Considerations regarding the regulation of gene transcription and messenger translation

The RNA sequences in the region of the coat protein gene of MS2/R17 phage, of the maturation protein gene ofQβ and of a 6s-RNA transcribed from a presumptive gene ofλ were examined. All but five of the 61 amino acid codons are present in these messages and although there is some evidence of a bias in the frequency of utilization of the codons, there is little evidence to suggest that any codons may be forbidden. It is shown that selection has not reduced useless protein synthesis by minimizing the number of out of register AUG's or maximizing the number of out of register terminating codons in messenger RNA. Secondary structures of the RNA's were formulated using a modification of the diagonal method of Tinocoet al. (1971). Of the 12 AUG triplets considered in the sequences only one is a primary attachment site for ribosomes and it is the only one of the 12 that appears in end loops with none of the bases paired. A thirteenth AUG triplet appears at the beginning of the 6s-RNAλ gene. Its occurrence in an end loop free of base pairing suggests that this is a ribosome binding site. It is speculated (1), that transcriptase may recognize its binding site on the DNA by a procedure that is in part the analogue of the protein synthetase recognizing its binding-initiation site, namely that as the DNA strands are separated, a secondary structure forms in the sense strand with a CAT in the end loop; (2), that reverse transcriptase might be useful as a means of keeping multiple copies of a gene identical if it were to correct the sense strand DNA in a DNA-RNA hybrid; and (3), that processing of RNA in the intercistronic region normally occurs in the same manner as translation, namely, moving the RNA through, three nucleotides at a time.