. | escherichia coli endonuclease viii (nei) excises oxidized pyrimidines from dna. it shares significant sequence homology and similar mechanism with fpg, a bacterial 8-oxoguanine glycosylase. the structure of a covalent nei-dna complex has been recently determined, revealing critical amino acid residues which are important for dna binding and catalysis. several fpg structures have also been reported; however, analysis of structural dynamics of fpg/nei family proteins has been hindered by the lack ... | 2005 | 16145054 |
| quantitative detection of hepatitis c virus (hcv) rna in saliva and gingival crevicular fluid of hcv-infected patients. | the search for hepatitis c virus (hcv) in body fluids other than blood is important when assessing possible nonparenteral routes of viral transmission. however, the role of oral fluids in hcv transmission remains controversial. here we quantitatively determined hcv rna in saliva and gingival crevicular fluid (gcf) of anti-hcv-positive patients. most patients (14 of 18; 78%) whose saliva specimens were negative had hcv rna in their gcf. most patients (20 of 26; 77%) had higher hcv rna levels in t ... | 2005 | 16145085 |
| investigating the secy plug movement at the secyeg translocation channel. | protein translocation occurs across the energy-conserving bacterial membrane at the secyeg channel. the crystal structure of the channel has revealed a possible mechanism for gating and opening. this study evaluates the plug hypothesis using cysteine crosslink experiments in combination with various allelic forms of the sec complex. the results demonstrate that the secy plug domain moves away from the center of the channel toward sece during polypeptide translocation, and further show that the t ... | 2005 | 16148946 |
| 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 |
| constraining ribosomal rna conformational space. | despite the potential for many possible secondary-structure conformations, the native sequence of ribosomal rna (rrna) is able to find the correct and universally conserved core fold. this study reports a computational analysis investigating two mechanisms that appear to constrain rrna secondary-structure conformational space: ribosomal proteins and rrna sequence composition. the analysis was carried out by using rrna-ribosomal protein interaction data for the escherichia coli 16s rrna and free ... | 2005 | 16155182 |
| dual-mode recognition of noncanonical trnas(ser) by seryl-trna synthetase in mammalian mitochondria. | the secondary structures of metazoan mitochondrial (mt) trnas(ser) deviate markedly from the paradigm of the canonical cloverleaf structure; particularly, trna(ser)(gcu) corresponding to the agy codon (y=u and c) is highly truncated and intrinsically missing the entire dihydrouridine arm. none of the mt serine isoacceptors possesses the elongated variable arm, which is the universal landmark for recognition by seryl-trna synthetase (serrs). here, we report the crystal structure of mammalian mt s ... | 2005 | 16163389 |
| protein activation of a ribozyme: the role of bacterial rnase p protein. | bacterial ribonuclease p (rnase p) belongs to a class of enzymes that utilize both rnas and proteins to perform essential cellular functions. the bacterial rnase p protein is required to activate bacterial rnase p rna in vivo, but previous studies have yielded contradictory conclusions regarding its specific functions. here, we use biochemical and biophysical techniques to examine all of the proposed functions of the protein in both escherichia coli and bacillus subtilis rnase p. we demonstrate ... | 2005 | 16163391 |
| crystal structure of tetrameric homoisocitrate dehydrogenase from an extreme thermophile, thermus thermophilus: involvement of hydrophobic dimer-dimer interaction in extremely high thermotolerance. | the crystal structure of homoisocitrate dehydrogenase involved in lysine biosynthesis from thermus thermophilus (tthicdh) was determined at 1.85-a resolution. arg85, which was shown to be a determinant for substrate specificity in our previous study, is positioned close to the putative substrate binding site and interacts with glu122. glu122 is highly conserved in the equivalent position in the primary sequence of icdh and archaeal 3-isopropylmalate dehydrogenase (ipmdh) but interacts with main- ... | 2005 | 16166541 |
