title: Nonlinearity in genetic decoding: homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting.
abstract: The tau and gamma subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. gamma is two-thirds the size of tau and shares virtually all its amino acid sequence with tau. E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between tau and gamma. Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller gamma protein. In E. coli, approximately 50% of initiating ribosomes translate the dnaX mRNA conventionally to give tau, but the other 50% shift into the -1 reading frame at a specific site (A AAA AAG) in the mRNA to produce gamma. 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 tau. The rest of the population of mRNAs (containing nine +/- nonmultiples of three As) puts ribosomes into the alternate reading frames to produce the gamma protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression.
authors.affiliation: Department of Human Genetics, University of Utah, 15 N 2030 East Building 533, Room 7410, Salt Lake City, UT 84112-5330, USA.
authors.forename: B
authors.initials: B
authors.lastname: Larsen
authors.forename: N M
authors.initials: NM
authors.lastname: Wills
authors.forename: C
authors.initials: C
authors.lastname: Nelson
authors.forename: J F
authors.initials: JF
authors.lastname: Atkins
authors.forename: R F
authors.initials: RF
authors.lastname: Gesteland
mesh_terms: D001426:Bacterial Proteins / Q000235:genetics* / Q000378:metabolism; D003001:Cloning, Molecular; D018388:Codon, Terminator / Q000235:genetics; D004258:DNA Polymerase III / Q000235:genetics* / Q000378:metabolism; D004926:Escherichia coli / Q000201:enzymology; D005786:Gene Expression Regulation; D013058:Mass Spectrometry; D014176:Protein Biosynthesis / Q000235:genetics*; D012329:RNA, Bacterial / Q000235:genetics; D012333:RNA, Messenger / Q000378:metabolism; D020133:Reverse Transcriptase Polymerase Chain Reaction; D012270:Ribosomes / Q000378:metabolism; D017421:Sequence Analysis; D016963:Thermus thermophilus / Q000201:enzymology; D014158:Transcription, Genetic / Q000235:genetics*
chemical_list: D001426:Bacterial Proteins; D018388:Codon, Terminator; C103076:DnaX protein, Bacteria; D012329:RNA, Bacterial; D012333:RNA, Messenger; D004258:DNA Polymerase III