Capreomycin binds across the ribosomal subunit interface using tlyA-encoded 2'-O-methylations in 16S and 23S rRNAs

The cyclic peptide antibiotics capreomycin and viomycin are generally effective against the bacterial pathogen Mycobacterium tuberculosis. However, recent virulent isolates have become resistant by inactivation of their tlyA gene. We show here that tlyA encodes a 2'-O-methyltransferase that modifies nucleotide C1409 in helix 44 of 16S rRNA and nucleotide C1920 in helix 69 of 23S rRNA. Loss of these previously unidentified rRNA methylations confers resistance to capreomycin and viomycin. Many bacterial genera including enterobacteria lack a tlyA gene and the ensuing methylations and are less susceptible than mycobacteria to capreomycin and viomycin. We show that expression of recombinant tlyA in Escherichia coli markedly increases susceptibility to these drugs. When the ribosomal subunits associate during translation, the two tlyA-encoded methylations are brought into close proximity at interbridge B2a. The location of these methylations indicates the binding site and inhibitory mechanism of capreomycin and viomycin at the ribosome subunit interface.     

Interaction between the ribosomal subunits: 16S rRNA suppressors of the lethal ΔA1916 mutation in the 23S rRNA of <Emphasis Type="Italic">Escherichia coli</Emphasis>

A1916 in 23S rRNA is located in one of the major intersubunit bridges of the 70S ribosome. Deletion of A1916 disrupts the intersubunit bridge B2a, promotes misreading of the genetic code and is lethal. In a genetic selection for suppressor mutations, two base substitutions in 16S rRNA were recovered that restored viability and also allowed expression of ΔA1916-associated capreomycin resistance. These mutations were G1048A in helix 34 and U1471C in helix 44. Restoration of function is incomplete, however, and the double mutants are slow-growing, defective in subunit association and support high levels of translational errors. In contrast, none of these parameters is affected by the single 16S suppressor mutations. U1471C likely affects another intersubunit contact, bridge B6, suggesting that interactions between different bridges and cross-talk between subunits contributes to ribosomal function.     

Capreomycin susceptibility is increased by TlyA-directed 2'-O-methylation on both ribosomal subunits

The binding site of the cyclic peptide antibiotics capreomycin and viomycin is located on the ribosomal subunit interface close to nucleotides C1409 in 16S rRNA and C1920 in 23S rRNA. In Mycobacterium tuberculosis, the 2'-hydroxyls of both nucleotides are methylated by the enzyme TlyA. Loss of these methylations through inactivation of TlyA confers resistance to capreomycin and viomycin. We report here that TlyA orthologues occur in diverse bacteria and fall into two distinct groups. One group, now termed TlyA(I) , has shorter N- and C-termini and methylates only C1920; the second group (now TlyA(II) ) includes the mycobacterial enzyme, and these longer orthologues methylate at both C1409 and C1920. Ribosomal subunits are the preferred substrates for both groups of orthologues. Amino acid substitutions at the N-terminus of TlyA(II) reduce its ability to methylate these substrates. Growing pairs of recombinant TlyA(II) Escherichia coli strains in competition shows that even subtle changes in the level of rRNA methylation lead to significant differences in susceptibility to sub-inhibitory concentrations of capreomycin. The findings reveal that 2'-O-methyls at both C1409 and C1920 play a role in facilitating the inhibitory effects of capreomycin and viomycin on the bacterial ribosome.     

Substrate specificity of the pseudouridine synthase RluD in Escherichia coli

Pseudouridine synthase RluD converts uridines at positions 1911, 1915, and 1917 of 23S rRNA to pseudouridines. These nucleotides are located in the functionally important helix-loop 69 of 23S rRNA. RluD is the only pseudouridine synthase that is required for normal growth in Escherichia coli. We have analyzed substrate specificity of RluD in vivo. Mutational analyses have revealed: (a) RluD isomerizes uridine in vivo only at positions 1911, 1915, and 1917, regardless of the presence of uridine at other positions in the loop of helix 69 of 23S rRNA variants; (b) substitution of one U by C has no effect on the conversion of others (i.e. formation of pseudouridines at positions 1911, 1915, and 1917 are independent of each other); (c) A1916 is the only position in the loop of helix 69, where mutations affect the RluD specific pseudouridine formation. Pseudouridines were determined in the ribosomal particles from a ribosomal large subunit defective strain (RNA helicase DeaD(-)). An absence of pseudouridines in the assembly precursor particles suggests that RluD directed isomerization of uridines occurs as a late step during the assembly of the large ribosomal subunit.     