| deacylated trna is released from the e site upon a site occupation but before gtp is hydrolyzed by ef-tu. | the presence or absence of deacylated trna at the e site sharply influences the activation energy required for binding of a ternary complex to the ribosomal a site indicating the different conformations that the e-trna imparts on the ribosome. here we address two questions: (i) whether or not peptidyltransferase--the essential catalytic activity of the large ribosomal subunit--also depends on the occupancy state of the e site and (ii) at what stage the e-trna is released during an elongation cyc ... | 2005 | 16166657 |
| amyloid formation of a protein in the absence of initial unfolding and destabilization of the native state. | in 5% (v/v) trifluoroethanol, ph 5.5, 25 degrees c one of the acylphosphatases from drosophila melanogaster (acpdro2) forms fibrillar aggregates that bind thioflavin t and congo red and have an extensive beta-sheet structure, as revealed by circular dichroism. atomic force microscopy indicates that the fibrils and their constituent protofilaments have diameters compatible with those of natural amyloid fibrils. spectroscopic and biochemical investigation, carried out using near- and far-uv circul ... | 2005 | 16169977 |
| expression of human ctp synthetase in saccharomyces cerevisiae reveals phosphorylation by protein kinase a. | ctp synthetase (ec 6.3.4.2, utp:ammonia ligase (adp-forming)) is an essential enzyme in all organisms; it generates the ctp required for the synthesis of nucleic acids and membrane phospholipids. in this work we showed that the human ctp synthetase genes, ctps1 and ctps2, were functional in saccharomyces cerevisiae and complemented the lethal phenotype of the ura7delta ura8delta mutant lacking ctp synthetase activity. the expression of the ctps1- and ctps2-encoded human ctp synthetase enzymes in ... | 2005 | 16179339 |
| high-level chromosomally mediated tetracycline resistance in neisseria gonorrhoeae results from a point mutation in the rpsj gene encoding ribosomal protein s10 in combination with the mtrr and penb resistance determinants. | neisseria gonorrhoeae becomes resistant to tetracycline by two major mechanisms: expression of a plasmid-encoded tetm protein and mutations in endogenous genes (chromosomally mediated resistance). early studies by sparling and colleagues (p. f. sparling f. a. j. sarubbi, and e. blackman, j. bacteriol. 124:740-749, 1975) demonstrated that three genes were involved in high-level chromosomally mediated tetracycline resistance (mic of tetracycline > or = 2 microg/ml): ery-2 (now referred to as mtrr) ... | 2005 | 16189114 |
| structural and mechanistic studies of vps4 proteins. | vps4 atpases function in multivesicular body formation and in hiv-1 budding. here, we report the crystal structure of monomeric apo human vps4b/skd1 (hvps4b), which is composed of five distinct elements: a poorly ordered n-terminal mit domain that binds escrt-iii substrates, large (mixed alpha/beta) and small (alpha) aaa atpase domains that closely resemble analogous domains in the p97 d1 atpase cassette, a three-stranded antiparallel beta domain inserted within the small atpase domain, and a no ... | 2005 | 16193069 |
| crystal structure of yeast yer010cp, a knotable member of the rraa protein family. | we present here the structure of yer010c protein of unknown function, solved by multiple anomalous diffraction and revealing a common fold and oligomerization state with proteins of the regulator of ribonuclease activity a (rraa) family. in escherichia coli, rraa has been shown to regulate the activity of ribonuclease e by direct interaction. the absence of ribonuclease e in yeast suggests a different function for this family member in this organism. yer010cp has a few supplementary secondary st ... | 2005 | 16195557 |
| global transcriptome analysis of shewanella oneidensis mr-1 exposed to different terminal electron acceptors. | to gain insight into the complex structure of the energy-generating networks in the dissimilatory metal reducer shewanella oneidensis mr-1, global mrna patterns were examined in cells exposed to a wide range of metal and non-metal electron acceptors. gene expression patterns were similar irrespective of which metal ion was used as electron acceptor, with 60% of the differentially expressed genes showing similar induction or repression relative to fumarate-respiring conditions. several groups of ... | 2005 | 16199584 |
| evidence for a role of initiation factor 3 in recycling of ribosomal complexes stalled on mrnas in escherichia coli. | specific interactions between ribosome recycling factor (rrf) and elongation factor-g (efg) mediate disassembly of post-termination ribosomal complexes for new rounds of initiation. the interactions between rrf and efg are also important in peptidyl-trna release from stalled pre-termination complexes. unlike the post-termination complexes (harboring deacylated trna), the pre-termination complexes (harboring peptidyl-trna) are not recycled by rrf and efg in vitro, suggesting participation of addi ... | 2005 | 16199751 |
