Proteins interaction with RNA

In contrast to its deoxy template, RNA exhibits a wider variety of interactions with proteins, because the three RNA species have a wider range of functions, involving various stages of protein synthesis. Table 2 lists some of the proteins we wish to consider. Proteins interacting with RNA include those that trim RNA before ribosome formation. Since in eukaryotes there are approximately 70 ribosomal structural proteins, it is expected, and realized that these structural proteins undergo multiple interactions with the species of RNA. For example, evidence suggests that the interaction of 5 S RNA with the L5, L18, and L25 proteins situated in the large ribosomal subunit is involved in translocation of the peptidyl tRNA. 

Fig. 2. Modulation of the RseA activity a working model. In the absence of non-native proteins in the periplasm, is bound to the RseA anti-sigma factor this binding is stabilized by RseB, a co-anti-sigma factor, in the periplasm. Upon accumulation of non-native proteins within the periplasm, RseB is released followed by dissociation of which interacts with RNA polymerase core enzyme to initiate transcription of the heat shock genes of the sigma-E regulon...

Detailed analysis of the lambda repressor led to the important concept that transcription regulatory proteins have several functional domains. For example, lambda repressor binds to DNA with high affinity. Repressor monomers form dimers, dimers interact with each other, and repressor interacts with RNA polymerase. The protein-DNA interface and the three protein-protein interfaces all involve separate and distinct domains of the repressor molecule. As will be noted below (see Figure 39—17), this is a characteristic shared by most (perhaps all) molecules that regulate transcription. 

The general types of protein-protein interactions that occur in cells include receptor-ligand, enzyme-substrate, multimeric complex formations, structural scaffolds, and chaperones. However, proteins interact with more targets than just other proteins. Protein interactions can include protein-protein or protein-peptide, protein-DNA/RNA or protein-nucleic acid, protein-glycan or protein-carbohydrate, protein-lipid or protein-membrane, and protein-small molecule or protein-ligand. It is likely that every molecule within a cell has some kind of specific interaction with a protein. 

Traviglia, S.L., Datwyler, S.A., and Meares, C.F. (1999) Mapping protein-protein interactions with a library of tethered cutting reagents The binding site of sigma (70) on Escherichia coli RNA polymerase. Biochemistry 38, 4259-4265. 

Regulation of RNA Polymerase II Activity Regulation of transcription at Pol II promoters is quite elaborate. It involves the interaction of a wide variety of other proteins with the preinitiation complex. Some of these regulatory proteins interact with transcription factors, others with Pol II itself. Many interact through TFIID, a complex of about 12 proteins, including TBP and certain... 

In addition to structural domains devoted to DNA binding and dimerization (or oligomerization), many regulatory proteins must interact with RNA polymerase, with unrelated regulatory proteins, or with both. At least three different types of additional domains for protein-protein interaction have been characterized (primarily in eukaryotes) glutamine-rich, proline-rich, and acidic domains, the names reflecting the amino acid residues that are especially abundant. 

FIGURE 28-16 CRP homodimer. (PDB ID 1RUN) Bound molecules of cAMP are shown in red. Note the bending of the DNA around the protein. The region that interacts with RNA polymerase is shaded yellow. 

Stutz, F., Bachi, A., Doerks, T., Braun, I.C., Seraphin, B., Wilm, M. et al. (2000) REF, an evolutionary conserved family of hnRNP-like proteins, interacts with TAP/Mex67p and participates in mRNA nuclear export. RNA, 6, 638-650. 

The bound factor then interacts with RNA polymerase III, which is then capable of initiation. During transcription, the multiple protein factors (called TFIIIs) remain bound to the transcribing gene. 

Transcription factors must recognize and bind to specific target DNA sequences located in promoters and enhancers. They must also activate transcription. The parts of the protein that are involved in these different functions usually lie in physically independent domains. There are many types of DNA-binding domains. Perhaps the best understood are the zinc lingers, in which a small group of conserved amino acids binds a zinc ion. The activation domains are less well understood. It is thought that they are involved in protein/protein interaction with other transcription factors and/or RNA polymerase. 

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