| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| 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 |
| ribosomes containing mutants of l4 ribosomal protein from thermus thermophilus display multiple defects in ribosomal functions and sensitivity against erythromycin. | protein l4 from thermus thermophilus (tthl4) was heterologously overproduced in escherichia coli cells. to study the implication of the extended loop of tthl4 in the exit-tunnel and peptidyltransferase functions, the highly conserved e56 was replaced by d or q, while the semiconserved g55 was changed to e or s. moreover, the sequence -g55e56- was inverted to -e55g56-. when we incorporated these mutants into e. coli ribosomes and investigated their impact on poly(phe) synthesis, high variations i ... | 2005 | 16244130 |
| solution probing of metal ion binding by helix 27 from escherichia coli 16s rrna. | helix (h)27 from escherichia coli 16s ribosomal (r)rna is centrally located within the small (30s) ribosomal subunit, immediately adjacent to the decoding center. bacterial 30s subunit crystal structures depicting mg(2+) binding sites resolve two magnesium ions within the vicinity of h27: one in the major groove of the g886-u911 wobble pair, and one within the gcaa tetraloop. binding of such metal cations is generally thought to be crucial for rna folding and function. to ask how metal ion-rna i ... | 2005 | 16244134 |
| kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase. | the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ... | 2006 | 16258041 |
| kinetic analysis of the metal binding mechanism of escherichia coli manganese superoxide dismutase. | the acquisition of a catalytic metal cofactor is an essential step in the maturation of every metalloenzyme, including manganese superoxide dismutase (mnsod). in this study, we have taken advantage of the quenching of intrinsic protein fluorescence by bound metal ions to continuously monitor the metallation reaction of escherichia coli mnsod in vitro, permitting a detailed kinetic characterization of the uptake mechanism. apo-mnsod metallation kinetics are "gated", zero order in metal ion for bo ... | 2006 | 16258041 |
| domain ii plays a crucial role in the function of ribosome recycling factor. | rrf (ribosome recycling factor) consists of two domains, and in concert with ef-g (elongation factor-g), triggers dissociation of the post-termination ribosomal complex. however, the function of the individual domains of rrf remains unclear. to clarify this, two rrf chimaeras, ecodi/ttedii and ttedi/ecodii, were created by domain swaps between the proteins from escherichia coli and thermoanaerobacter tengcongensis. the ribosome recycling activity of the rrf chimaeras was compared with their wild ... | 2006 | 16262604 |
| identification of pilus-like structures and genes in microcystis aeruginosa pcc7806. | four putative type iv pilus genes from the toxic, naturally transformable microcystis aeruginosa pcc7806 were identified. three of these genes were clustered in an arrangement which is identical to that from other cyanobacterial genomes. type iv pilus-like appendages were also observed by electron microscopy. | 2005 | 16269818 |
| homology-model-guided site-specific mutagenesis reveals the mechanisms of substrate binding and product-regulation of adenosine kinase from leishmania donovani. | despite designating catalytic roles of asp299 and arg131 during the transfer of gamma-phosphate from atp to ado (adenosine) [r. datta, das, sen, chakraborty, adak, mandal and a. k. datta (2005) biochem. j. 387, 591-600], the mechanisms that determine binding of substrate and cause product inhibition of adenosine kinase from leishmania donovani remained unclear. in the present study, employing homology-model-guided site-specific protein mutagenesis, we show that asp16 is indispensable, since its ... | 2006 | 16271040 |
| structural basis for transcription inhibition by tagetitoxin. | tagetitoxin (tgt) inhibits transcription by an unknown mechanism. a structure at a resolution of 2.4 a of the thermus thermophilus rna polymerase (rnap)-tgt complex revealed that the tgt-binding site within the rnap secondary channel overlaps that of the stringent control effector ppgpp, which partially protects rnap from tgt inhibition. tgt binding is mediated exclusively through polar interactions with the beta and beta' residues whose substitutions confer resistance to tgt in vitro. important ... | 2005 | 16273103 |
