Ribosome

Ribosomes are essential molecular machines found in all living cells, responsible for synthesizing proteins from genetic information encoded in messenger RNA. They play a central role in cellular function and growth, making them critical for life. Understanding ribosome structure and function is fundamental to both molecular biology and medicine.

Structure of Ribosome

Ribosomal Subunits

Ribosomes are composed of two unequal subunits, each with distinct roles in protein synthesis. These subunits differ in size and composition between prokaryotic and eukaryotic cells.

• Large subunit: In prokaryotes, the large subunit is 50S, while in eukaryotes it is 60S. It contains the peptidyl transferase center, which catalyzes peptide bond formation.
• Small subunit: In prokaryotes, the small subunit is 30S, and in eukaryotes it is 40S. It is responsible for decoding the mRNA sequence and ensuring correct tRNA binding.

Ribosomal RNA (rRNA)

Ribosomal RNA forms the structural and functional core of ribosomes, providing the scaffold for ribosomal proteins and participating directly in catalysis.

• Prokaryotic ribosomes contain 16S rRNA in the small subunit and 23S and 5S rRNAs in the large subunit.
• Eukaryotic ribosomes contain 18S rRNA in the small subunit and 28S, 5.8S, and 5S rRNAs in the large subunit.
• rRNA is crucial for maintaining ribosome structure and facilitating peptide bond formation during translation.

Ribosomal Proteins

Ribosomal proteins surround the rRNA core, stabilizing its three-dimensional structure and contributing to ribosome function.

• Prokaryotic ribosomes contain approximately 55 proteins, while eukaryotic ribosomes contain about 80 proteins.
• These proteins assist in proper folding of rRNA, interact with tRNAs and translation factors, and can influence the accuracy of protein synthesis.

Types of Ribosomes

Prokaryotic Ribosomes

Prokaryotic ribosomes are 70S in size, composed of 50S and 30S subunits. They are found freely in the cytoplasm, where they synthesize proteins necessary for cell survival.

Eukaryotic Ribosomes

Eukaryotic ribosomes are larger, measuring 80S, with 60S and 40S subunits. They are present both as free ribosomes in the cytoplasm and attached to the rough endoplasmic reticulum, where they produce proteins for secretion or membrane localization.

Free vs Membrane-Bound Ribosomes

Ribosomes can exist freely in the cytosol or be bound to cellular membranes, with functional distinctions.

• Free ribosomes: Synthesize proteins that function in the cytoplasm, nucleus, mitochondria, or other organelles.
• Membrane-bound ribosomes: Associated with the rough endoplasmic reticulum and produce proteins destined for secretion, lysosomes, or incorporation into membranes.

Ribosome Biogenesis

rRNA Transcription and Processing

Ribosome biogenesis begins in the nucleolus, where ribosomal RNA genes are transcribed and processed into mature rRNA molecules. This process is essential for assembling functional ribosomal subunits.

• In eukaryotes, the nucleolus synthesizes 18S, 5.8S, and 28S rRNAs, while 5S rRNA is transcribed separately by RNA polymerase III.
• Pre-rRNA undergoes cleavage, chemical modifications, and folding to form mature rRNA molecules.
• Processing is guided by small nucleolar RNAs (snoRNAs) and associated proteins, ensuring accurate ribosome assembly.

Assembly of Ribosomal Subunits

The assembly of ribosomal subunits involves the integration of rRNA with ribosomal proteins to form the small and large subunits, which are then transported to the cytoplasm for final maturation.

• Ribosomal proteins are synthesized in the cytoplasm and imported into the nucleolus for assembly with rRNA.
• Pre-assembly complexes form intermediate structures that are processed into mature 40S and 60S subunits in eukaryotes, or 30S and 50S subunits in prokaryotes.
• Export to the cytoplasm involves nuclear transport factors and ensures that only fully assembled subunits participate in translation.

Function of Ribosomes

Protein Synthesis

The primary function of ribosomes is to translate messenger RNA into polypeptide chains, producing proteins required for cellular structure and function.

• Ribosomes read the codons on mRNA and recruit the corresponding transfer RNA (tRNA) molecules carrying specific amino acids.
• Each codon-anticodon interaction ensures the correct amino acid sequence is incorporated into the growing polypeptide chain.

Peptide Bond Formation

Ribosomes catalyze the formation of peptide bonds between amino acids, a critical step in elongating the polypeptide chain.

• The peptidyl transferase activity is located in the large subunit and is responsible for linking amino acids together.
• This enzymatic activity is RNA-based, highlighting the catalytic role of rRNA in ribosome function.

Regulation of Translation

Translation by ribosomes is tightly regulated to ensure proper protein synthesis according to cellular needs.

• Initiation factors guide the assembly of ribosomal subunits on mRNA to start translation.
• Elongation factors facilitate the addition of amino acids to the growing polypeptide chain.
• Termination factors recognize stop codons and release the completed protein from the ribosome.
• Regulatory mechanisms respond to cellular stress, nutrient availability, and signaling pathways to modulate translation efficiency.

Ribosome and Cellular Processes

Response to Cellular Stress

Ribosomes play a critical role in the cellular response to stress, adjusting protein synthesis to maintain homeostasis and survival.

• Under stress conditions such as nutrient deprivation or oxidative stress, ribosomes can stall on mRNA, leading to the formation of stress granules.
• These granules temporarily store mRNA and translation factors, allowing the cell to quickly resume protein synthesis once stress is alleviated.
• Ribosome-associated quality control pathways detect defective mRNAs and nascent polypeptides, preventing accumulation of incomplete or misfolded proteins.

