Recognition of diverse RNAs by a single protein structural framework

Dissection and prediction of RNA-binding sites on proteins

RNA-binding proteins are involved in many important regulatory processes in cells and their study is essential for a complete understanding of living organisms. They show a large variability from both structural and functional points of view. However, several recent studies performed on protein-RNA crystal structures have revealed interesting common properties. RNA-binding sites usually constitute patches of positively charged or polar residues that make most of the specific and non-specific contacts with RNA. Negatively charged or aliphatic residues are less frequent at protein-RNA interfaces, although they can also be found either forming aliphatic and positive-negative pairs in protein RNA-binding sites or contacting RNA through their main chains. Aromatic residues found within these interfaces are usually involved in specific base recognition at RNA single-strand regions. This specific recognition, in combination with structural complementarity, represents the key source for specificity in protein-RNA association. From all this knowledge, a variety of computational methods for prediction of RNA-binding sites have been developed based either on protein sequence or on protein structure. Some reported methods are really successful in the identification of RNA-binding proteins or the prediction of RNA-binding sites. Given the growing interest in the field, all these studies and prediction methods will undoubtedly contribute to the identification and comprehension of protein-RNA interactions.

Crystal structure of the bacteriophage Qβ coat protein in complex with the RNA operator of the replicase gene

The coat proteins of single-stranded RNA bacteriophages specifically recognize and bind to a hairpin structure in their genome at the beginning of the replicase gene. The interaction serves to repress the synthesis of the replicase enzyme late in infection and contributes to the specific encapsidation of phage RNA. While this mechanism is conserved throughout the Leviviridae family, the coat protein and operator sequences from different phages show remarkable variation, serving as prime examples for the co-evolution of protein and RNA structure. To better understand the protein-RNA interactions in this virus family, we have determined the three-dimensional structure of the coat protein from bacteriophage Qβ bound to its cognate translational operator. The RNA binding mode of Qβ coat protein shares several features with that of the widely studied phage MS2, but only one nucleotide base in the hairpin loop makes sequence-specific contacts with the protein. Unlike in other RNA phages, the Qβ coat protein does not utilize an adenine-recognition pocket for binding a bulged adenine base in the hairpin stem but instead uses a stacking interaction with a tyrosine side chain to accommodate the base. The extended loop between β strands E and F of Qβ coat protein makes contacts with the lower part of the RNA stem, explaining the greater length dependence of the RNA helix for optimal binding to the protein. Consequently, the complex structure allows the proposal of a mechanism by which the Qβ coat protein recognizes and discriminates in favor of its cognate RNA.

An RNA aptamer with high affinity and high specificity for the 5S RNA binding zinc finger proteins TFIIIA and p43

The Xenopus zinc finger proteins TFIIIA and p43 bind to 5S RNA in immature oocytes to form 7S and 42S ribonucleoprotein storage particles. To probe the similarities and differences in the RNA binding domains of these two proteins, a library of random RNA molecules was enriched using TFIIIA as the bait protein. One of the abundant aptamers isolated, RNA22, bound to both TFIIIA and p43 derived zinc finger peptides with high affinity and specificity even though the predicted secondary structure of the RNA was unrelated to that of 5S RNA. The interactions of TFIIIA and p43 peptides with RNA22 were compared to their interactions with 5S RNA by characterizing the effects of assay conditions, mutations in RNA22, and mutations in the zinc finger proteins. The similarities and differences in the mechanisms by which these two zinc finger proteins interact with 5S RNA compared to RNA22 suggest they share a common platform for RNA binding with enough flexibility to form specific interactions with both RNAs.

