ABSTRACT
Nonnucleoside reverse transcriptase inhibitors (NNRTIs) are important components of current combination therapies for the treatment of human immunodeficiency virus type 1 (HIV-1) infection. However, their low genetic barriers against resistance development, cross-resistance and serious side effects can compromise the benefits of the first generation compounds in this class (efavirenz and nevirapine). To study potential pathways leading to resistance against the novel diphenylether NNRTI, RO-0335, sequential passage experiments at low multiplicity of infection (MOI) were performed to solicit a stepwise selection of resistance mutations. Two pathways to loss of susceptibility to RO-0335 were observed, containing patterns of amino acid changes at either V106I/A plus F227C (with additional contributions from A98G, V108I, E138K, M230L and P236L) or V106I/Y188L (with a potential contribution from L100I, E138K and Y181C). Characterization of the observed mutations by site-directed mutagenesis in the isogenic HXB2D background demonstrated that a minimum of two or more mutations were required for significant loss of susceptibility, with the exception of Y188L, which requires a two-nucleotide change. Patterns containing F227C or quadruple mutations selected by RO-0335 showed a low relative fitness value when compared to wild-type HXB2D.
Subject(s)
Anti-HIV Agents/pharmacology , Drug Resistance, Viral , HIV Reverse Transcriptase/antagonists & inhibitors , HIV-1/drug effects , Reverse Transcriptase Inhibitors/pharmacology , Amino Acid Substitution/genetics , Anti-HIV Agents/chemistry , Cell Line , DNA Mutational Analysis , Humans , Molecular Structure , Mutagenesis, Site-Directed , Mutation, Missense , Reverse Transcriptase Inhibitors/chemistry , Serial PassageABSTRACT
A newly developed 30 S subunit reconstitution system using a complete set of recombinant proteins was used to study the ribosomal RNA (rRNA) neighborhood of ribosomal protein S5 in 30 S subunits and 70 S ribosomes by directed hydroxyl radical probing. Using three cysteine-containing mutant S5 proteins derivatized with 1-(p-bromoacetamidobenzyl)-Fe(II)-EDTA, we expanded on experiments carried out earlier using a natural protein reconstitution system. Natural 16 S rRNA, Fe(II)-S5, and the other recombinant ribosomal proteins were reconstituted into 30 S subunits. Both 30 S subunits and 70 S ribosomes containing Fe(II)-S5 were purified, and hydroxyl radicals were generated in situ from the tethered Fe(II). In 30 S subunits, 16 S rRNA nucleotides targeted by two positions on S5, C21 and C99, were virtually identical to those observed in the previous work, supporting the validity of the recombinant protein reconstitution system for probing studies. Interestingly, new cleavages were detected using Fe(II)-C129-S5, possibly reflecting incorporation of more derivatized protein into 30 S subunits due to the increased reconstitution efficiency of the recombinant protein system. These newly targeted positions overlap, but are distinct from, those observed using Fe(II) tethered to C21, which is near C129 in the S5 structure. In 70 S ribosomes, the cleavage pattern of 16 S rRNA was very similar to that observed in 30 S subunits for all target sites except for the absence of those at the extreme 5' end of 16 S rRNA. Additionally, probing of 70 S ribosomes from Fe-C99-S5 results in cleavage of 23 S rRNA in the 1690-1770 region of domain IV. These data provide constraints for the three-dimensional location of nucleotides within domain IV of 23 S ribosomal RNA relative to known features of the 30 S subunit.
Subject(s)
Bacterial Proteins/chemistry , Edetic Acid/analogs & derivatives , Nucleic Acid Conformation , Organometallic Compounds/chemistry , Protein Conformation , RNA, Bacterial/chemistry , RNA, Ribosomal/chemistry , Ribosomal Proteins/chemistry , Ribosomes/chemistry , Cell-Free System , Edetic Acid/chemistry , Escherichia coli/chemistry , Escherichia coli/ultrastructure , Hydroxyl Radical , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 23S/chemistry , Recombinant Fusion Proteins/chemistryABSTRACT
The NS3 protein of hepatitis C virus contains a bipartite structure consisting of an N-terminal serine protease and a C-terminal DEAD box helicase. We show that the C-terminal domain has ATPase and panhelicase activities. The integrity of the helicase function is dependent on the conserved DEAD motif and can be abolished by a His-Ala point mutation, leaving a fully functional nucleoside triphosphatase.
