Errors and alternatives in reading the universal genetic code

The fidelity of biological information flow is critical. Deoxyribonucleic acid (DNA) replication, with its attendant proofreading and repair processes, has an error level in the range of 10-8 to 10-11 (71, 183). Different kinds of mutations occur at different frequencies, and sequences are known in which errors occur preferentially and at a higher frequency (see, e.g., references 15, 80, and 268). However, in an average Escherichia coli cell the great majority of genes will have been copied error free. For such a cell to function correctly, each of the subsequent steps in information flow from DNA to protein must also occur with reasonable fidelity. However, it is not obvious what constitutes reasonable fidelity. From the relatively few measurements of the accuracy of transcription, it seems that this process is much less accurate than DNA replication, if only because of the apparent lack of repair pathways. The in vivo error level for transcription may be on the order of lo(258), and such errors may also be context dependent (259). The universal genetic code was elucidated in the late 1960s primarily by in vitro biochemical means (see reference 324). It is substantiated by an enormous and growing body of data generated by comparing DNA and protein sequences. Therefore, given a DNA sequence, it seems simple to predict the sequence of its protein product. Indeed, reputable journals contain articles that routinely discuss "codons" such as TAT or ATG, as if ribosomes in cells read DNA directly. There can be dramatic pitfalls in this practice. Intron splicing creates rather large differences between transcripts and messenger ribonucleic acids (mRNAs). More subtle RNA editing processes, in which there are specific insertions or deletions of one or a few bases internally in a transcript (14, 273), or even a specific base substitution (47, 63, 247), can also occur. Knowledge of these different RNA-processing and editing mechanisms adds an element of caution when translating DNA directly to protein (and the mechanisms themselves introduce new possibilities for error). Note that in each case the problem can be overcome if the sequence of the mRNA is known. Although this is also true of protein made from mRNA containing transcriptional or processing errors, these few error-containing mRNAs will almost certainly be impossible to detect. In addition, several organisms and organelles that use genetic codes slightly different from the universal code have now been discovered. In each of these codes there are one or a few codons which have different assignments. These alternative codes have recently been reviewed by Fox (85). Alternative codes are translated correctly only when the translational apparatus has appropriate and corresponding predictable changes. As is the case for RNA-processing or transcriptional errors, knowledge of the mRNA sequence and the appropriate codon table is required for predicting protein sequence. However, even disallowing posttranslational modifications, proteins whose primary sequence cannot be predicted from the most simple reading of the RNA code will be synthesized in the cell. Some of these will arise because of errors in the translation process. Errors are of interest because they allow insight into the normal functioning of the translational machinery and its evolution. However, not all differences between the predicted sequence of a protein and its actual sequence are the result of errors (see below). In some cases it is clear that certain codons or mRNA sequences can have alternative readings and that organisms have taken advantage of this flexibility in reading the genetic code. The primary concerns of this review are the types of errors