| crystal structures of the editing domain of escherichia coli leucyl-trna synthetase and its complexes with met and ile reveal a lock-and-key mechanism for amino acid discrimination. | aarss (aminoacyl-trna synthetases) are responsible for the covalent linking of amino acids to their cognate trnas via the aminoacylation reaction and play a vital role in maintaining the fidelity of protein synthesis. leurs (leucyl-trna synthetase) can link not only the cognate leucine but also the nearly cognate residues ile and met to trna(leu). the editing domain of leurs deacylates the mischarged ile-trna(leu) and met-trna(leu). we report here the crystal structures of ecleurs-ed (the editin ... | 2006 | 16277600 |
| structure of a central stalk subunit f of prokaryotic v-type atpase/synthase from thermus thermophilus. | the crystal structure of subunit f of vacuole-type atpase/synthase (prokaryotic v-atpase) was determined to of 2.2 a resolution. the subunit reveals unexpected structural similarity to the response regulator proteins that include the escherichia coli chemotaxis response regulator chey. the structure was successfully placed into the low-resolution em structure of the prokaryotic holo-v-atpase at a location indicated by the results of crosslinking experiments. the crystal structure, together with ... | 2005 | 16281059 |
| crystal structure and rna binding of the rpb4/rpb7 subunits of human rna polymerase ii. | the rpb4 and rpb7 subunits of eukaryotic rna polymerase ii (rnap(ii)) form a heterodimer that protrudes from the 10-subunit core of the enzyme. we have obtained crystals of the human rpb4/rpb7 heterodimer and determined the structure to 2.7 a resolution. the presence of putative rna-binding domains on the rpb7 subunit and the position of the heterodimer close to the rna exit groove in the 12 subunit yeast polymerase complex strongly suggests a role for the heterodimer in binding and stabilizing ... | 2005 | 16282592 |
| extending ribosomal protein identifications to unsequenced bacterial strains using matrix-assisted laser desorption/ionization mass spectrometry. | a protocol has been developed that allows protein identifications using available dna-based or protein sequences from a reference strain of a bacterial species to be extended to bacterial strains for which no prior dna-based or protein sequence information exists. the protocol is predicated on careful isolation of a specific sub-cellular group of proteins. in this study, ribosomal proteins were chosen due to their high relative abundance and similarity in copy number per cell. after isolation of ... | 2005 | 16287167 |
| control of phosphate release from elongation factor g by ribosomal protein l7/12. | ribosomal protein l7/12 is crucial for the function of elongation factor g (ef-g) on the ribosome. here, we report the localization of a site in the c-terminal domain (ctd) of l7/12 that is critical for the interaction with ef-g. single conserved surface amino acids were replaced in the ctd of l7/12. whereas mutations in helices 5 and 6 had no effect, replacements of v66, i69, k70, and r73 in helix 4 increased the michaelis constant (km) of ef-g.gtp for the ribosome, suggesting an involvement of ... | 2005 | 16292341 |
| a guild of 45 crispr-associated (cas) protein families and multiple crispr/cas subtypes exist in prokaryotic genomes. | clustered regularly interspaced short palindromic repeats (crisprs) are a family of dna direct repeats found in many prokaryotic genomes. repeats of 21-37 bp typically show weak dyad symmetry and are separated by regularly sized, nonrepetitive spacer sequences. four crispr-associated (cas) protein families, designated cas1 to cas4, are strictly associated with crispr elements and always occur near a repeat cluster. some spacers originate from mobile genetic elements and are thought to confer "im ... | 2005 | 16292354 |