pH-dependent structural changes of helix 69 from Escherichia coli 23S ribosomal RNA

Helix 69 in 23S rRNA is a region in the ribosome that participates in a considerable number of RNA-RNA and RNA-protein interactions. Conformational flexibility is essential for such a region to interact and accommodate protein factors at different stages of protein biosynthesis. In this study, pH-dependent structural and stability changes were observed for helix 69 through a variety of spectroscopic techniques, such as circular dichroism spectroscopy, UV melting, and nuclear magnetic resonance spectroscopy. In Escherichia coli 23S rRNA, helix 69 contains pseudouridine residues at positions 1911, 1915, and 1917. The presence of these pseudouridines was found to be essential for the pH-induced conformational changes. Some of the pH-dependent changes appear to be localized to the loop region of helix 69, emphasizing the importance of the highly conserved nature of residues in this region.     

Pseudouridylation of 23S rRNA helix 69 promotes peptide release by release factor RF2 but not by release factor RF1

Pseudouridine [Ψ] is a frequent base modification in the ribosomal RNA [rRNA] and may be involved in the modulation of the conformational flexibility of rRNA helix-loop structures during protein synthesis. Helix 69 of 23S rRNA contains pseudouridines at the positions 1911, 1915 and 1917 which are formed by the helix 69-specific synthase RluD. The growth defect caused by the lack of RluD can be rescued by mutations in class I release factor RF2, indicating a role for helix 69 pseudouridines in translation termination. We investigated the role of helix 69 pseudouridines in peptide release by release factors RF1 and RF2 in an in vitro system consisting of purified components of the Escherichia coli translation apparatus. Lack of all three pseudouridines in helix 69 compromised the activity of RF2 about 3-fold but did not significantly affect the activity of RF1. Reintroduction of pseudouridines into helix 69 by RluD-treatment restored the activity of RF2 in peptide release. A Ψ-to-C substitution at the 1917 position caused an increase in the dissociation rate of RF1 and RF2 from the postrelease ribosome. Our results indicate that the presence of all three pseudouridines in helix 69 stimulates peptide release by RF2 but has little effect on the activity of RF1. The interactions around the pseudouridine at the 1917 position appear to be most critical for a proper interaction of helix 69 with release factors.     

Ribosomal Intersubunit Bridge B2a Is Involved in Factor-Dependent Translation Initiation and Translational Processivity

Intersubunit bridges are important for holding together subunits in the 70S ribosome. Moreover, a number of intersubunit bridges have a role in modulating the activity of the ribosome during translation. Ribosomal intersubunit bridge B2a is formed by the interaction between the conserved 23S rRNA helix-loop 69 (H69) and the top of the 16S rRNA helix 44. Within the 70S ribosome, bridge B2a contacts translation factors and the A-site tRNA. In addition to bridging the subunits, bridge B2a has been invoked in a number of other ribosomal functions from initiation to termination. In the present work, single-nucleotide substitutions were inserted at positions 1912 and 1919 of Escherichia coli 23S rRNA (helix 69), which are involved in important intrahelical and intersubunit tertiary interactions in bridge B2a. The resulting ribosomes had a severely reduced activity in a cell-free translation elongation assay, but displayed a nearly wild-type-level peptidyl transferase activity. In vitro reassociation efficiency decreased with all of the H69 variant 50S subunits, but was severest with the A1919C and ΔH69 variants. The mutations strongly affected initiation-factor-dependent 70S initiation complex formation, but exhibited a minor effect on the nonenzymatic initiation process. The mutations decreased ribosomal processivity in vitro and caused a progressive depletion of 50S subunits in polysomal fractions in vivo. Mutations at position 1919 decreased the stability of a dipeptidyl-tRNA in the A-site, whereas the binding of the dipeptidyl-tRNA was rendered more stable with 1912 and ΔH69 mutations. Our results suggest that the H69 of 23S rRNA functions as a control element during enzymatic steps of translation.     