Subject(s)
Acid Anhydride Hydrolases/chemistry , RNA Nucleotidyltransferases/chemistry , Viral Nonstructural Proteins/chemistry , Acid Anhydride Hydrolases/physiology , Nucleoside-Triphosphatase , Point Mutation , RNA Helicases , RNA Nucleotidyltransferases/physiology , Structure-Activity Relationship , Viral Nonstructural Proteins/physiologyABSTRACT
Directed hydroxyl radical probing was used to probe the rRNA neighborhood around protein S13 in the 30S ribosomal subunit. The unique cysteine at position 84 of S13 served as a tethering site for attachment of Fe(II)-1-(p-bromoacetamidobenzyl)-EDTA. Derivatized S13 (Fe-C84-S13) was then assembled into 30S ribosomal subunits by in vitro reconstitution with 16S rRNA and a mixture of the remaining 30S subunit proteins. Hydroxyl radicals generated from the tethered Fe(II) resulted in cleavage of the RNA backbone in two localized regions of the 3' major domain of 16S rRNA. One region spans nt 1308-1333 and is close to a site previously crosslinked to S13. A second set of cleavages is found in the 950/1230 helix. Both regions have been implicated in binding of S13 by previous chemical footprinting studies using base-specific chemical probes and solution-based hydroxyl radical probing. These results place both regions of 16S rRNA in proximity to position C84 of S13 in the three-dimensional structure of the 30S ribosomal subunit.
Subject(s)
Bacterial Proteins/chemistry , Escherichia coli/chemistry , RNA, Bacterial/chemistry , RNA, Ribosomal/chemistry , Ribosomal Proteins/chemistry , Cysteine/chemistry , Edetic Acid/analogs & derivatives , Escherichia coli Proteins , Hydrogen Peroxide , Hydroxyl Radical , Iron , Models, Molecular , Molecular Probes , Nucleic Acid Conformation , Organometallic Compounds , UltracentrifugationABSTRACT
Cysteine residues were introduced into three different positions distributed on the surface of ribosomal protein S5, to serve as targets for derivatization with an Fe(II)-ethyl-enediaminetetraacetic acid linker. Hydroxyl radicals generated locally from the tethered Fe(II) in intermediate ribonucleoprotein particles or in 30S ribosomal subunits reconstituted from derivatized S5 caused cleavage of the RNA, resulting in characteristically different cleavage patterns for the three different tethering positions. These findings provide constraints for the three-dimensional folding of 16S ribosomal RNA (rRNA) and for the orientation of S5 in the 30S subunit, and they further suggest that antibiotic resistance and accuracy mutations in S5 may involve perturbation of 16S rRNA.
Subject(s)
Hydroxyl Radical/chemistry , RNA, Ribosomal/chemistry , Ribosomal Proteins/chemistry , Anti-Bacterial Agents/pharmacology , Cloning, Molecular , Cysteine/chemistry , Edetic Acid/analogs & derivatives , Escherichia coli , Ferrous Compounds/chemistry , Models, Molecular , Molecular Probes , Mutagenesis, Site-Directed , Nucleic Acid Conformation , Organometallic Compounds , Protein Conformation , RNA, Ribosomal, 16S/chemistry , RNA, Ribosomal, 16S/drug effects , Ribosomal Proteins/genetics , Spectinomycin/pharmacologyABSTRACT
A refined model has been developed for the folding of 16S rRNA in the 30S subunit, based on additional constraints obtained from new experimental approaches. One set of constraints comes from hydroxyl radical footprinting of each of the individual 30S ribosomal proteins, using free Fe(2+)-EDTA complex. A second approach uses localized hydroxyl radical cleavage from a single Fe2+ tethered to unique positions on the surface of single proteins in the 30S subunit. This has been carried out for one position on the surface of protein S4, two on S17, and three on S5. Nucleotides in 16S rRNA that are essential for P-site tRNA binding were identified by a modification interference strategy. Ribosomal subunits were partially inactivated by chemical modification at a low level. Active, partially modified subunits were separated from inactive ones by binding 3'-biotinderivatized tRNA to the 30S subunits and captured with streptavidin beads. Essential bases are those that are unmodified in the active population but modified in the total population. The four essential bases, G926, 2mG966, G1338, and G1401 are a subset of those that are protected from modification by P-site tRNA. They are all located in the cleft of our 30S subunit model. The rRNA neighborhood of the acceptor end of tRNA was probed by hydroxyl radical probing from Fe2+ tethered to the 5' end of tRNA via an EDTA linker. Cleavage was detected in domains IV, V, and VI of 23S rRNA, but not in 5S or 16S rRNA. The sites were all found to be near bases that were protected from modification by the CCA end of tRNA in earlier experiments, except for a set of E-site cleavages in domain IV and a set of A-site cleavages in the alpha-sarcin loop of domain VI. In vitro genetics was used to demonstrate a base-pairing interaction between tRNA and 23S rRNA. Mutations were introduced at positions C74 and C75 of tRNA and positions 2252 and 2253 of 23S rRNA. Interaction of the CCA end of tRNA with mutant ribosomes was tested using chemical probing in conjunction with allele-specific primer extension. The interaction occurred only when there was a Watson-Crick pairing relationship between positions 74 of tRNA and 2252 of 23S rRNA. Using a novel chimeric in vitro reconstitution method, it was shown that the peptidyl transferase reaction depends on this same Watson-Crick base pair.