| regulation through the rna polymerase secondary channel. structural and functional variability of the coiled-coil transcription factors. | gre factors enhance the intrinsic endonucleolytic activity of rna polymerase to rescue arrested transcription complexes and are thought to confer the high fidelity and processivity of rna synthesis. the gre factors insert the extended alpha-helical coiled-coil domains into the rna polymerase secondary channel to position two invariant acidic residues at the coiled-coil tip near the active site to stabilize the catalytic metal ion. gfh1, a grea homolog from thermus thermophilus, inhibits rather t ... | 2006 | 16298991 |
| accessibility of 18s rrna in human 40s subunits and 80s ribosomes at physiological magnesium ion concentrations--implications for the study of ribosome dynamics. | protein biosynthesis requires numerous conformational rearrangements within the ribosome. the structural core of the ribosome is composed of rna and is therefore dependent on counterions such as magnesium ions for function. many steps of translation can be compromised or inhibited if the concentration of mg(2+) is too low or too high. conditions previously used to probe the conformation of the mammalian ribosome in vitro used high mg(2+) concentrations that we find completely inhibit translation ... | 2005 | 16314459 |
| an assembly landscape for the 30s ribosomal subunit. | self-assembling macromolecular machines drive fundamental cellular processes, including transcription, messenger rna processing, translation, dna replication and cellular transport. the ribosome, which carries out protein synthesis, is one such machine, and the 30s subunit of the bacterial ribosome is the preeminent model system for biophysical analysis of large rna-protein complexes. our understanding of 30s assembly is incomplete, owing to the challenges of monitoring the association of many c ... | 2005 | 16319883 |
| compatible solutes of the hyperthermophile palaeococcus ferrophilus: osmoadaptation and thermoadaptation in the order thermococcales. | the effect of salinity and growth temperature on the accumulation of intracellular organic solutes was examined in the hyperthermophilic archaeon palaeococcus ferrophilus. the genus palaeococcus represents a deep-branching lineage of the order thermococcales, which diverged before thermococcus and pyrococcus. palaeococcus ferrophilus accumulated mannosylglycerate, glutamate, and aspartate as major compatible solutes. unlike members of the genera pyrococcus and thermococcus, palaeococcus ferrophi ... | 2005 | 16332790 |
| the proficiency of a thermophilic chorismate mutase enzyme is solely through an entropic advantage in the enzyme reaction. | a study of the thermus thermophilus chorismate mutase (ttcm) is described by using quantum mechanics (self-consistent-charge density-functional tight binding)/molecular mechanics, umbrella sampling, and the weighted histogram analysis method. the computed free energies of activation for the reactions in water and ttcm are comparable to the experimental values. the free energies for formation of near attack conformer have been determined to be 8.06 and 0.05 kcal/mol in water and ttcm, respectivel ... | 2005 | 16344484 |
| resistance of thermus spp. to potassium tellurite. | two members of the genus thermus were examined for their resistance to toxic inorganic compounds. they both proved to be fairly resistant to tellurite and selenite and to many other heavy metal salts. cell extracts of thermus thermophilus hb8 and of t. flavus at-62 catalyze the reduction of k(2)teo(3) in a reaction which is dependent on nadh oxidation. | 1988 | 16347571 |
| production and extracellular secretion of aqualysin i (a thermophilic subtilisin-type protease) in a host-vector system for thermus thermophilus. | aqualysin i is synthesized as a large precursor, processed, and secreted into the culture medium by thermus aquaticus yt-1. an expression plasmid for the aqualysin i gene in t. thermophilus hb27 was constructed. t. thermophilus cells harboring the recombinant plasmid produced correctly processed aqualysin i, and the mature enzyme was secreted into the culture medium. | 1991 | 16348594 |
| recombination-deficient mutants of an extreme thermophile, thermus thermophilus. | recombination-deficient strains of the extreme thermophile thermus thermophilus have been prepared from a leucine-isoleucine mutant strain (nm6). the availability of such recombination-deficient thermophilic bacterial strains may provide especially good hosts for work with plasmid vectors. | 1993 | 16349029 |
