RNA secondary structure models

A completely different class of landscape models has developed from studies of RNA secondary structure folding (recent review in Ref. 66, software available in Ref. 102). These studies are reviewed by Schuster elsewhere in this collection, so I will only summarize certain relevant results here. 

The NK, p-spin and other models described above all assign fitnesses directly to sequences. In contrast, the secondary structure landscapes are best thought of in two parts  

---

Most of the studies of the ability of neutral evolution to discover new phenotypes have been carried out on RNA secondary structure models. Here, the neutral network is defined as a connected region of sequence... 

The knowledge of the primary structure was the basis for the construction of models of the secondary structure of the RNA molecules. Different approaches have been used in several laboratories to get experimental support for developing secondary structure models for example, chemic modification of the RNA, treatment with single- or double-strand-specihc nucleases, intramolecular RNA cross-linking, isolation and sequence analysis of double-stranded RNA, and, last but not least, comparison of ribosomal RNA sequences from different organisms (reviewed by Brimacombe et al., 1983). 

Figure 29-2 (A) Secondary structure model for the 1542-residue E. coli 16S rRNA based on comparative sequence analysis.733 Dots indicate G U or A G pairs dashes indicate G C or A U pairs. Strongly implied tertiary interactions are shown by solid green lines. Helix numbering according to Brimacombe. Courtesy of Robin Gutell. (B) Simplified schematic drawing of type often used. (C) Positions of the A, P, and E sites on the 30S ribosomal subunit from Carter et al7° (D) Stereoscopic view of the three-dimensional fold of the 16S RNA from Thermus thermophilus as revealed by X-ray structural analysis at 0.3 nm resolution. Features labeled are the head (H), beak (Be), neck (N), platform (P), shoulder (Sh), spur (Sp), and body (Bo). (E-H) Selected parts of the 16S RNA. In (E) and (F) the helices are numbered as in (A). (F) and (H) are stereoscopic views. The decoding site...

Figure 29-17 Partial sequence and secondary structure model of RNA of bacteriophage MS2. The initiation and termination codons for each of the three genes (A protein, coat protein, and replicase) are enclosed in boxes as is the second stop signal that is in-frame for the A protein gene but out-of-frame for the coat protein gene. The entire coat protein gene is shown but less them one-third of the entire sequence is given. From W. Fiers and associates.499-501...

Recall that the secondary-structure model for RNA is a model - and a crude one at that. It neglects pseudo knots and other tertiary interactions, does not take deviations from the additive nearest neighbor energy model into account, and is based on thermodynamic parameters extracted from melting experiments by means of multidimensional fitting procedures. Thus, you cannot expect perfect predictions for each individual sequence. Rather, the accuracy is on the order of 50% of the base pairs for the minimum free energy structure. 

Figure 4.2 The hammerhead and hairpin ribozymes. Secondary structures for both the hammerhead and hairpin ribozymes are depicted. N=any nucleotide, R=Purine and Y=Pyrimidine. A diagram of the tertiary structure of the hammerhead ribozyme is depicted above the secondary structure model. The corresponding stems I, II and III in both structures are shown. In the hammerhead ribozyme H=A, C or U at the cleavage site. In the hairpin ribozymes HI, H2, etc. refer to the helical regions of the RNA structure.

Search on RNA secondary structure landscapes is distinctly different from search on the spin glass-like models. The difference is a result of the neutral networks that percolate the space. Note that, in practice, the sequences on neutral networks need not have exactly the same fitness, but fitnesses whose differences are below a threshold determined by the mutation rate and noise in the system. As with search on spin glass landscapes, this topic is quite extensive and is reviewed in several papers [39,67,69,113] as well as in Schuster s contribution to this collection, so I will only touch on a few key points. 

The first limitation is that the landscape models are very abstract. Their results apply to molecular search in a general way, but are difficult to relate to laboratory concerns. Ideally, future work will combine the mathematical rigor of landscape-based search with the chemical and experimental details of the laboratory technique-based models. Some work along these lines has started with calculating mutation rates for SELEX schemes based on RNA secondary structure landscape models [114],... 

TrpR, which is a DNA binding repressor protein, regulates transcription initiation of the E. coli trpEDCBA operon. Under tryptophan limiting conditions, TrpR represses transcription initiation, whereas repression is relieved in the presence of excess tryptophan. Once transcription initiates the elongating transcription complex is subject to control by transcription attenuation (reviewed in References 5 and 6). The leader transcript can form three RNA secondary structures that are referred to as the pause hairpin, the antiterminator structure, and an intrinsic terminator hairpin. Because the antiterminator shares nucleotides in common with the terminator, their formation is mutually exclusive. The pause hairpin has two additional roles in this transcription attenuation mechanism it serves as an anti-antiterminator stmc-ture that prevents antiterminator formation, and it codes for a leader peptide. A model of the E. coli trp operon transcription attenuation mechanism is presented in Fig. 2a. 

Ruschak AM, Mathews DH, Bibillo A, Spinelli SL, Childs JL, Eickbush TH, Turner DH. Secondary structure models of the 3 untranslated regions of diverse R2 RNAs. RNA 2004 10(6) 978-987. 

Fig. 4.7. Illustration of an RNA footprint experiment, (a) Autoradiogram showing the altered chemical and ribonuclease reactivities in the presence (+) and in the absence (-) of a binding protein. The extension is from an end-labelled primer, (b) Reactivites which are altered in the presence of the protein is indicated on a secondary structure model. Protein induced protection of RNase T1 and T2 are indicated by arrows outside the backbone, while arrows penetrating the backbone indicate sites protected against CVE. Bases protected against DMS (circles), ke-thoxal (stars) and CMCT (boxed residues) are indicated. The small vertical arrows indicate enhanced base reactivities.

Johnson and Gray have applied their method of analysis to the secondary structure of Escherichia coli 5 S RNA, an RNA for which several secondary structural models have been proposed, based on extensive sequence data. The results were in good agreement with two of the proposed models but showed substantial differences with two other models. Thus, this method of secondary structure analysis for RNA can provide a test for proposed models based on sequence analysis. 

Clary DO, Wolstenholme DR (1987) Drosophila mitochondrial DNA conserved sequence in the A+T rich region and supporting evidence for a secondary structure model of the small ribosomal RNA. J Mol Evol 25 116-125... 

---