| entropic stabilization of proteins and its proteomic consequences. | evolutionary traces of thermophilic adaptation are manifest, on the whole-genome level, in compositional biases toward certain types of amino acids. however, it is sometimes difficult to discern their causes without a clear understanding of underlying physical mechanisms of thermal stabilization of proteins. for example, it is well-known that hyperthermophiles feature a greater proportion of charged residues, but, surprisingly, the excess of positively charged residues is almost entirely due to ... | 2005 | 16201009 |
| 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 |
| mechanisms of product feedback regulation and drug resistance in cytidine triphosphate synthetases from the structure of a ctp-inhibited complex. | cytidine triphosphate synthetases (ctpss) synthesize ctp and regulate its intracellular concentration through direct interactions with the four ribonucleotide triphosphates. in particular, ctp product is a feedback inhibitor that competes with utp substrate. selected ctps mutations that impart resistance to pyrimidine antimetabolite inhibitors also relieve ctp inhibition and cause a dramatic increase in intracellular ctp concentration, indicating that the drugs act by binding to the ctp inhibito ... | 2005 | 16216072 |
| an inexpensive and rapid diagnostic method of koi herpesvirus (khv) infection by loop-mediated isothermal amplification. | koi herpesvirus (khv) affects both juvenile and adult common carp and koi, and is especially lethal to fry. the high mortalities caused by the disease have had a negative impact on the international koi trade. different diagnostic techniques have been used to detect khv, including: isolation of the virus in cell culture, electron microscopy, several pcr tests, elisa and in situ hybridisation. all of these methods are time consuming, laborious and require specialised equipment. | 2005 | 16216123 |
| single-molecule forster resonance energy transfer study of protein dynamics under denaturing conditions. | proteins are highly complex systems, exhibiting a substantial degree of structural variability in their folded state. in the presence of denaturants, the heterogeneity is greatly enhanced, and fluctuations among vast numbers of folded and unfolded conformations occur via many different pathways. here, we have studied the structure and dynamics of the small enzyme ribonuclease hi (rnase h) in the presence of the chemical denaturant guanidinium chloride (gdmcl) using single-molecule fluorescence m ... | 2005 | 16221762 |
| evolutionary, structural and functional relationships revealed by comparative analysis of syntenic genes in rhizobiales. | comparative genomics has provided valuable insights into the nature of gene sequence variation and chromosomal organization of closely related bacterial species. however, questions about the biological significance of gene order conservation, or synteny, remain open. moreover, few comprehensive studies have been reported for rhizobial genomes. | 2005 | 16229745 |
| combining two genomes in one cell: stable cloning of the synechocystis pcc6803 genome in the bacillus subtilis 168 genome. | cloning the whole 3.5-megabase (mb) genome of the photosynthetic bacterium synechocystis pcc6803 into the 4.2-mb genome of the mesophilic bacterium bacillus subtilis 168 resulted in a 7.7-mb composite genome. we succeeded in such unprecedented large-size cloning by progressively assembling and editing contiguous dna regions that cover the entire synechocystis genome. the strain containing the two sets of genome grew only in the b. subtilis culture medium where all of the cloning procedures were ... | 2005 | 16236728 |
| 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 |
| characterization of the family i inorganic pyrophosphatase from pyrococcus horikoshii ot3. | a gene encoding for a putative family i inorganic pyrophosphatase (ppase, ec 3.6.1.1) from the hyperthermophilic archaeon pyrococcus horikoshii ot3 was cloned and the biochemical characteristics of the resulting recombinant protein were examined. the gene (accession no. 1907) from p. horikoshii showed some identity with other family i inorganic pyrophosphatases from archaea. the recombinant ppase from p. horikoshii (phppase) has a molecular mass of 24.5 kda, determined by sds-page. this enzyme s ... | 2005 | 16243777 |