Ribosome in Development and Growth

Ribosomes are essential for cell growth, proliferation, and differentiation, supporting the high demand for protein synthesis during development.

• Cells with high proliferation rates, such as embryonic and stem cells, contain abundant ribosomes to meet protein synthesis needs.
• Regulation of ribosome biogenesis and activity is tightly linked to growth signals and nutrient availability.

Specialized Ribosomes

Recent studies suggest that ribosomes are not uniform; specialized ribosomes may selectively translate specific subsets of mRNAs.

• Ribosome heterogeneity can arise from variations in ribosomal protein composition or rRNA modifications.
• Specialized ribosomes may regulate gene expression during development, stress response, or in specific tissues.

Ribosome-Targeting Antibiotics

Prokaryotic Ribosome Inhibitors

Many antibiotics exert their effects by selectively targeting prokaryotic ribosomes, inhibiting bacterial protein synthesis without affecting eukaryotic ribosomes.

• Examples include tetracyclines, which block tRNA binding to the ribosome, and macrolides, which inhibit peptide chain elongation.
• Aminoglycosides cause misreading of mRNA, leading to production of faulty proteins.

Clinical Significance

Understanding how antibiotics target ribosomes is essential for effective treatment of bacterial infections and combating antibiotic resistance.

• Ribosome-targeting antibiotics form the basis of many clinical therapies for bacterial diseases.
• Mutations in ribosomal RNA or proteins can confer resistance, emphasizing the need for new drugs and therapeutic strategies.

Ribosomopathies

Genetic Disorders Affecting Ribosomes

Ribosomopathies are a group of genetic disorders caused by mutations in ribosomal proteins or rRNA processing factors, leading to impaired ribosome function.

• Diamond-Blackfan anemia: Characterized by defective red blood cell production due to mutations in ribosomal protein genes.
• Shwachman-Diamond syndrome: Results from mutations affecting ribosome biogenesis, leading to bone marrow failure and pancreatic insufficiency.
• Other ribosomopathies include Treacher Collins syndrome and Dyskeratosis congenita, affecting craniofacial development and telomere maintenance respectively.

Pathophysiology

Impaired ribosome function in ribosomopathies disrupts normal protein synthesis, affecting rapidly dividing cells and leading to tissue-specific defects.

• Defective ribosomes activate cellular stress pathways and p53-mediated apoptosis.
• Altered translation of specific mRNAs can contribute to disease phenotypes, such as anemia or developmental abnormalities.

Experimental Techniques for Studying Ribosomes

Electron Microscopy

Electron microscopy allows visualization of ribosome structure at high resolution, providing insights into subunit organization and ribosomal complexes.

• Transmission electron microscopy (TEM) and cryo-electron microscopy (cryo-EM) reveal ribosome architecture and conformational changes during translation.

Ribosome Profiling

Ribosome profiling is a high-throughput technique that maps ribosome positions on mRNA, revealing translation dynamics and identifying actively translated genes.

• This method provides nucleotide-level resolution of ribosome occupancy and translation efficiency across the transcriptome.

X-ray Crystallography and Cryo-EM

X-ray crystallography and cryo-EM have been instrumental in determining the three-dimensional structures of ribosomes and ribosome-ligand complexes.

• These structural studies inform our understanding of translation mechanisms, antibiotic binding sites, and ribosome evolution.

References

1. Alberts B, Johnson A, Lewis J, Raff M, Roberts K, Walter P. Molecular Biology of the Cell. 6th edition. New York: Garland Science; 2014.
2. Lodish H, Berk A, Kaiser CA, Krieger M, Bretscher A, Ploegh H, et al. Molecular Cell Biology. 8th edition. New York: W.H. Freeman; 2016.
3. Ban N, Nissen P, Hansen J, Capel M, Moore PB, Steitz TA. The complete atomic structure of the large ribosomal subunit at 2.4 Å resolution. Science. 2000;289(5481):905-920.
4. Wool IG. Ribosomal proteins. In: Neidhardt FC, Curtis R, Ingraham JL, Lin ECC, Low KB, Magasanik B, et al., editors. Escherichia coli and Salmonella: Cellular and Molecular Biology. 2nd edition. Washington, DC: ASM Press; 1996. p. 263-283.
5. Warner JR. The economics of ribosome biosynthesis in yeast. Trends Biochem Sci. 1999;24(11):437-440.
6. Baretić D, LaRiviere FJ, Milek M, Chen Y, Fox T, Oeffinger M, et al. Ribosome biogenesis and the regulation of cell growth. Cold Spring Harb Perspect Biol. 2015;7(6):a019320.
7. De Keersmaecker K, Sulima SO, Dinman JD. Ribosomopathies and the paradox of cellular hypo- to hyperproliferation. Blood. 2015;125(9):1377-1382.
8. Sharma MR, Ling C, Baasov T, Joseph S. Structure of the ribosome at atomic resolution: implications for antibiotic binding. Annu Rev Biophys Biomol Struct. 2007;36:197-216.
9. Ingolia NT, Ghaemmaghami S, Newman JR, Weissman JS. Genome-wide analysis in vivo of translation with nucleotide resolution using ribosome profiling. Science. 2009;324(5924):218-223.
10. Steitz TA. Ribosome structures: new windows into protein synthesis. Cold Spring Harb Perspect Biol. 2010;2(5):a003771.