Subject(s)
RNA, Ribosomal/chemistry , Models, Biological , Models, Molecular , Nucleic Acid Conformation , RNA, Ribosomal/genetics , RNA, Ribosomal, 23S/chemistry , RNA, Transfer/genetics , RNA-Binding Proteins/chemistry , Structure-Activity RelationshipABSTRACT
Localized hydroxyl radical probing has been used to explore the rRNA neighborhood around a unique position in the structure of the Escherichia coli 30S ribosomal subunit. Fe(II) was attached to ribosomal protein S4 at Cys-31 via the reagent 1-(p-bromoacetamidobenzyl)-EDTA. [Fe-Cys31]S4 was then complexed with 16S rRNA or incorporated into active 30S ribosomal subunits by in vitro reconstitution with 16S rRNA and a mixture of the remaining 30S subunit proteins. Hydroxyl radicals generated from the tethered Fe resulted in cleavage of the 16S rRNA chain in two localized regions of its 5' domain. One region spans positions 419-432 and is close to the multihelix junction previously placed at the RNA binding site of S4 by chemical and enzymatic protection (footprinting) and crosslinking studies. A second site of directed cleavage includes nucleotides 297-303, which overlap a site that is protected from chemical modification by protein S16, a near neighbor of S4 in the ribosome. These results provide useful information about the three-dimensional organization of 16S rRNA and indicate that these two regions of its 5' domain are in close spatial proximity to Cys-31 of protein S4.
Subject(s)
Hydroxyl Radical/chemistry , Iron/chemistry , RNA, Ribosomal, 16S/chemistry , Ribosomal Proteins/chemistry , Escherichia coli/chemistryABSTRACT
The binding site and probable site of action have been determined for the universal antibiotic amicetin which inhibits peptide bond formation. Evidence from in vivo mutants, site-directed mutations and chemical footprinting all implicate a highly conserved motif in the secondary structure of the 23S-like rRNA close to the central circle of domain V. We infer that this motif lies at, or close to, the catalytic site in the peptidyl transfer centre. The binding site of amicetin is the first of a group of functionally related hexose-cytosine inhibitors to be localized on the ribosome.
Subject(s)
Anti-Bacterial Agents/pharmacology , Halobacterium salinarum/genetics , RNA, Ribosomal, 23S/genetics , Anti-Bacterial Agents/metabolism , Base Sequence , Conserved Sequence , Drug Resistance, Microbial/genetics , Escherichia coli/drug effects , Halobacterium salinarum/metabolism , Molecular Sequence Data , Nucleic Acid Conformation , Point Mutation , Protein Biosynthesis/drug effects , Pyrimidine Nucleosides/metabolism , Pyrimidine Nucleosides/pharmacology , RNA, Ribosomal, 23S/metabolismABSTRACT
The primary giant-cell tumour is a semimalignant bone tumour which occurs primarily on the epiphysis of the long tubular bones and the methaphysis. The present case report describes the bilateral occurrence of this tumour in the region of the osseous thorax. The paper also deals with diagnostic, therapeutical and prognostic problems.
