The topography of ribosomal proteins on the surface of the 30S subunit of Escherichia coli

Sensitivity and correlation of hypervariable regions in 16S rRNA genes in phylogenetic analysis

Background

Prokaryotic 16S ribosomal RNA (rRNA) sequences are widely used in environmental microbiology and molecular evolution as reliable markers for the taxonomic classification and phylogenetic analysis of microbes. Restricted by current sequencing techniques, the massive sequencing of 16S rRNA gene amplicons encompassing the full length of genes is not yet feasible. Thus, the selection of the most efficient hypervariable regions for phylogenetic analysis and taxonomic classification is still debated. In the present study, several bioinformatics tools were integrated to build an in silico pipeline to evaluate the phylogenetic sensitivity of the hypervariable regions compared with the corresponding full-length sequences.

Results

The correlation of seven sub-regions was inferred from the geodesic distance, a parameter that is applied to quantitatively compare the topology of different phylogenetic trees constructed using the sequences from different sub-regions. The relationship between different sub-regions based on the geodesic distance indicated that V4-V6 were the most reliable regions for representing the full-length 16S rRNA sequences in the phylogenetic analysis of most bacterial phyla, while V2 and V8 were the least reliable regions.

Conclusions

Our results suggest that V4-V6 might be optimal sub-regions for the design of universal primers with superior phylogenetic resolution for bacterial phyla. A potential relationship between function and the evolution of 16S rRNA is also discussed.

Electronic supplementary material

The online version of this article (doi:10.1186/s12859-016-0992-y) contains supplementary material, which is available to authorized users.

The genesis of ribosome structure: how a protein generates RNA structure in real time

Ribosomal subunit assembly is initiated by the binding of several primary binding proteins. Results from chemical modification studies show that 16S ribosomal RNA undergoes striking structural rearrangements when protein S17 is bound. For the first time, we are able to distinguish and order these structural rearrangements by using time-dependent chemical probing. Initially, protein S17 binds to a portion of helix 11, inducing a kink-turn in that helix that bends helix 7 toward the S17-helix 11 complex in a hairpin-like manner, allowing helix 7 to bind to protein S17. This structural change is rapidly stabilized by interactions at the distal and proximal ends of both RNA helices. Identifying the dynamic nature of interactions between RNA and proteins is not only essential in unraveling ribosome assembly, but also has more general application to all protein-RNA interactions.

Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. III. Functional analysis of the 690 loop

An instant-evolution experiment was performed on the eight nucleotides comprising the loop region of the 690 hairpin in Escherichia coli 16 S ribosomal RNA. Positions 690 to 697 were randomly mutated and 101 unique functional mutants were isolated, sequenced and analyzed for function in vivo. Non-random nucleotide distributions were observed at each of the mutated positions except 693 and 694. Nucleotide identity significantly affected ribosome function at positions 690, 695, 696 and 697. Pyrimidines were absent at position 696 in the instant-evolution pool as were C at position 691 and G at position 697. A highly significant covariation was observed between nucleotides 690 and 697. No functional double mutants at positions 691 and 696 were obtained from the instant-evolution pool. In our NMR structure of the 690 loop, both the G690.U697 and G691.A696 form sheared hydrogen-bonded mismatches. To further examine the functional constraints between these paired nucleotides, one set of site-directed mutations was constructed at positions 690:697 and another set was constructed at positions 691:696. Functional analysis of the site-directed mutants is consistent with our instant-evolution findings and revealed constraints on the placement of specific functional groups observed in the NMR structure. Ten instant-evolution mutants were isolated that are more functional than the wild-type. Hyperactivity in these mutants correlates with a single mutation at position 693.

Structure and function of the conserved 690 hairpin in Escherichia coli 16 S ribosomal RNA. II. NMR solution structure

The solution structure of the conserved 690 hairpin from Escherichia coli 16 S rRNA was determined by NMR spectroscopy. The 690 loop is located at the surface of the 30 S subunit in the platform region and has been implicated in interactions with P-site bound tRNA, E-site mRNA, S11 binding, IF3 binding, and in RNA-RNA interactions with the 790 loop of 16 S rRNA and domain IV of 23 S rRNA. The structure reveals a novel sheared type G690.U697 base-pair with a single hydrogen bond from the G690 amino to U697-04. G691 and A696 also form a sheared pair and U692 forms a U-turn with an H-bond to the A695 non-bridging phosphate oxygen. The sheared pairs and U-turn result in the continuous single-stranded stacking of five residues from 6693 to U697 with their Watson-Crick functional groups exposed in the minor groove. The overall fold of the 690 hairpin is similar to the anticodon loop of tRNA. The structure provides an explanation for chemical protection patterns in the loop upon interaction with tRNA, the 50 S subunit, and S11. In vivo genetic studies demonstrate the functional importance of the motifs observed in the solution structure of the 690 hairpin.

Nucleotides in 16S rRNA protected by the association of 30S and 50S ribosomal subunits

We have studied the interaction of 16S rRNA in 30S subunits with 50S subunits using a series of chemical probes that monitor the accessibility of the RNA bases and backbone. The probes include 1-cyclohexyl-3-(2-morpholinoethyl) carbodiimide metho-p-toluene sulfonate (CMCT; to probe U at N-3 and G at N-1), diethylpyrocarbonate (DEPC; to probe A at N-7), dimethyl sulfate (DMS; to probe A at N-1, and C at N-3), kethoxal (to probe G at N-1 and N-2), hydroxyl radicals generated by free Fe(II)-EDTA (to probe the backbone ribose groups) and Pb(II). The sites of reaction were identified by primer extension of the probed RNA. Association of the subunits protects the bases of 11 nucleotides and the ribose groups of over 90 nucleotides of 16S rRNA. The nucleotides protected from the base-specific probes are often adjacent to one another and surrounded by sugar-phosphate backbone protections; thus, the results obtained with the different probes confirmed each other. Most of the protected nucleotides occur in five extended-stem-loop structures around positions 250, 700, 790, 900, and 1408-1495. These regions are located in the platform and bottom of the subunit in the general vicinity of inter-subunit bridges that are visible in reconstructed electron micrographs. Our results provide an extensive map of the nucleotides in 16S rRNA that are likely to be involved in subunit-subunit interactions.

Conformational variability of the N-terminal helix in the structure of ribosomal protein S15

BACKGROUND

Ribosomal protein S15 is a primary RNA-binding protein that binds to the central domain of 16S rRNA. S15 also regulates its own synthesis by binding to its own mRNA. The binding sites for S15 on both mRNA and rRNA have been narrowed down to less than a hundred nucleotides each, making the protein an attractive candidate for the study of protein-RNA interactions.

RESULTS

The crystal structure of S15 from Bacillus stearothermophilus has been solved to 2.1 A resolution. The structure consists of four alpha helices. Three of these helices form the core of the protein, while the N-terminal helix protrudes out from the body of the molecule to make contacts with a neighboring molecule in the crystal lattice. S15 contains a large conserved patch of basic residues which could provide a site for binding 16S rRNA.

CONCLUSIONS

The conformation of the N-terminal alpha helix is quite different from that reported in a recent NMR structure of S15 from Thermus thermophilus. The intermolecular contacts that this alpha helix makes with a neighboring molecule in the crystal, however, closely resemble the intramolecular contacts that occur in the NMR structure. This conformational variability of the N-terminal helix has implications for the range of possible S15-RNA interactions. A large, conserved basic patch at one end of S15 and a cluster of conserved but exposed aromatic residues at the other end provide two possible RNA-binding sites on S15.

The structure of ribosomal protein S7 at 1.9 A resolution reveals a beta-hairpin motif that binds double-stranded nucleic acids

BACKGROUND

Ribosomal protein S7, a crucial RNA-binding component of the ribosome, is one of two proteins that initiates assembly of the 30S ribosomal subunit. It is required for proper folding of a large 3' domain of 16S ribosomal RNA. S7 regulates its own synthesis by binding to its own mRNA. This ability of S7 to bind both messenger and ribosomal RNAs makes determination of its mode of RNA recognition particularly interesting.

