Ribosomal RNA


Ribosomal ribonucleic acid is a type of non-coding RNA which is the primary component of ribosomes, essential to all cells. rRNA is a ribozyme which carries out protein synthesis in ribosomes. Ribosomal RNA is transcribed from ribosomal DNA and then bound to ribosomal proteins to form small and large ribosome subunits. rRNA is the physical and mechanical factor of the ribosome that forces transfer RNA and messenger RNA to process and translate the latter into proteins. Ribosomal RNA is the predominant form of RNA found in most cells; it makes up about 80% of cellular RNA despite never being translated into proteins itself. Ribosomes are composed of approximately 60% rRNA and 40% ribosomal proteins, though this ratio differs between prokaryotes and eukaryotes.

Structure

Although the primary structure of rRNA sequences can vary across organisms, base-pairing within these sequences commonly forms stem-loop configurations. The length and position of these rRNA stem-loops allow them to create three-dimensional rRNA structures that are similar across species. Because of these configurations, rRNA can form tight and specific interactions with ribosomal proteins to form ribosomal subunits. These ribosomal proteins contain basic residues and aromatic residues allowing them to form chemical interactions with their associated RNA regions, such as stacking interactions. Ribosomal proteins can also cross-link to the sugar-phosphate backbone of rRNA with binding sites that consist of basic residues. All ribosomal proteins have been identified. These interactions along with the association of the small and large ribosomal subunits result in a functioning ribosome capable of synthesizing proteins.
Ribosomal RNA organizes into two types of major ribosomal subunit: the large subunit and the small subunit. One of each type come together to form a functioning ribosome. The subunits are at times referred to by their size-sedimentation measurements. In prokaryotes, the LSU and SSU are called the 50S and 30S subunits, respectively. In eukaryotes, they are a little larger; the LSU and SSU of eukaryotes are termed the 60S and 40S subunits, respectively.
In the ribosomes of prokaryotes such as bacteria, the SSU contains a single small rRNA molecule while the LSU contains one single small rRNA and a single large rRNA molecule. These are combined with ~50 ribosomal proteins to form ribosomal subunits. There are three types of rRNA found in prokaryotic ribosomes: 23S and 5S rRNA in the LSU and 16S rRNA in the SSU.
In the ribosomes of eukaryotes such as humans, the SSU contains a single small rRNA while the LSU contains two small rRNAs and one molecule of large rRNA. Eukaryotic rRNA has over 70 ribosomal proteins which interact to form larger and more polymorphic ribosomal units in comparison to prokaryotes. There are four types of rRNA in eukaryotes: 3 species in the LSU and 1 in the SSU. Yeast has been the traditional model for observation of eukaryotic rRNA behavior and processes, leading to a deficit in diversification of research. It has only been within the last decade that technical advances have allowed for preliminary investigation into ribosomal behavior in other eukaryotes. In yeast, the LSU contains the 5S, 5.8S and 28S rRNAs. The combined 5.8S and 28S are roughly equivalent in size and function to the prokaryotic 23S rRNA subtype, minus expansion segments that are localized to the surface of the ribosome which were thought to occur only in eukaryotes. However recently, the Asgard phyla, namely, Lokiarchaeota and Heimdallarchaeota, considered the closest archaeal relatives to Eukarya, were reported to possess two supersized ESs in their 23S rRNAs. Likewise, the 5S rRNA contains a 108‐nucleotide insertion in the ribosomes of the halophilic archaeon Halococcus morrhuae.
A eukaryotic SSU contains the 18S rRNA subunit, which also contains ESs. SSU ESs are generally smaller than LSU ESs.
SSU and LSU rRNA sequences are widely used for study of evolutionary relationships among organisms, since they are of ancient origin, are found in all known forms of life and are resistant to horizontal gene transfer. rRNA sequences are conserved over time due to their crucial role in the function of the ribosome. Phylogenic information derived from the 16s rRNA is currently used as the main method of delineation between similar prokaryotic species by calculating nucleotide similarity. The canonical tree of life is the lineage of the translation system.
LSU rRNA subtypes have been called ribozymes because ribosomal proteins cannot bind to the catalytic site of the ribosome in this area.
The SSU rRNA subtypes decode mRNA in its decoding center. Ribosomal proteins cannot enter the DC.
The structure of rRNA is able to drastically change to affect tRNA binding to the ribosome during translation of other mRNAs. In 16S rRNA, this is thought to occur when certain nucleotides in the rRNA appear to alternate base pairing between one nucleotide or another, forming a "switch" that alters the rRNA's conformation. This process is able to affect the structure of the LSU and SSU, suggesting that this conformational switch in the rRNA structure affects the entire ribosome in its ability to match a codon with its anticodon in tRNA selection as well as decode mRNA.

