The three most prominent roles of RNA are that of mRNA, tRNA and rRNA. Apart from these RNAs there is another class of RNAs referred as noncoding RNAs (ncRNAs) that perform a variety of functions such as in gene expression/regulation, protein synthesis, modification of macromolecules in particular RNA and cleavage of other RNA molecules. It has been observed that the RNA secondary structure plays a vital role in making these molecules perform their diverse functions. The following are some of the most common noncoding RNA types and certain prominent secondary structural changes of mRNAs which bring about the regulation of cellular phenomenon:
mRNA-secondary-structural changes and other regulatory elements – (Riboswitches, prokaryotic intrinsic terminators, certain Protein responsive elements such as Iron Response Elements etc).
- miRNA : involved in the regulation of the expression of mRNA.
- siRNA : small, bind to complementary RNA sequences targeting them for destruction.
- snRNA : involved with the processing of larger precursor RNA molecules.
- snoRNA : involved in making ribosomes and telomeres.
- XIST RNA : inactivates one of the two X chromosomes in females.
A riboswitch is a part of the sequence of an mRNA molecule where a small target molecule can bind and bring about a change in the gene’s activity, making the mRNA that contains a riboswitch to control its owns expression depending on the presence or absence of its target molecule. A typical riboswitch can be divided into two parts based on the molecule binding regions; an aptamer and an expression platform. The aptamer is the sequence where the protein binding takes place and this binding of the protein induces a conformational change in the aptamer region. Expression platform occurs downstream to the aptamer (upstream to the coding region) and the conformation change in the aptamer activates its function of regulating the expression. The expression platform shows more than one method of regulating the expression, which include:
1. Formation of transcription termination hairpins (intrinsic transcription terminator).
2. Sequestering ribosome binding site to block translation.
3. Splicing control (aptamer domain is flanked by consensus splice site sequences).
4. Self cleavage – riboswitch contains a ribozyme (enzyme made up of RNA) that cleaves itself in the presence of sufficient concentrations of its metabolite.
Most of the riboswitches discovered so far are in bacteria, where as in eukaryotes only a single riboswitch is discovered till date (TPP riboswitch). However, the RNAs that match the consensus sequence of TPP riboswitch have been observed in several plant and fungal species. The following are the known riboswitches:
1. B12-riboswitch (also called Cobalamin riboswitch) binds adenosylcobalamin and regulates the biosynthesis and transport of cobalamin and similar metabolites.
2. FMN riboswitch (also called RFN element) binds flavin mononucleotide and regulates its transport.
3. TPP riboswitch (also called THI- element) – binds thiamin pyrophosphate and regulates biosynthesis of thiamin and its transport.
4. Lysine riboswitch (also called L-box) binds lysine and regulates biosynthesis, catabolism and transport of lysine.
5. SAM riboswitch binds S-adenosyl methionine and regulates biosynthesis and transport of methionine. Three distinct SAM riboswitches (SAM-I, II and MK) are found that have no similarities in terms of sequence or structure.
6. Purine riboswitch binds purines and regulate metabolism and transport of purines. Different forms are observed; in G-box (can bind either guanine or adenine), the specificity depends on interactions with a single pyrimidine in the riboswitch at Y74 position. In guanine riboswitch this residue is always a cytosine (C74), where as in adenine riboswitch it is always a uracil (U74).
7. Glycine riboswitch binds glycine and regulates glycine metabolism genes.
8. glmS riboswitch it is a ribozyme that cleaves itself in the presence of sufficient concentrations of glucosamine 6 phosphate.
9. Mg+2 riboswitch regulates magnesium transport by sensing Mg+2 ions. This is the only known ion-sensing riboswitch.
Sequence analysis of all the above riboswitches has revealed conserved aptamer domains in different organisms for each riboswitch. Thus the presence of these consensus sequences in the aptamer domains and the expression platforms of the riboswitches play an important role in determining the secondary conformation and the specific functions of these riboswitches.