Protein synthesis, a fundamental process in all living organisms, involves converting genetic information into functional proteins. This intricate cellular machinery, known as translation, decodes messenger RNA (mRNA) sequences into specific chains of amino acids, which then fold into three-dimensional proteins. Proteins are the workhorses of the cell, performing diverse functions from providing structural support to catalyzing metabolic reactions. While the core steps of protein synthesis are universally conserved, significant differences exist in the translational machinery and processes between bacterial (prokaryotic) and eukaryotic cells.
Distinct Ribosome Structures
Ribosomes, the cellular machines responsible for protein synthesis, exhibit notable structural variations between bacteria and eukaryotes. Bacterial ribosomes are smaller, with a sedimentation coefficient of 70S, while eukaryotic ribosomes are larger at 80S. The ‘S’ in these designations refers to Svedberg units, which indicate a particle’s sedimentation rate during centrifugation, reflecting its size and density.
Each ribosome is composed of two subunits. The bacterial 70S ribosome consists of a large 50S subunit and a small 30S subunit. Each bacterial subunit contains specific ribosomal RNA (rRNA) molecules and numerous proteins. In contrast, the eukaryotic 80S ribosome comprises a large 60S subunit and a small 40S subunit, each also containing distinct rRNAs and proteins.
These structural distinctions, particularly in their ribosomal RNA components and associated proteins, are a basis for selective targeting by antibiotics. Many clinically used antibiotics exploit these differences by binding specifically to bacterial ribosomes, thereby inhibiting protein synthesis in bacteria without significantly affecting host eukaryotic cells.
Initiation: The Starting Line
Initiation, the process where protein synthesis begins, shows marked differences between bacterial and eukaryotic cells. In bacteria, the ribosome directly recognizes specific sequences on the messenger RNA (mRNA) to start translation. A key element is the Shine-Dalgarno sequence, a purine-rich region located a few nucleotides upstream of the start codon, typically AUG. This sequence base-pairs with a complementary anti-Shine-Dalgarno sequence found on the 16S ribosomal RNA (rRNA) of the small 30S ribosomal subunit, precisely positioning the ribosome for initiation.
Bacterial translation typically begins with a modified amino acid, N-formylmethionine (fMet), carried by a specialized initiator tRNA. This fMet-tRNA binds to the P-site of the small ribosomal subunit, guided by bacterial initiation factors (IFs). These factors coordinate the assembly of the initiation complex. Once the small subunit, mRNA, and fMet-tRNA are correctly aligned, the large 50S subunit joins, forming the complete 70S initiation complex, and the initiation factors dissociate.
Eukaryotic initiation, on the other hand, is generally more complex and involves a scanning mechanism. Translation typically begins with the small 40S ribosomal subunit binding to the 5′ cap structure of the mRNA. This binding is mediated by a complex array of eukaryotic initiation factors (eIFs) that recognize the cap. The 40S subunit then scans along the mRNA in a 5′ to 3′ direction until it encounters the first AUG start codon within a favorable sequence context.
This favorable sequence context is known as the Kozak sequence, which surrounds the AUG start codon and enhances initiation efficiency. Unlike bacteria, eukaryotes use regular methionine, not fMet, as the first amino acid, delivered by a specific initiator tRNA. A larger number of eIFs coordinate the recruitment of the initiator tRNA, the scanning process, and the eventual joining of the large 60S ribosomal subunit to form the complete 80S ribosome, marking the start of protein synthesis.
Transcriptional-Translational Linkage
A striking difference between bacterial and eukaryotic gene expression lies in the spatial and temporal relationship between transcription and translation. In bacteria, these two processes are intimately linked, occurring simultaneously within the cytoplasm. As messenger RNA (mRNA) is being synthesized from a DNA template by RNA polymerase, ribosomes can immediately attach to the nascent mRNA strand and begin protein synthesis. This phenomenon, known as coupled transcription-translation, allows for a rapid cellular response to environmental changes.
The lack of a nuclear membrane in bacteria enables this direct coupling. Ribosomes can follow closely behind the RNA polymerase, with the nascent mRNA immediately threaded into the ribosome. This tight coordination ensures efficient protein production and can also play a role in gene regulation. Multiple ribosomes can translate a single mRNA molecule even as it is still being transcribed, leading to a rapid amplification of protein levels.
In contrast, eukaryotic cells exhibit a clear separation of transcription and translation. Transcription occurs within the nucleus, where the DNA is located. The newly synthesized pre-mRNA undergoes extensive processing steps within the nucleus before it is exported to the cytoplasm. This nuclear envelope acts as a physical barrier, ensuring that transcription and translation cannot occur concurrently in the same compartment.
This spatial and temporal separation provides eukaryotes with additional opportunities for gene regulation and mRNA processing. It allows for complex modifications to the mRNA, such as splicing, to occur before translation begins. Once the mRNA is fully processed, it is then transported out of the nucleus into the cytoplasm, where ribosomes are located and translation can commence.
mRNA Preparation and Organization
The journey of messenger RNA (mRNA) from its initial synthesis to its role as a template for protein production differs significantly between bacteria and eukaryotes, particularly in the preparatory steps. Eukaryotic mRNA undergoes extensive post-transcriptional modifications within the nucleus before it is ready for translation. These modifications include the addition of a 5′ cap, a 3′ poly-A tail, and the process of splicing.
The 5′ cap, a modified guanine nucleotide, is added to the beginning of the mRNA molecule shortly after transcription begins. This cap protects the mRNA from degradation by enzymes and plays a role in its export from the nucleus and its recognition by ribosomes during translation. At the other end, a poly-A tail, a long chain of adenine nucleotides, is added to the 3′ end of the mRNA. The poly-A tail also contributes to mRNA stability, nuclear export, and translation efficiency.
Perhaps the most intricate modification in eukaryotes is splicing, where non-coding regions called introns are removed from the pre-mRNA, and the coding regions, known as exons, are precisely joined together. Introns do not carry information for protein synthesis and must be excised to ensure that the final protein sequence is accurate. These processing steps collectively ensure the stability, transport, and proper translation of eukaryotic mRNA.
In stark contrast, bacterial mRNA generally does not undergo such extensive processing. Bacterial mRNA molecules are typically ready for translation as soon as they are transcribed, lacking the 5′ cap, poly-A tail, and introns characteristic of eukaryotic mRNA. This simplicity aligns with the coupled transcription-translation observed in bacteria, allowing for immediate protein synthesis.
Another organizational difference lies in the coding capacity of mRNA. Bacterial mRNA is often polycistronic, meaning a single mRNA molecule can encode multiple different proteins, typically those involved in a common metabolic pathway. This allows bacteria to efficiently coordinate the synthesis of several related proteins from one transcript. Conversely, eukaryotic mRNA is predominantly monocistronic, carrying the genetic information for only one specific protein.