23S ribosomal RNA (rRNA) is a fundamental molecule found within bacterial cells. This ribonucleic acid plays a significant part in the cellular machinery responsible for creating proteins. It functions as a foundational component of the ribosome, the cell’s factory for assembling proteins.
The Ribosomal Context of 23S rRNA
23S rRNA is an integral part of the prokaryotic ribosome, often referred to as the 70S ribosome. This bacterial ribosome is composed of two main subunits: a smaller 30S subunit and a larger 50S subunit. The 23S rRNA molecule is a major structural and functional component located within this larger 50S subunit. It constitutes a substantial portion of the subunit’s mass and intricate three-dimensional structure.
The “S” in “23S,” “30S,” “50S,” and “70S” refers to the Svedberg unit, a measure of a particle’s sedimentation rate. This unit reflects a combination of a particle’s mass, density, and shape. The Svedberg values of the individual subunits do not simply add up to the value of the complete ribosome because the compaction and interaction of the subunits influence their overall sedimentation rate.
Catalytic Function in Protein Synthesis
Beyond its structural role, 23S rRNA is an active enzymatic molecule, a ribozyme. Its primary biological function involves catalyzing the formation of peptide bonds between individual amino acids, which is the chemical reaction that builds proteins. This enzymatic activity occurs specifically within the peptidyl transferase center (PTC) of the large ribosomal subunit. The PTC is a highly conserved region formed predominantly by the 23S rRNA itself.
During protein synthesis, transfer RNA (tRNA) molecules deliver specific amino acids to the ribosome’s A-site. The growing polypeptide chain, attached to a tRNA, resides in the P-site. The 23S rRNA within the PTC facilitates the transfer of the polypeptide chain to the incoming amino acid, extending the protein by one unit.
A Target for Antibiotics
The 23S rRNA molecule holds significant importance in medicine because it serves as an effective target for certain classes of antibiotics. Since 23S rRNA is fundamental for bacterial survival and possesses distinct structural features compared to its human counterpart (28S rRNA), it presents an appealing target for drug development. This structural difference allows antibiotics to selectively inhibit bacterial protein synthesis without significantly harming human cells.
Specific antibiotic classes achieve their antibacterial effect by binding directly to the 23S rRNA, often within or near the peptidyl transferase center. For example, macrolide antibiotics, which include common drugs like erythromycin and azithromycin, bind to a region of the 23S rRNA, effectively blocking the nascent polypeptide exit tunnel or interfering with peptidyl transferase activity. Lincosamides, such as clindamycin, also interact with the 23S rRNA, inhibiting peptide bond formation or translocation. This binding physically obstructs the ribosome’s ability to form peptide bonds, thereby halting the production of new bacterial proteins and ultimately leading to the cessation of bacterial growth or outright bacterial death.
Role in Bacterial Identification and Phylogeny
The gene sequence that codes for 23S rRNA is a valuable molecular marker used in microbiology for identifying different species of bacteria and understanding their evolutionary relationships. While the 16S rRNA gene is more frequently utilized for broad bacterial classification, the 23S rRNA gene offers distinct advantages. Its larger size, typically around 2,900 to 3,000 base pairs, often contains more variable regions than the 16S rRNA gene. This increased variability can provide a higher resolution for distinguishing between very closely related bacterial species or even subspecies.
The sequence differences in the 23S rRNA gene accumulate over evolutionary time, allowing scientists to construct phylogenetic trees that illustrate the genetic distances and relationships among various bacterial groups. This application is particularly useful in areas such as clinical microbiology for rapid and accurate pathogen identification, and in environmental studies for characterizing microbial communities. By comparing 23S rRNA gene sequences, researchers can gain insights into the diversity and relatedness of bacteria found in various habitats.