Genetic and structural analysis of base substitutions in the central pseudoknot of Thermus thermophilus 16S ribosomal RNA

Characterization of base substitutions in rRNAs has provided important insights into the mechanism of protein synthesis. Knowledge of the structural effects of such alterations is limited, and could be greatly expanded with the development of a genetic system based on an organism amenable to both genetics and structural biology. Here, we describe the genetic analysis of base substitutions in 16S ribosomal RNA of the extreme thermophile Thermus thermophilus, and an analysis of the conformational effects of these substitutions by structure probing with base-specific modifying agents. Gene replacement methods were used to construct a derivative of strain HB8 carrying a single 16S rRNA gene, allowing the isolation of spontaneous streptomycin-resistant mutants and subsequent genetic mapping of mutations by recombination. The residues altered to give streptomycin resistance reside within the central pseudoknot structure of 16S rRNA comprised of helices 1 and 27, and participate in the U13–U20–A915 base triple, the G21–A914 type II sheared G–A base pair, or the G885–C912 Watson–Crick base pair closing helix 27. Substitutions at any of the three residues engaged in the base triple were found to confer resistance. Results from structure probing of the pseudoknot are consistent with perturbation of RNA conformation by these substitutions, potentially explaining their streptomycin-resistance phenotypes.     

Modulation of 16S rRNA function by ribosomal protein S12

Ribosomal protein S12 is a critical component of the decoding center of the 30S ribosomal subunit and is involved in both tRNA selection and the response to streptomycin. We have investigated the interplay between S12 and some of the surrounding 16S rRNA residues by examining the phenotypes of double-mutant ribosomes in strains of Escherichia coli carrying deletions in all chromosomal rrn operons and expressing total rRNA from a single plasmid-borne rrn operon. We show that the combination of S12 and otherwise benign mutations at positions C1409-G1491 in 16S rRNA severely compromises cell growth while the level and range of aminoglycoside resistances conferred by the G1491U/C substitutions is markedly increased by a mutant S12 protein. The G1491U/C mutations in addition confer resistance to the unrelated antibiotic, capreomycin. S12 also interacts with the 912 region of 16S rRNA. Genetic selection of suppressors of streptomycin dependence caused by mutations at proline 90 in S12 yielded a C912U substitution in 16S rRNA. The C912U mutation on its own confers resistance to streptomycin and restricts miscoding, properties that distinguish it from a majority of the previously described error-promoting ram mutants that also reverse streptomycin dependence.     

Cross-resistant relationships among the aminoglucoside antibiotics in Mycobacterium tuberculosis.

Phenotypes of isolates of Mycobacterium tuberculosis H37RV showing resistance to the aminoglucoside antibiotics streptomycin, viomycin, kanamycin, capreomycin, tuberactinomycin N, lividomycin and paromomycin could be grouped into the following types: (I) resistant only to different levels of streptomycins; (2) resistant only to a low level of kanamycin; (3) triply resistant, to low levels of viomycin, tuberactinomycin N and capreomycin; (4) triply resistant, to a low level of kanamycin and high levels of lividomycin and paromomycin; (5) quadruply resistant, to a low level of capreomycin and high levels of kanamycin, lividomycin and paromomycin; (6) hextuply resistant, to high levels of viomycin, tuberactinomycin N, capreomycin, kanamycin, lividomycin, and paromomycin. Three modificatied types of the latter were also observed. Appearance rates of the six types were estimated as 10(-6) to 10(-9), 10(-6), 10(-6) to 10(-7), 10(-8), 10(-8), and 10(-8) to 10(-9), respectively, in a total viable population of the parent strain. Mutations to all phenotypes were considered to be produced by single mutations. According to cross-resistance relationships, aminoglucoside antibiotics were classified into three groups: (I) streptomycin; (II) viomycin, tuberactinomycin N and capreomycin; (III) kanamycin, lividomycin and paromomycin. No cross-resistance relationship between streptomycin and other antibiotics was observed. Resistances to viomycin, tuberactinomycin N and capreomycin occurred by single mutation to type 3. Resistances to kanamycin, lividomycin and paromomycin occurred by single mutations to types 4 and 5. Low resistance to capreomycin was produced by mutation to type 5. Therefore capreomycin was considered to be an intermediate between the second and third groups. These two groups had a close relationship, as resistance to all six agents in these groups could be produced by a single mutation to type 6 (and its modified types).     

