While antibiotics are designed to directly hinder bacterial translation, their efficacy is significantly reduced when pathogens develop drug resistance through a variety of mechanisms, which include ribosomal modifications, translation elongation factors, ribosomal protection proteins, and mistranslation.
The challenge that lies before us, therefore, is to prevent the spread of multidrug-resistant pathogens in a post-antibiotic world. Can it be done? Thankfully, there are several options available to help overcome the most common mechanisms of drug resistance – and these can be done by targeting the rRNA translation process.
Ribosomal RNA: Structure and Function
Ribosomal RNA is the primary component of ribosomes and is the most predominant form of RNA in cells, comprising about 80% of the cellular RNA. While rRNA in itself is not translated into proteins, it plays an important role in synthesizing the genetic code into proteins by regulating the action of the transfer RNA and messenger RNA.
Ribosomal RNA has two distinct subunits: the large ribosomal subunit (LSU) and small ribosomal subunit (SSU). Each of these units are composed of different rRNA types. In prokaryotes, the LSU is composed of a single small rRNA and one large rRNA molecule (approximately 3000 nucleotides) while the SSU has a single small rRNA molecule (approximately 1500 nucleotides). In eukaryotes, the LSU contains one large and two small rRNAs (approximately 50000 nucleotides) while the SSU has a single small rRNA (approximately 1800 nucleotides).
Prokaryotic ribosomes contain three types of rRNA (5S and 23S rRNA in the LSU, 16S rRNA in the SSU) while eukaryotic ribosomes contain four types of rRNA (5S, 5.8S, and 28S rRNA in the LSU and 18S rRNA in the SSU). The LSU rRNA (specifically the peptidyl transferase center or PTC) is classified as a ribozyme because it catalyzes specific biochemical reactions (i.e. peptide bond formation and peptide release).
rRNA and Drug Resistance Formation
Considering its significance in protein synthesis, many antibiotics (e.g., streptomycin, spectinomycin, tetracycline, lincomycin, clindamycin, chloramphenicol) target rRNA to reduce protein translation and inhibit bacterial growth. Additionally, rRNAs are the most likely targets, since they have numerous binding sites for antibacterial agents. Here’s how different antibiotics work.
- Aminoglycosides (i.e., streptomycin, spectinomycin) bind on the prokaryotic rRNA A-site to kill bacterial cells.
- Tetracycline discourages the binding of the RNA to the ribosomes by influencing binding to the A-site, binding of Ac-Phe-tRNA to the P-site, or by incorporating itself into the ribosomal proteins (in the absence of ribonucleoproteins).
- Lincomycin and its derivative clindamycin inhibit bacterial action by targeting the site of peptide bond formation.
- Chloramphenicol targets the 50S ribosomal subunit to inhibit peptidyl transferase activity.
However, drug resistance develops when alterations or mutations occur in the rRNA. For example, methylation in the LSU 23S rRNA will result in the modification of the ribosome and inhibit the action of drugs that attack the PTC of the bacterial ribosome, while mutations in E. coli 16S rRNA affects its response to streptomycin.
In some cases, bacterial species use ribosomal protection proteins (RPPs) to induce a structural change in the ribosome, which then inhibits drug activity or dislodges drugs that target the 30S or 50S subunit without permanently modifying ribosomal activity. Some RPPs also work by binding and hydrolyzing adenosine triphosphate (ATP) and other nucleotide triphosphates (NTPs). Upon binding to the 50S subunit, the linker domain extends to the PTC to induce conformational change and drug release.
Antibiotic resistance can also be induced when fusidic acid is used to bind and inhibit the action of elongation factor G (EF-G), a translation factor that catalyzes the translocation of tRNA through the ribosome. Although it can effectively hinder translation, it can also trigger point mutation in EF-G which will initiate resistance formation.
Moreover, antibiotic resistance may also result from mistranslation. The ribosome may fail to match codons with their corresponding aminoacylated tRNA, resulting in enhanced or diminished decoding accuracy. Errors in the pairing between tRNAs and their cognate amino acids can also disrupt the fidelity of aminoacylation.
