Abstract
The molecular mechanisms for repairing DNA damages and point mutations have been well understood but it remains unclear how a frameshift mutation is repaired. Here we report that frameshift reversion occurs in E. coli more frequently than expected and appears to be a targeted gene repair signaled by premature termination codons (PTCs), producing high-level variations in the repaired genes. Genome resequencing shows that the revertant genome is highly stable, and the single-molecule variations in the repaired genes are derived from RNA editing. A multi-omics analysis shows that the expression levels change greatly in most the DNA and RNA manipulating genes. DNA replication, transcription, RNA editing, RNA degradation, nucleotide excision repair, mismatch repair, and homologous recombination were upregulated in the frameshift or revertant, but the base excision repair was not. Moreover, genes and transposons in a duplicate region silenced in wild type E. coli were activated in the frameshift. Finally, we propose a nonsense-mediated gene revising (NMGR) model for frame repair, which also acts as a driving force for molecular evolution. In essence, nonsense mRNAs are recognized, edited, and transported to template the repair of the coding gene by RNA-directed DNA repair, nucleotide excision, mismatch repair, and homologous recombination. Thanks to NMGR, the mutation rate temporarily rises in a frameshift gene, bringing genetic diversity while repairing the frameshift mutation and accelerating the evolution process without a high mutation rate in the genome.
Competing Interest Statement
The authors have declared no competing interest.
Footnotes
Revision summary 1.The title is changed, the text is reorganized and polished for language problems. 2.The proposed model is changed from nonsense-mediated gene repair (NMGR) to nonsense-mediated gene revising (NMGR) because the frameshift gene is not only repaired but also evolved, the NMGR process acts as both a mechanism for frame repair and a driving force for molecular evolution, bringing genetic diversity to the gene while reparing the reading frame. 3.The genome data are re-analyzed, the SNP densities in the genome and the plasmid are corrected; SNPs are compared between the frameshift and the revertant. 4.The transcriptome data are re-analyzed, the differentially expressed genes/pathways are updated; in the previous version, only great changes (fold change >=2.0) are considered; in this version, moderate changes (1.2<fold change<2.0) are also considered, and many more genes are found also involved in frame repair, including most DNA or RNA manipulating pathways. 5.New data are added, includes: (1) The base substitutions in the revertant are derived from RNA editing (section 3.7); (2) Identifying frameshift repair genes in the duplicate regions (section 3.9) (3) Detection of the proteins by quantitative analysis of global proteome (section 3.10) 6.The previous Fig 2D, 4B, 4C, 4D, their legend and description are removed. 7.The previous Fig 1 are merged into Fig 2; Fig 3 are renamed as Fig 1, Fig 4 as Fig3, Fig 5 as Fig 4, Fig 6 as Fig 5, Fig 7 as Fig 6, and their legend and description are updated. 8.Previous Table 4-5 are removed, a new Table 4 is created. 9.The detailed materials and methods, a review of previous studies, and the supplementary tables S1-S12 are described in a supplementary file.