Nonlinearity in Genetic Decoding: Homologous DNA Replicase Genes Use Alternatives of Transcriptional Slippage or Translational Frameshifting

• Published in: Proceedings of the National Academy of Sciences - PNAS Vol. 97; no. 4; pp. 1683 - 1688
• Main Authors: Larsen, Bente, Wills, Norma M., Nelson, Chad, Atkins, John F., Gesteland, Raymond F.
• Format: Journal Article
• Language: English
• Published: United States National Academy of Sciences of the United States of America 15-02-2000; National Acad Sciences; National Academy of Sciences; The National Academy of Sciences
• Subjects: Average linear density; Bacterial Proteins - genetics; Bacterial Proteins - metabolism; Biological Sciences; Cloning, Molecular; Codon, Terminator - genetics; Complementary DNA; Deoxyribonucleic acid; DNA; DNA Polymerase III - genetics; DNA Polymerase III - metabolism; DNA replicase; dnaX gene; Escherichia coli; Escherichia coli - enzymology; Gene Expression Regulation; Genes; Genetics; Genomics; Mass Spectrometry; Mass spectroscopy; Messenger RNA; Molecules; Polymerase chain reaction; Protein Biosynthesis - genetics; Proteins; Reverse Transcriptase Polymerase Chain Reaction; Ribonucleic acid; Ribosomes - metabolism; RNA; RNA, Bacterial - genetics; RNA, Messenger - metabolism; Sequence Analysis; Thermus thermophilus; Thermus thermophilus - enzymology; Transcription, Genetic - genetics
• DOI: 10.1073/pnas.97.4.1683
• EISSN: 1091-6490
• ISSN: 0027-8424

The τ and γ subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. γ is two-thirds the size of τ and shares virtually all its amino acid sequence with τ . E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between τ and γ . Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller γ protein. In E. coli, ≈ 50% of initiating ribosomes translate the dnaX mRNA conventionally to give τ , but the other 50% shift into the -1 reading frame at a specific site (A AAA AAG) in the mRNA to produce γ . In T. thermophilus ribosomal frameshifting is not required: the dnaX mRNA is a heterogeneous population of molecules with different numbers of A residues arising from transcriptional slippage on a run of nine T residues in the DNA template. Translation of the subpopulation containing nine As (or +/- multiples of three As) yields τ . The rest of the population of mRNAs (containing nine +/- nonmultiples of three As) puts ribosomes into the alternative reading frames to produce the γ protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression.