RRNA structure

FIGURE 1 The 50S subunit of a bacterial ribosome (PDB ID 1 NKW). The protein backbones are shown as blue wormlike structures the rRNA components are transparent. The unstructured extensions of many of the ribosomal proteins snake into the rRNA structures, helping to stabilize them. 

Fig. 4.9. Diagrammatic representations of the secondary structures of the nSSU (left) and mtSSU (right) rRNAs. Universal helices are shown in solid black. Helices present in eukaryotic expansion segments of neodermatans are not shaded. Expansion segments are numbered as V1 to V9, following De Rijk et al. (1992). The equivalent numbering scheme used by Gerbi (1996) is indicated in parentheses. Note that the V7 region adjacent to helix 43 might have a different, as yet unknown, structure in cestodes. The mtSSU rRNA structure is based on that for Fasciola hepatica (Le ef al., 2001). Diagram modified from one supplied by Dr Jan Wuyts.

It is likely that protein binding and other macromolecular interactions also play a role in stabilizing the rRNA structures. A recent analysis12 reveals that the binding of specific ribosomal protein to rRNA in vitro results in changes within the rRNA modification patterns. Because the experiments detailed herein examine a population of rRNA within the cell, and thus may be analyzing a variety of RNA conformations, it is remarkable that very consistent results are observed. However, the consequence of polysome assembly and translation on the structure of the rRNA and how these structures might be distinct are not addressed in this analysis. In vitro DMS modification of soybean RNA has revealed some differences in base reactivity relative to that observed on RNA modified in vivo as described herein.36 ... 

These findings are interpreted to indicate that erythromycin resistance mutation in domain II caused an increase in the peptide and disrupted an indirectly functional interaction between domains II and V, because such a mutation could affect alteration of the stability of a secondary rRNA structure (hairpin sequence structure) in domain II. In addition, the Shine-Dalgamo (SD) sequence of the rRNA-encoded E-peptide ORE is sequestered in the hairpin structure. Thereby, SD and E-peptide codon are not accessible to ribosomes of wild-type E. coli. The conformational change of the hairpin structure by erythromycin resistance mutation can be recognized by ribosomes for the initiation of translation of E-peptide. Thus, the increase of the peptide is expected to show resistance to macrolide antibiotics such as erythromycin, oleandomycin, and spiramycin but not clindamycin and chloramphenicol without preventing their binding to the target. 

The NAST [16, 34] model represents each nucleotide by one pseudoatom at the C3 atom of the ribose group. NAST utilizes MD simulations and a force field parameterized from solved rRNA structures. NAST relies upon information from an accurate secondary structure and can also include experimental constraints. These constraints are modeled by a harmonic energy term. The bonded energy terms of distance, angle, and dihedral are further modeled by a harmonic potential, parameterized according to a Boltzmann inversion. Non-bonded interactions are modeled by a Lennard-Jones potential with a hard sphere radii of 5 A. Due to the low-resolution representation of one pseudoatom per nt, the conversion from the CG model to the all-atom model is complex and may produce steric overlaps. In order to overcome this difficulty, Jonikas et al. developed a program C2A [35] which is able to insert and minimize the all atom structure. 

To our knowledge this is the first exarrple of an aminoglycosphingo-lipid in a procaryote. It may be significant that this lipid is found in green sulfur bacteria which are related to the bacteroides/ flavobacteria by the criterion of 16S rRNA structure (7). These are the only two groups of bacteria known to contain sphingolipids. 

This work is aimed to clarify some aspects of the role played by Mg " ions in the E. coli ribosomes, i.e. to which extent the rRNA structure, both inside and outside the ribosome, is determined by the interaction with the Mg ions. 

More sequence conservation is observed for ribosomal proteins than for rRNA. Structural similarities are significant enough that cross-species RNA interactions were shown possible for proteins LI, LI 1, and SI5. At a minimum, then, the RNA-binding features of these proteins are conserved. 

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