Nonlinearity in genetic decoding: Homologous DNA replicase genes use alternatives of transcriptional slippage or translational frameshifting

Abstract

The and ␥ subunits of DNA polymerase III are both encoded by a single gene in Escherichia coli and Thermus thermophilus. ␥ is two-thirds the size of and shares virtually all its amino acid sequence with . E. coli and T. thermophilus have evolved very different mechanisms for setting the approximate 1:1 ratio between and ␥. Both mechanisms put ribosomes into alternate reading frames so that stop codons in the new frame serve to make the smaller ␥ protein. In E. coli, Ϸ50% of initiating ribosomes translate the dnaX mRNA conventionally to give , but the other 50% shift into the ؊1 reading frame at a specific site (A AAA AAG) in the mRNA to produce ␥. 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 . The rest of the population of mRNAs (containing nine ؉͞؊ nonmultiples of three As) puts ribosomes into the alternate reading frames to produce the ␥ protein(s). It is surprising that two rather similar dnaX sequences in E. coli and T. thermophilus lead to very different mechanisms of expression.

Endosymbiont gene functions impaired and rescued by polymerase infidelity at poly(A) tracts

“…This rules out selection on out-of-frame homopolymers to compensate for indel mutations and/or RNA polymerase slippage at other locations in the gene or vice versa. In rare cases, alternative decoding is used to produce two overlapping gene products in different stoichiometry from the same sequence (6,7,21). However, subfunctionalization by alternative decoding seems unlikely to explain the data presented here, because no novel gene functions are anticipated for the truncated forms of the frameshifted gene products.…”

“…Likewise, transcriptional slippage, or slippage of RNA polymerase along a homopolymeric stretch, generates a heterogeneous pool of mRNA products with varied tract lengths and reading phases. Such slippage can restore the reading frame of genes with frameshifts in the genomic DNA, such as some IS elements (6), and may lead to the synthesis of alternate functional proteins, such as the ␥ and subunits of Thermus thermophilus DNA polymerase III (7).…”

DNA Polymerase III Holoenzyme from Thermus thermophilus Identification, Expression, Purification of Components, and Use to Reconstitute a Processive Replicase

“…A dnaX-like mRNA was independently isolated by a PCR approach and expressed in E. coli, resulting in synthesis of ␥-and -like proteins (41). It was recently discovered that Tth ␥ and are translated from distinct mRNAs that result from transcriptional slippage at a stretch of adenosine residues located at the same site as the E. coli translational frameshift site (42).…”

Identification and characterization of a -1 reading frameshift in the heavy chain constant region of an IgG1 recombinant monoclonal antibody produced in CHO cells

“…13, theoretically there were 3 possible mechanisms of the -1 frameshift: 1) insertion of a G within the GGGGGG repeat at DNA level; 2) insertion of a G within the GGGGGG at RNA level; or 3) a shift of the ribosome one nucleotide position toward the 5' direction at the codon GGG (Gly231) or GGA (Gly232) during translation. Although none of the 3 possible mechanisms could be completely ruled out, it appeared that insertion of a nucleotide (likely G) within the GGGGGG repeat at DNA level is more likely than the other 2 mechanisms since insertion at RNA level has only been reported for A/T but not G/C repeats, 33,34 and frameshifts on Gstring are predominately C1 rather than -1 frameshift. 50,52 A homology search of the Mab-1 frameshifted peptide sequence SCDKTHTCPPCPAPELLGGTVSLPLPPKTQGHPHDLPDP in the NCBI Genbank database (Cur_NR_Prot) 53 using BLAST 54 found that it was partially shared by sequences of 3 IgG HC fragments in mAb samples prepared with peripheral blood lymphocytes of patients.…”

“…31 On the RNA level, although the transcription error rate is considered much lower than those during DNA replication, 32 insertion or deletion of a nucleotide can also occur during transcription leading to a frameshift. 33,34,35 The insertion/deletion is believed to involve a slippage between the DNA and RNA strands similar to the Streisinger DNA slippage model, and also tends to occur more frequently on mononucleotide repeats. However, according to the reported examples to date, insertion/deletions during transcription appear to be more prone to occur on A or T repeats rather than G or C repeats, 33,34 a preference that is opposite to that in DNA replication.…”