Many aspects of human health are affected by the process of genetic adaptation. Somatic cells escape growth control and become malignant. Pathogens evade host defenses and cause disease. Inherited disorders would be more easily associated with mutations by knowing how genetic changes occur. Adaptation can be very rapid, despite very low mutation rates. We propose that experimental genetics has missed a major pathway of genetic adaptation. Genetics focuses on rare large-effect mutations that are easier to identify and simpler to analyze. This ignores the two commonest mutation types (missense and copy number changes). Most point mutations and copy number changes have very small phenotypes and are hard to remove from the population (if deleterious) and hard to detect experimentally (if beneficial). Both types are carried as frequent polymorphisms in populations. When selection is imposed, the resident small effect mutant alleles can amplify under selection and provide an increased phenotype with a greater selective advantage. Amplification provides more copies of the growth-limiting gene and more gene targets for mutational improvement. Once the problem is solved, selection is relaxed, the amplification is lost and only the improved allele is retained Selection thus appears to induce mutagenesis and direct mutations to beneficial sites. We suggest that most gene duplications are initiated by palindromic sequences, which can form snap-back structures and prime repair synthesis leading to a symmetrical tandem inversion duplication (sTID) - abcd-d'c'b'a'-abcd. These duplications amplify under selection and are stabilized by join point deletions that shorten the repeated unit, improve fitness and allow even higher amplification. We will look for the predicted intermediate unstable symmetric TID junctions using a new non-selective trapping methods. We suggest that the initiating palindromic sequences are activated by transcription, which allows secondary (snap back) structures to form in the non- template DNA strand of R-loops. This is most likely to occur during transcription of A/T-rich, G/C skewed sequences and in operons that include palindromic dispersed repeats - REP(BIMES), ERIC, AelRep and LasRep. Other potential sources of TID-initiating palindromes are the highly- transcribed, palindromic ribosomal RNA (rrn) genes.

Public Health Relevance

In cancer and infectious disease, growth-limited cell populations acquire mutations that allow them to proliferate despite host controls and defenses. The speed adaptation is often due to common small-effect mutations that gain a larger phenotype by selected increases in gene copy number. We will test a model by which duplications are initiated by palindromic sequences whose transcription allows them to form snap-back (hairpin) structures in an R- loop. Cutting allows these snap-backs to initiate repair synthesis leading to tandem arrays of inverse-order copies.

Agency
National Institute of Health (NIH)
Institute
National Institute of General Medical Sciences (NIGMS)
Type
Research Project (R01)
Project #
5R01GM027068-39
Application #
9518937
Study Section
Prokaryotic Cell and Molecular Biology Study Section (PCMB)
Program Officer
Ainsztein, Alexandra M
Project Start
1979-12-01
Project End
2019-06-30
Budget Start
2018-07-01
Budget End
2019-06-30
Support Year
39
Fiscal Year
2018
Total Cost
Indirect Cost
Name
University of California Davis
Department
Microbiology/Immun/Virology
Type
Schools of Medicine
DUNS #
047120084
City
Davis
State
CA
Country
United States
Zip Code
95618
Maisnier-Patin, Sophie; Roth, John R (2018) Selection and Plasmid Transfer Underlie Adaptive Mutation in Escherichia coli. Genetics 210:821-841
Yamayoshi, Itsugo; Maisnier-Patin, Sophie; Roth, John R (2018) Selection-Enhanced Mutagenesis of lac Genes Is Due to Their Coamplification with dinB Encoding an Error-Prone DNA Polymerase. Genetics 208:1009-1021
Roth, John R; Maisnier-Patin, Sophie (2016) Reinterpreting Long-Term Evolution Experiments: Is Delayed Adaptation an Example of Historical Contingency or a Consequence of Intermittent Selection? J Bacteriol 198:1009-12
Maisnier-Patin, Sophie; Roth, John R (2015) The Origin of Mutants Under Selection: How Natural Selection Mimics Mutagenesis (Adaptive Mutation). Cold Spring Harb Perspect Biol 7:a018176
Reams, Andrew B; Roth, John R (2015) Mechanisms of gene duplication and amplification. Cold Spring Harb Perspect Biol 7:a016592
Sano, Emiko; Maisnier-Patin, Sophie; Aboubechara, John Paul et al. (2014) Plasmid copy number underlies adaptive mutability in bacteria. Genetics 198:919-33
Reams, Andrew B; Kofoid, Eric; Duleba, Natalie et al. (2014) Recombination and annealing pathways compete for substrates in making rrn duplications in Salmonella enterica. Genetics 196:119-35
Huseby, Douglas L; Roth, John R (2013) Evidence that a metabolic microcompartment contains and recycles private cofactor pools. J Bacteriol 195:2864-79
Näsvall, Joakim; Sun, Lei; Roth, John R et al. (2012) Real-time evolution of new genes by innovation, amplification, and divergence. Science 338:384-7
Reams, Andrew B; Kofoid, Eric; Kugelberg, Elisabeth et al. (2012) Multiple pathways of duplication formation with and without recombination (RecA) in Salmonella enterica. Genetics 192:397-415

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