RESULTS

The crystal structure of S7 from Thermus thermophilus was determined by a two-wavelength anomalous diffraction experiment using the LIII edge of mercury. The S7 structure consists of a bundle of six helices and an extended beta hairpin between helices 3 and 4, with two or more RNA-binding sites on its surface. The hairpin, along with portions of helices 1, 4 and 6, forms a large, positively charged, concave surface that has the appropriate curvature and dimensions to bind double-stranded RNA. A second putative RNA-binding site comprises parts of loop 2 and the helix 4-loop 5 turn.

CONCLUSIONS

Structural similarity between S7 and the IHF/HU family of proteins strongly suggests that the beta hairpin of S7 binds to a groove of double-stranded RNA. The beta hairpin of S7 is also similar to those from other nucleic acid binding proteins, such as ribosomal protein L14 and BIV Tat, suggesting that it belongs to an extended family of such motifs, all of which bind to a groove of double-stranded nucleic acid. The residues in S7 loop 2 that belong to the second putative RNA-binding site may have a role analogous to the N-terminal residues of IHF/HU which grip an unbent portion of double helix.

Identification of two antibody-interaction sites on the surface of Panulirus interruptus hemocyanin

Negatively stained complexes of Panulirus interruptus (spiny lobster) hemocyanin with two different monoclonal antibodies, named E and J, were studied by electron microscopy and image processing. The attachment site of the antibodies to the hexameric hemocyanin molecule was deduced from two perpendicular views of hemocyanin/antibody complexes, in which either the threefold axis or one of the twofold axes was oriented perpendicular to the supporting film. Images of complexes in these orientations were searched with reference images simulated from the known X-ray structure of P. interruptus hemocyanin. The two sites were further characterized by combining our results from electron microscopy with structural data obtained by X-ray diffraction and other methods. These two antibodies recognize different non-overlapping epitopes. The epitope for clone E is located on domain 3 at the surface of the beta barrel and consists of certain loops, which form connections between beta-strand structures. The epitope for clone J is situated on domain 1 at the surface of an alpha-helical region and consists mainly of certain alpha-helices connecting loops. The orientation of the hemocyanin hexamers in the two complexes is very different, as is demonstrated most clearly when they form chains. Clone E forms complexes with the threefold axes perpendicular to the chain direction, while for clone J the threefold axes seem to be parallel to the main direction. The angle between the Fab part of an IgG molecule and the threefold axis of the hexamer is 60 +/- 5 degrees for clone E and 35 +/- 7 degrees for clone J. This observation is clearly related to the difference in orientation of the hexamers for the two complexes.

Structural dynamics of translating ribosomes: 16S ribosomal RNA bases that may move twice during translocation

Recent footprinting, sedimentation and neutron-scattering results obtained in vivo or on pre-translocation and post-translocation ribosomal complexes are integrated with cross-linking and immunoelectron microscopy information. It is proposed that the 30S subunit pulses during translocation and that its pre- and post-translocation structures are not necessarily identical. Accordingly, translocation is characterized by three consecutive conformational states of the 30S and 50S subunits. State 1 (the pre-translocation state) lasts until the elongation factor EF-G.GTP complex binds to the ribosome or adopts the GTPase conformation. State 2 (the translocation state, or the peak or plateau of the pulse) follows and lasts until EF-G adopts a subsequent conformation or is released from the ribosome. State 3 (the post-translocation state) ensues and lasts until A (aminoacyl) site binding of aminoacyl-tRNA. In state 2, 16S RNA hairpins 26 and 33-33A, located in the platform and the head of the 30S subunit, respectively, become kinked or twisted, and residue A1503, near the decoding site, becomes exposed. A platform twist is associated with P (peptide) to E (exit) site tRNA movements and a head twist with pivoting of the peptidyl-tRNA elbow from the A to the P site, around a (retractable?) S19 domain. These twists result in an unlocking of the platform and the head from the 50S subunit. Exposure of A1503 is tentatively associated with movements of mRNA or tRNA anticodon stem-loops. These twisted or otherwise-exposed residues readopt their previous setting upon completion of translocation, i.e. states 1 and 3 of 16S RNA differ more from state 2 than from each other.(ABSTRACT TRUNCATED AT 250 WORDS)

