Elongation of Protein Synthesis: Structural Basis of the Process of Decoding.
The information for the amino acid sequence
of proteins is encoded in the nucleotide sequence of the DNA.
Gene expression or the synthesis of a protein
encoded in the gene comprises two main phases,
transcription of one DNA strand into the complementary RNA copy messenger RNA or mRNA and
translation of the mRNA into a protein by polymerizing
amino acids in the sequence specified by the nucleotide sequence of the mRNA.
Genetic information is maintained and expressed with remarkable fidelity.
Replication of the genome,
which transmits genetic information from one generation to the next,
is extremely accurate with error rates as low as
10 to the -8 in bacteria or below 10 to the -10 in eukaryotes.
Not surprisingly, DNA replication has sophisticated
error correction mechanisms including editing and repair.
The error rate of transcription in vivo in
E. coli has been estimated to be in 10 to the -4 by
nucleotide or four times 10 to the -4 per
Codon which is considerably higher than that of replication.
Error rates of translation in vivo have been
estimated to be on the order of 10 to the -3,
to 10 to the -4.
Errors in translation can arise from incorrect amino acylation of
a particular tRNA by the specific enzymes catalyzing amino acylation,
or from incorrect translation by the ribosome.
The tRNA amino acylation step has been known to be very accurate because
the synthetases possess specific binding sites
that are tailored to recognize one particular substrate.
Correct recognition by the ribosome of a tRNA matching the Codon is more difficult.
It is because in every new round of decoding,
a different Codon is presented for reading and a different correct,
also called cognate tRNA, has to be selected.
Furthermore, decoding on the ribosome has to be
very fast to support the high speed of protein synthesis.
On the average, 10 amino acids incorporated into a peptide per second.
Therefore, the overall accuracy of gene expression is not as high as one might expect,
and rather represents a compromise that
optimizes the evolutionary fitness of the organism.
The mechanistic and structural basis underlying the accuracy of
protein synthesis has been the subject of over four decades of investigations.
In this lecture, we will discuss how recent structures
of the ribosome and the dissection of kinetics of
aminoacyl-tRNA selection shed light on the mechanism of translational accuracy
and clarified many longstanding questions
about the mechanism of decoding on the ribosome.