| protein-protein interactions of the hyperthermophilic archaeon pyrococcus horikoshii ot3. | although 2,061 proteins of pyrococcus horikoshii ot3, a hyperthermophilic archaeon, have been predicted from the recently completed genome sequence, the majority of proteins show no similarity to those from other organisms and are thus hypothetical proteins of unknown function. because most proteins operate as parts of complexes to regulate biological processes, we systematically analyzed protein-protein interactions in pyrococcus using the mammalian two-hybrid system to determine the function o ... | 2005 | 16356270 |
| asnb is involved in natural resistance of mycobacterium smegmatis to multiple drugs. | mycobacteria are naturally resistant to most common antibiotics and chemotherapeutic agents. the underlying molecular mechanisms are not fully understood. in this paper, we describe a hypersensitive mutant of mycobacterium smegmatis, ms 2-39, which was isolated by screening for transposon insertion mutants of m. smegmatis mc2155 that exhibit increased sensitivity to rifampin, erythromycin, or novobiocin. the mutant ms 2-39 exhibited increased sensitivity to all three of the above mentioned antib ... | 2006 | 16377694 |
| the allosteric transition in dnak probed by infrared difference spectroscopy. concerted atp-induced rearrangement of the substrate binding domain. | the biological activity of dnak, the bacterial representative of the hsp70 protein family, is regulated by the allosteric interaction between its nucleotide and peptide substrate binding domains. despite the importance of the nucleotide-induced cycling of dnak between substrate-accepting and releasing states, the heterotropic allosteric mechanism remains as yet undefined. to further characterize this mechanism, the nucleotide-induced absorbance changes in the vibrational spectrum of wild-type dn ... | 2006 | 16384998 |
| production of recombinant and tagged proteins in the hyperthermophilic archaeon sulfolobus solfataricus. | many systems are available for the production of recombinant proteins in bacterial and eukaryotic model organisms, which allow us to study proteins in their native hosts and to identify protein-protein interaction partners. in contrast, only a few transformation systems have been developed for archaea, and no system for high-level gene expression existed for hyperthermophilic organisms. recently, a virus-based shuttle vector with a reporter gene was developed for the crenarchaeote sulfolobus sol ... | 2006 | 16391031 |
| involvement of nark1 and nark2 proteins in transport of nitrate and nitrite in the denitrifying bacterium pseudomonas aeruginosa pao1. | two transmembrane proteins were tentatively classified as nark1 and nark2 in the pseudomonas genome project and hypothesized to play an important physiological role in nitrate/nitrite transport in pseudomonas aeruginosa. the nark1 and nark2 genes are located in a cluster along with the structural genes for the nitrate reductase complex. our studies indicate that the transcription of all these genes is initiated from a single promoter and that the gene complex nark1k2ghji constitutes an operon. u ... | 2006 | 16391109 |
| bioinformatic analysis of an unusual gene-enzyme relationship in the arginine biosynthetic pathway among marine gamma proteobacteria: implications concerning the formation of n-acetylated intermediates in prokaryotes. | the n-acetylation of l-glutamate is regarded as a universal metabolic strategy to commit glutamate towards arginine biosynthesis. until recently, this reaction was thought to be catalyzed by either of two enzymes: (i) the classical n-acetylglutamate synthase (nags, gene arga) first characterized in escherichia coli and pseudomonas aeruginosa several decades ago and also present in vertebrates, or (ii) the bifunctional version of ornithine acetyltransferase (oat, gene argj) present in bacteria, a ... | 2006 | 16409639 |