Ribosomal proteins S7 and L1 are located close to the decoding site of E. coli ribosome--affinity labeling studies with modified tRNAs carrying photoreactive probes attached adjacent to the 3'-end of the anticodon

Two photoreactive azidonitrophenyl probes have been attached to Yeast methionine elongator tRNA by chemical modification of the N6-(threoninocarbonyl)adenosine located next to the 3'-end of the anticodon. The maximum distance between the purine ring and the azido group estimated for the two probes is 16-17 and 23-24A, respectively. Binding and cross-linking of the uncharged, modified tRNAs to E. coli ribosomes have been studied with and without poly(A,U,G) as a message, under conditions directing uncharged tRNAs preferentially to the P-site. The modified tRNAs retain their binding activity and upon irradiation bind covalently to the ribosome with very high yields. Protein S7 is the major cross-linking target for both modified tRNAs, in the presence or absence of poly(A,U,G). Protein L1 and to a lesser extent proteins L33 and L27 have been found to be cross-linked with the short probe. Cross-linking to 168 rRNA reaches significant levels only in the absence of the message.

Immunoblotting analysis of protein-protein crosslinks within the 50S ribosomal subunit of Escherichia coli. A study using dimethylsuberimidate as crosslinking reagent

50S ribosomal subunits of Escherichia coli have been crosslinked with the bifunctional imidoester dimethyl-suberimidate and the protein-protein crosslinks have been analyzed by immunoblotting, using antisera specific for the individual ribosomal proteins of the large ribosomal subunit. Crosslinked protein pairs which occurred in yields higher than 5% have been unambiguously identified. Thus 13 crosslinks have been identified, namely L1-L33, L5-L7/12, L6-L19, L7/12-L10, L7/12-L11, L9-L28, L10-L11, L13-L20, L16-L27, L17-L32, L18-L22, L19-L25 and L27-L33. These data, together with the results which we will be presenting elsewhere, contribute considerably to our knowledge of the protein topography of the 50S ribosomal proteins as determined by immunoelectron microscopy. We can now propose the approximate locations of ten proteins that have not previously been localized.

Localization of proteins L4, L5, L20 and L25 on the ribosomal surface by immuno-electron microscopy

Ribosomal proteins L4, L5, L20 and L25 have been localized on the surface of the 50S ribosomal subunit of Escherichia coli by immuno-electron microscopy. The two 5S RNA binding proteins L5 and L25 were both located at the central protuberance extending towards its base, at the interface side of the 50S particle. L5 was localized on the side of the central protuberance that faces the L1 protuberance, whereas L25 was localized on the side that faces the L7/L12 stalk. Proteins L4 and L20 were both located at the back of the 50S subunit; L4 was located in the vicinity of proteins L23 and L29, and protein L20 was localized between proteins L17 and L10 and is thus located below the origin of the L7/L12 stalk.

Amino acid sequences of ribosomal proteins S11 from Bacillus stearothermophilus and S19 from Halobacterium marismortui. Comparison of the ribosomal protein S11 family

The complete amino acid sequences of ribosomal proteins S11 from the Gram-positive eubacterium Bacillus stearothermophilus and of S19 from the archaebacterium Halobacterium marismortui have been determined. A search for homologous sequences of these proteins revealed that they belong to the ribosomal protein S11 family. Homologous proteins have previously been sequenced from Escherichia coli as well as from chloroplast, yeast and mammalian ribosomes. A pairwise comparison of the amino acid sequences showed that Bacillus protein S11 shares 68% identical residues with S11 from Escherichia coli and a slightly lower homology (52%) with the homologous chloroplast protein. The halophilic protein S19 is more related to the eukaryotic (45-49%) than to the eubacterial counterparts (35%).