Structural basis of RNA binding discrimination between bacteriophages Qbeta and MS2

Sequence-specific interactions between RNA stem-loops and coat protein (CP) subunits play vital roles in the life cycles of the RNA bacteriophages, e.g., by allowing translational repression of their replicase cistrons and tagging their own RNA genomes for encapsidation. The CPs of bacteriophages Qbeta and MS2 each discriminate in favor of their cognate translational operators, even in the presence of closely related operators from other phages in vivo. Discrete mutations within the MS2 CP have been shown to relax this discrimination in vitro. We have determined the structures of eight complexes between such mutants and both MS2 and Qbeta stem-loops with X-ray crystallography. In conjunction with previously determined in vivo repression data, the structures enable us to propose the molecular basis for the discrimination mechanism.

A cryptic lysis gene near the start of the Qbeta replicase gene in the +1 frame

The maturation/lysis (A2) protein encoded by the group B single-stranded RNA bacteriophage Qbeta mediates lysis of host Escherichia coli cells. We found a frameshift mutation in the replicase (beta-subunit) gene of Qbeta cDNA causes cell lysis. The mutant has a single base deletion 73 nucleotides (nt) 3' from the start of the replicase gene with consequent translation termination at a stop codon 129-131 nt further 3'. The 43-amino acid C-terminal part of the 67-amino acid product encoded by what in WT (wild-type) is the +1 frame, is rich in basic amino acids This 67-aa protein can mediate cell lysis whose characteristics indicate that the protein may cause lysis by a different mechanism and via a different target, than that caused by the A2 maturation/lysis protein. Synthesis of a counterpart of the newly discovered lysis product in wild-type phage infection would require a hypothetical ribosomal frameshifting event. The lysis gene of group A RNA phages is also short, 75 codons in MS2, and partially overlaps the first part of their equivalently located replicase gene, raising significant evolutionary implications for the present finding.

High-affinity binding site for a group II intron-encoded reverse transcriptase/maturase within a stem-loop structure in the intron RNA

Mobile group II introns encode proteins that have reverse transcriptase and maturase activities and bind specifically to the intron RNA to promote both RNA splicing and intron mobility. Previous studies with the Lactococcus lactis Ll.LtrB intron showed that the intron-encoded protein (LtrA) has a high-affinity binding site in intron subdomain DIVa, an idiosyncratic structure containing the translation initiation region of the LtrA open reading frame, and that this binding site consists of a small stem-loop emanating from a purine-rich internal loop. The binding of LtrA to DIVa is important for translational regulation, RNA splicing, and intron mobility. Here, we show by in vitro selection that part of the purine-rich internal loop can be closed by base pairing, enabling the LtrA binding site to be represented as an extended stem-loop structure with a bulged A (A556) required for tight binding of LtrA. The deletion or pairing of A556 has relatively little effect on maturase-promoted RNA splicing, but significantly inhibits intron mobility. The wild-type DIVa structure has a second bulged A (A553), which is selected against in tightly binding variants. As expected from the selection, the deletion or pairing of A553 results in tighter binding of LtrA, but surprisingly, also inhibits intron mobility. These findings suggest that the binding of LtrA to DIVa is delicately balanced, so that either too weak or too tight binding can be deleterious. The nature of the maturase/DIVa interaction and its role in translational regulation are reminiscent of the coat protein/RNA hairpin interactions of single-stranded RNA phages.

RNA recognition site of PP7 coat protein

The coat proteins of different single-strand RNA phages use a common protein tertiary structural framework to recognize different RNA hairpins and thus offer a natural model for understanding the molecular basis of RNA-binding specificity. Here we describe the RNA structural requirements for binding to the coat protein of bacteriophage PP7, an RNA phage of Pseudomonas. Its recognition specificity differs substantially from those of the coat proteins of its previously characterized relatives such as the coliphages MS2 and Qbeta. Using designed variants of the wild-type RNA, and selection of binding-competent sequences from random RNA sequence libraries (i.e. SELEX) we find that tight binding to PP7 coat protein is favored by the existence of an 8 bp hairpin with a bulged purine on its 5' side separated by 4 bp from a 6 nt loop having the sequence Pu-U-A-G/U-G-Pu. However, another structural class possessing only some of these features is capable of binding almost as tightly.