Assembly

Ribosomal RNA's integration and assembly into ribosomes begins with their folding, modification, processing and assembly with ribosomal proteins to form the two ribosomal subunits, the LSU and the SSU. In Prokaryotes, rRNA incorporation occurs in the cytoplasm due to the lack of membrane-bound organelles. In Eukaryotes, however, this process primarily takes place in the nucleolus and is initiated by the synthesis of pre-RNA. This requires the presence of all three RNA polymerases. In fact, the transcription of pre-RNA by RNA polymerase I accounts for about 60% of cell's total cellular RNA transcription. This is followed by the folding of the pre-RNA so that it can be assembled with ribosomal proteins. This folding is catalyzed by endo- and exonucleases, RNA helicases, GTPases and ATPases. The rRNA subsequently undergoes endo- and exonucleolytic processing to remove external and internal transcribed spacers. The pre-RNA then undergoes modifications such as methylation or pseudouridinylation before ribosome assembly factors and ribosomal proteins assemble with the pre-RNA to form pre-ribosomal particles. Upon going under more maturation steps and subsequent exit from the nucleolus into the cytoplasm, these particles combine to form the ribosomes. The basic and aromatic residues found within the primary structure of rRNA allow for favorable stacking interactions and attraction to ribosomal proteins, creating a cross-linking effect between the backbone of rRNA and other components of the ribosomal unit.

Function

Universally conserved secondary structural elements in rRNA among different species show that these sequences are some of the oldest discovered. They serve critical roles in forming the catalytic sites of translation of mRNA. During translation of mRNA, rRNA functions to bind both mRNA and tRNA to facilitate the process of translating mRNA's codon sequence into amino acids. rRNA initiates the catalysis of protein synthesis when tRNA is sandwiched between the SSU and LSU. In the SSU, the mRNA interacts with the anticodons of the tRNA. In the LSU, the amino acid acceptor stem of the tRNA interacts with the LSU rRNA. The ribosome catalyzes ester-amide exchange, transferring the C-terminus of a nascent peptide from a tRNA to the amine of an amino acid. These processes are able to occur due to sites within the ribosome in which these molecules can bind, formed by the rRNA stem-loops. A ribosome has three of these binding sites called the A, P and E sites:
A single mRNA can be translated simultaneously by multiple ribosomes. This is called a polysome.
In prokaryotes, much work has been done to further identify the importance of rRNA in translation of mRNA. For example, it has been found that the A site consists primarily of 16S rRNA. Apart from various protein elements that interact with tRNA at this site, it is hypothesized that if these proteins were removed without altering ribosomal structure, the site would continue to function normally. In the P site, through the observation of crystal structures it has been shown the 3' end of 16s rRNA can fold into the site as if a molecule of mRNA. This results in intermolecular interactions that stabilize the subunits. Similarly, like the A site, the P site primarily contains rRNA with few proteins. The peptidyl transferase center, for example, is formed by nucleotides from the 23S rRNA subunit. In fact, studies have shown that the peptidyl transferase center contains no proteins, and is entirely initiated by the presence of rRNA. Unlike the A and P sites, the E site contains more proteins. Because proteins are not essential for the functioning of the A and P sites, the E site molecular composition shows that it is perhaps evolved later. In primitive ribosomes, it is likely that tRNAs exited from the P site. Additionally, it has been shown that E-site tRNA bind with both the 16S and 23S rRNA subunits.

Subunits and associated ribosomal RNA

Both prokaryotic and eukaryotic ribosomes can be broken down into two subunits, one large and one small. The exemplary species used in the table below for their respective rRNAs are the bacterium Escherichia coli and human. Note that "nt" represents the length of the rRNA type in nucleotides and the "S" represents Svedberg units.
TypeSizeLarge subunit Small subunit
prokaryotic70S50S 30S
eukaryotic 80S60S 40S
eukaryotic 55S39S 16S 28S 12S

S units of the subunits cannot simply be added because they represent measures of sedimentation rate rather than of mass. The sedimentation rate of each subunit is affected by its shape, as well as by its mass. The nt units can be added as these represent the integer number of units in the linear rRNA polymers.
Gene clusters coding for rRNA are commonly called "ribosomal DNA" or rDNA.