A mutation in the decoding center of Thermus thermophilus 16S rRNA suggests a novel mechanism of streptomycin resistance

A spontaneous kanamycin resistance and capreomycin resistance mutation, A1408G, in the decoding center of 16S rRNA, was identified in the extreme thermophile Thermus thermophilus. Unexpectedly, this mutation also confers resistance to streptomycin. We propose a novel mechanism of streptomycin resistance by which A1408G influences conformational changes in 16S rRNA during tRNA selection.     

Functional interactions within 23S rRNA involving the peptidyltransferase center.

A molecular genetic approach has been employed to investigate functional interactions within 23S rRNA. Each of the three base substitutions at guanine 2032 has been made. The 2032A mutation confers resistance to the antibiotics chloramphenicol and clindamycin, which interact with the 23S rRNA peptidyltransferase loop. All three base substitutions at position 2032 produce an erythromycin-hypersensitive phenotype. The 2032 substitutions were compared with and combined with a 12-bp deletion mutation in domain II and point mutations at positions 2057 and 2058 in the peptidyltransferase region of domain V that also confer antibiotic resistance. Both the domain II deletion and the 2057A mutation relieve the hypersensitive effect of the 2032A mutation, producing an erythromycin-resistant phenotype; in addition, the combination of the 2032A and 2057A mutations confers a higher level of chloramphenicol resistance than either mutation alone. 23S rRNAs containing mutations at position 2058 that confer clindamycin and erythromycin resistance become deleterious to cell growth when combined with the 2032A mutation and, additionally, confer hypersensitivity to erythromycin and sensitivity to clindamycin and chloramphenicol. Introduction of the domain II deletion into these double-mutation constructs gives rise to erythromycin resistance. The results are interpreted as indicating that position 2032 interacts with the peptidyltransferase loop and that there is a functional connection between domains II and V.     

Conserved loop sequence of helix 69 in Escherichia coli 23 S rRNA is involved in A-site tRNA binding and translational fidelity

Ribosomal (r) RNAs play a crucial role in the fundamental structure and function of the ribosome. Helix 69 (H69) (position 1906-1924), a highly conserved stem-loop in domain IV of the 23 S rRNA of bacterial 50 S subunits, is located on the surface for intersubunit association with the 30 S subunit by connecting with helix 44 of 16 S rRNA with the bridge B2a. H69 directly interacts with A/T-, A-, and P-site tRNAs during each translation step. To investigate the functional importance of the highly conserved loop sequence (1912-1918) of H69, we employed a genetic method that we named SSER (systematic selection of functional sequences by enforced replacement). This method allowed us to identify and select from the randomized loop sequences of H69 in Escherichia coli 23 S rRNA functional sequences that are absolutely required for ribosomal function. From a library consisting of 16,384 sequence variations, 13 functional variants were obtained. A1912 and U(Psi)1917 were selected as essential residues in all variants. An E. coli strain having 23 S rRNA with a U to A mutation at position 1915 showed a severe growth phenotype and low translational fidelity. The result could be explained by the fact that the A1915-ribosome variant has weak subunit association, weak A-site tRNA binding, and decreased translational activity. This study proposes that H69 plays an important role in the control of translational fidelity by modulating A-site tRNA binding during the decoding process.     

Protein-RNA sequence covariation in a ribosomal protein-rRNA complex

Comparative sequence analysis has successfully predicted secondary structure and tertiary interactions in ribosomal and other RNAs. Experiments presented here ask whether the scope of comparative sequence-based predictions can be extended to specific interactions between proteins and RNA, using as a system the well-characterized C-terminal RNA binding domain of ribosomal protein L11 (L11-C76) and its 58 nucleotide binding region in 23S rRNA. The surface of L11-C76 alpha-helix 3 is known to contact RNA; position 69 in this helix is conserved as serine in most organisms but varies to asparagine (all plastids) or glutamine (Mycoplasma). RNA sequence substitutions unique to these groups of organisms occur at base pairs 1062/1076 or 1058/1080, respectively. The possibility that rRNA base pair substitutions compensate for variants in L11 alpha-helix 3 has been tested by measuring binding affinities between sets of protein and RNA sequence variants. Stability of the RNA tertiary structure, as measured by UV melting experiments, was unexpectedly affected by a 1062/1076 base pair substitution; additional mutations were required to restore a stably folded structure to this RNA. The results show that the asparagine variant of L11-C76 residue 69 has been compensated by substitution of a 1062/1076 base pair, and plausibly suggest a direct contact between the amino acid and base pair. For some of the protein and RNA mutations studied, changes in binding affinity probably reflect longer-range adjustments of the protein-RNA contact surface.     

