The central dogma of molecular biology suggests that DNA contains information for encoding all of our proteins and that three different types of RNA passively convert this code into polypeptides. In particular, the RNA messenger (mRNA) transfers the protein plan from the DNA of the cell to its ribosomes, which are the “machines” that control protein synthesis. Then, RNA (tRNA) transfers the corresponding amino acids to the ribosome for inclusion in a new protein. Meanwhile, the ribosomes themselves consist mainly of molecules of ribosomal RNA (rRNA).
However, over the half century that has passed since the DNA structure was first developed, scientists have learned that RNA plays a much larger role than simply participating in protein synthesis. For example, it was found that many types of RNA are catalytic, that is, they carry out biochemical reactions in the same way as enzymes. In addition, it was found that many other types of RNA play complex regulatory roles in cells.
Thus, RNA molecules play numerous roles both in normal cellular processes and in disease states. Typically, those RNA molecules that do not take the form of mRNA are called non-coding, since they do not encode proteins. The participation of non-coding mRNAs is in many regulatory processes. Their prevalence and variety of functions led to the hypothesis that the “RNA world” could precede the evolution of DNA and RNA functions in the cell, and participation in protein biosynthesis.
Non-coding RNA in eukaryotes
In eukaryotes, non-coding RNA can be of several varieties. Most noticeably, they carry RNA (tRNA) and ribosomal RNA (rRNA). As mentioned earlier, both tRNA and rRNA play an important role in the translation of mRNA into proteins. For example, Francis Crick suggested the existence of adapter RNA molecules that could bind to the mRNA nucleotide code, thereby facilitating the transfer of amino acids into growing polypeptide chains.
The work of Hoagland et al. (1958) did confirm that a specific fraction of cellular RNA was covalently linked to amino acids. Later, the fact that rRNA turned out to be a structural component of ribosomes suggested that, like tRNA, rRNA also does not encode.
In addition to rRNA and tRNA, a number of other non-coding RNAs exist in eukaryotic cells. These molecules help in many of the important energy storage functions of RNA in the cell that are still being listed and defined. These RNAs are often referred to as small regulatory RNAs (sRNAs), and in eukaryotes they have been further classified into a number of subcategories. Together, regulatory RNAs exert their effects through a combination of complementary base pairing, complexation with proteins, and their own enzymatic activity.
Small nuclear RNA
One important subcategory of small regulatory RNAs is composed of molecules known as small nuclear RNAs (snRNAs). These molecules play an important role in the regulation of genes by RNA splicing. SnRNAs are found in the nucleus and are usually closely associated with proteins in complexes called snRNPs (small nuclear ribonucleoproteins, sometimes referred to as “snurps”). The most common of these molecules are particles U1, U2, U5 and U4 / U6, which are involved in splicing of pre-mRNA with the formation of mature mRNA.
MicroRNA
Another topic of great interest to researchers is microRNAs (microRNAs), which are small regulatory RNAs with a length of approximately 22 to 26 nucleotides. The existence of miRNAs and their contractile RNA functions in the cell in gene regulation was initially detected in the C. elegans nematode (Lee et al., 1993; Wightman et al., 1993). Since their discovery of miRNAs, they have been identified in many other species, including flies, mice, and humans. To date, several hundred miRNAs have been identified. There may be many more (He & Hannon, 2004).
MicroRNAs have been shown to inhibit gene expression by repression of translation. For example, miRNAs encoded by C. elegans, lin-4 and let-7 bind to the 3'-untranslated region of their target mRNAs, preventing the formation of functional proteins at certain stages of larval development. So far, most of the miRNAs studied seem to control gene expression by binding to target mRNAs by imperfect base pairing and subsequent translation inhibition, although some exceptions have been noted.
Additional studies show that miRNAs also play an important role in cancer and other diseases. For example, the species miR-155 is enriched in B cells derived from Burkitt’s lymphoma, and its sequence also correlates with a known chromosomal translocation (DNA exchange between chromosomes).
Small interfering RNA
Small interfering RNAs (siRNAs) are another class of RNA. Although these molecules are only 21 to 25 base pairs long, they also work to suppress gene expression. In particular, a single strand of a double-stranded siRNA molecule can be incorporated into a complex called RISC. This RNA-containing complex can then inhibit the transcription of the mRNA molecule, which has a sequence complementary to its RNA component.
MiRNAs were first identified by their participation in RNA interference (RNAi). They could develop as a protective mechanism against double-stranded RNA viruses. SiRNAs are derived from longer transcripts in a process similar to that by which miRNAs occur and both types of RNA processing involve the same enzyme, Dicer. These two classes seem to differ in their repression mechanisms, but exceptions have been found in which siRNAs exhibit more typical miRNAs behavior and vice versa (He & Hannon, 2004).
Small Nucleolar RNA
Inside the eukaryotic nucleus, the nucleolus is a structure in which rRNA processing and ribosomal assembly occur. Molecules called small nucleolar RNAs (snoRNAs) were isolated from nucleolar extracts due to their abundance in this structure. These molecules function to process rRNA molecules, which often leads to methylation and pseudo-uridylation of specific nucleosides. Modifications are mediated by one of two classes of snoRNAs: the C / D box or the H / ACA box family, which usually involves the addition of methyl groups or isomerization of uradine in immature rRNA molecules, respectively.
Non-coding RNA in prokaryotes
However, eukaryotes did not drive the market into non-coding RNAs with specific regulatory energy functions of RNA in the cell. Bacteria also have a class of small regulatory RNAs. Bacterial rRNAs are involved in processes ranging from virulence to the transition from growth to the stationary phase, which occurs when a bacterium encounters a situation such as nutrient deprivation.
One example of bacterial rRNA is 6S RNA found in Escherichia coli. This molecule has been well characterized; its initial sequencing took place in 1980. 6S RNA is conserved in many types of bacteria, which indicates its important role in the regulation of genes.
RNA has been shown to affect the activity of RNA polymerase (RNAP), the molecule that transcribes the RNA messenger from DNA. 6S RNA inhibits this activity by binding to the polymerase subunit, which stimulates transcription during growth. Due to this mechanism, 6S RNA inhibits the expression of genes that stimulate active growth and helps cells enter the stationary phase (Jabri, 2005).
Riboswitches
The regulation of genes - in both prokaryotes and eukaryotes - is affected by regulatory RNA elements called riboswitches (or RNA switches). Riboswitches are RNA sensors that detect and respond to environmental or metabolic signals and, accordingly, affect gene expression.
A simple example of this group is the RNA temperature sensor found in the virulence genes of the bacterial pathogen Listeria monocytogenes. When this bacterium enters the host, the elevated temperature inside the host body melts the secondary structure of the segment in the 5'-untranslated region of the mRNA produced by the bacterial prfA gene. As a result of this, changes in the secondary structure occur.
It has been shown that additional riboswitches respond to heat and cold shocks in various organisms, and also regulate the synthesis of metabolites, such as sugars and amino acids. Although riboswitches are apparently more common in prokaryotes, many of them have also been found in eukaryotic cells.