| comparative genomics of multidrug resistance in acinetobacter baumannii. | acinetobacter baumannii is a species of nonfermentative gram-negative bacteria commonly found in water and soil. this organism was susceptible to most antibiotics in the 1970s. it has now become a major cause of hospital-acquired infections worldwide due to its remarkable propensity to rapidly acquire resistance determinants to a wide range of antibacterial agents. here we use a comparative genomic approach to identify the complete repertoire of resistance genes exhibited by the multidrug-resist ... | 2006 | 16415984 |
| structure-function analysis of the kinase-cpd domain of yeast trna ligase (trl1) and requirements for complementation of trna splicing by a plant trl1 homolog. | trl1 is an essential 827 amino acid enzyme that executes the end-healing and end-sealing steps of trna splicing in saccharomyces cerevisiae. trl1 consists of two domains--an n-terminal ligase component and a c-terminal 5'-kinase/2',3'-cyclic phosphodiesterase (cpd) component--that can function in trna splicing in vivo when expressed as separate polypeptides. to understand the structural requirements for the kinase-cpd domain, we performed an alanine scan of 30 amino acids that are conserved in t ... | 2006 | 16428247 |
| function and evolution of plasmid-borne genes for pyrimidine biosynthesis in borrelia spp. | the thyx gene for thymidylate synthase of the lyme borreliosis (lb) agent borrelia burgdorferi is located in a 54-kb linear plasmid. in the present study, we identified an orthologous thymidylate synthase gene in the relapsing fever (rf) agent borrelia hermsii, located it in a 180-kb linear plasmid, and demonstrated its expression. the functions of the b. hermsii and b. burgdorferi thyx gene products were evaluated both in vivo, by complementation of a thymidylate synthase-deficient escherichia ... | 2006 | 16428394 |
| characterization of the biosynthetic pathway of glucosylglycerate in the archaeon methanococcoides burtonii. | the pathway for the synthesis of the organic solute glucosylglycerate (gg) is proposed based on the activities of the recombinant glucosyl-3-phosphoglycerate synthase (gpgs) and glucosyl-3-phosphoglycerate phosphatase (gpgp) from methanococcoides burtonii. a mannosyl-3-phosphoglycerate phosphatase gene homologue (mpgp) was found in the genome of m. burtonii (http://www.jgi.doe.gov), but an mpgs gene coding for mannosyl-3-phosphoglycerate synthase (mpgs) was absent. the gene upstream of the mpgp ... | 2006 | 16428406 |
| crystal structures of nitroalkane oxidase: insights into the reaction mechanism from a covalent complex of the flavoenzyme trapped during turnover. | nitroalkane oxidase (nao) from fusarium oxysporum catalyzes the oxidation of neutral nitroalkanes to the corresponding aldehydes or ketones with the production of h(2)o(2) and nitrite. the flavoenzyme is a new member of the acyl-coa dehydrogenase (acad) family, but it does not react with acyl-coa substrates. we present the 2.2 a resolution crystal structure of nao trapped during the turnover of nitroethane as a covalent n5-fad adduct (es*). the homotetrameric structure of es* was solved by mad p ... | 2006 | 16430210 |
| identification and characterization of rsme, the founding member of a new rna base methyltransferase family. | a variety of rna methyltransferases act during ribosomal rna maturation to modify nucleotides in a site-specific manner. however, of the 10 base-methylated nucleotides present in the small ribosomal subunit of escherichia coli, only three enzymes responsible for modification of four bases are known. here, we show that the protein encoded by yggj, a member of the uncharacterized duf558 protein family of predicted alpha/beta (trefoil) knot methyltransferases is responsible for methylation at u1498 ... | 2006 | 16431987 |
| mutations conferring aminoglycoside and spectinomycin resistance in borrelia burgdorferi. | we have isolated and characterized in vitro mutants of the lyme disease agent borrelia burgdorferi that are resistant to spectinomycin, kanamycin, gentamicin, or streptomycin, antibiotics that target the small subunit of the ribosome. 16s rrna mutations a1185g and c1186u, homologous to escherichia coli nucleotides a1191 and c1192, conferred >2,200-fold and 1,300-fold resistance to spectinomycin, respectively. a 16s rrna a1402g mutation, homologous to e. coli a1408, conferred >90-fold resistance ... | 2006 | 16436695 |