The kink-turn: a new RNA secondary structure motif

Analysis of the Haloarcula marismortui large ribosomal subunit has revealed a common RNA structure that we call the kink-turn, or K-turn. The six K-turns in H.marismortui 23S rRNA superimpose with an r.m.s.d. of 1.7 A. There are two K-turns in the structure of Thermus thermophilus 16S rRNA, and the structures of U4 snRNA and L30e mRNA fragments form K-turns. The structure has a kink in the phosphodiester backbone that causes a sharp turn in the RNA helix. Its asymmetric internal loop is flanked by C-G base pairs on one side and sheared G-A base pairs on the other, with an A-minor interaction between these two helical stems. A derived consensus secondary structure for the K-turn includes 10 consensus nucleotides out of 15, and predicts its presence in the 5'-UTR of L10 mRNA, helix 78 in Escherichia coli 23S rRNA and human RNase MRP. Five K-turns in 23S rRNA interact with nine proteins. While the observed K-turns interact with proteins of unrelated structures in different ways, they interact with L7Ae and two homologous proteins in the same way.     

Increased Bacterial Hemolytic Activity is Conferred by Expression of TlyA Methyltransferase but not by its 2′-O-methylation of the Ribosome

Bacterial 2′-O-methyltransferase TlyA methylates either both nucleotide C1409 of 16S rRNA and C1920 of 23S rRNA or only the C1920. Both ribosomal methylations increase bacterial susceptibility to ribosome-targeting antibiotics capreomycin and viomycin. However, TlyA has been suggested to also function as a hemolysin. Here, heterologous expression of TlyA from six diverse bacteria (including Mycobacterium tuberculosis and M. smegmatis) was found to increase hemolytic ability in the Escherichia coli host. Characterizing E. coli strains expressing mycobacterial TlyA with mutated rRNA recognition domain and impaired rRNA methylations showed that the abolished C1409 methylation altogether with significantly reduced C1920 methylation did not affect E. coli hemolytic activity. Thus, the increased bacterial hemolytic function is not likely a consequence of TlyA-mediated methylations of the ribosome. Purified water-soluble TlyA showed a weak concentration-dependent hemolysis in vitro. Therefore, the TlyA isoform alone is not a potent hemolysin. The results suggested that the bacterial hemolytic function might relate to the over-expression of TlyA and its interaction to other non-ribosomal target that is associated with the hemolytic ability.     

The structure of helix 89 of 23S rRNA is important for peptidyl transferase function of Escherichia coli ribosome

Helix 89 of the 23S rRNA connects ribosomal peptidyltransferase center and elongation factor binding site. Secondary structure of helix 89 determined by X-ray structural analysis involves less base pairs then could be drawn for the helix of the same primary structure. It can be that alternative secondary structure might be realized at some stage of translation. Here by means of site-directed mutagenesis we stabilized either the "X-ray" structure or the structure with largest number of paired nucleotides. Mutation UU2492-3C which aimed to provide maximal pairing of the helix 89 of the 23S rRNA was lethal. Mutant ribosomes were unable to catalyze peptide transfer independently either with aminoacyl-tRNA or puromycin.     

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 regions of the Escherichia coli 16S rRNA. Using a genetic complementation approach, we selected mutations in 16S rRNA that compensate for a 900 tetraloop mutation, A900G, which severely impairs subunit association and translational fidelity. Mutations were randomly introduced in 16S rRNA, using either a mutagenic XL1-Red E. coli strain or an error-prone PCR strategy. Gain-offunction mutations were selected in vivo with a specialized ribosome system. Two mutations, the deletion of U12 and the U12C substitution, were thus independently selected in helix 1 of 16S rRNA. This helix is located in the vicinity of helix 27, but does not directly contact the 900 tetraloop in the crystal structures of the ribosome. Both mutations correct the subunit association and translational fidelity defects caused by the A900G mutation, revealing an unanticipated functional interaction between these two regions of 16S rRNA.