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Organisms are capable of detecting and fixing nucleotide mismatches that occur during DNA replication. This sophisticated process requires identifying the new strand and replacing the erroneous bases with correct nucleotides. Mismatch repair is coordinated by many proteins in both prokaryotes and eukaryotes.
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Mutations are heritable changes in an organism’s genome involving alterations in the base sequence of DNA or RNA. These changes can influence cellular processes and phenotypic traits, potentially transforming the unaltered wild type into a mutant form. Such changes, termed forward mutations, are pivotal in shaping the genetic diversity of organisms.RNA viruses exhibit the highest mutation rates due to the absence of robust proofreading mechanisms during genome replication. In contrast,...
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The genomes of eukaryotes are punctuated by long stretches of sequence which do not code for proteins or RNAs. Although some of these regions do contain crucial regulatory sequences, the vast majority of this DNA serves no known function. Typically, these regions of the genome are the ones in which the fastest change, in evolutionary terms, is observed, because there is typically little to no selection pressure acting on these regions to preserve their sequences.
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Spontaneous mutations arise infrequently during DNA replication due to errors in the process. A key factor behind these errors is tautomeric shifts in nitrogenous bases, where bases transition from keto to enol forms or amino to imino forms. This shift can alter base-pairing rules, leading to mutations. Additionally, reactive oxygen species (ROS) arising from aerobic metabolism can damage DNA, resulting in depurination (loss of a purine base) or depyrimidination (loss of a pyrimidine base).
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Point mutations are genetic alterations involving the change of a single nucleotide base pair in DNA. Depending on how the alteration affects protein synthesis, they can lead to various consequences.Point mutations fall into the following types:Silent mutations occur when a nucleotide change does not alter the amino acid sequence due to the redundancy of the genetic code. For instance, changing ACC to ACA still encodes threonine, leaving the protein function unaffected. This occurs because...
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Synonymous mutations in representative yeast genes are mostly strongly non-neutral.

Xukang Shen1, Siliang Song1, Chuan Li2,3

  • 1Department of Ecology and Evolutionary Biology, University of Michigan, Ann Arbor, MI, USA.

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Most synonymous mutations significantly impact gene fitness, challenging the assumption of neutrality. This finding necessitates re-evaluating biological conclusions drawn from mutation and selection studies.

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Area of Science:

  • Molecular Biology
  • Genetics
  • Evolutionary Biology

Background:

  • Synonymous mutations, which do not alter amino acid sequences, are traditionally considered neutral.
  • This assumption has underpinned many biological models in genetics and evolution.

Purpose of the Study:

  • To experimentally test the long-held presumption that synonymous mutations are neutral.
  • To investigate the fitness effects of synonymous mutations in endogenous yeast genes.

Main Methods:

  • Created 8,341 yeast mutants with synonymous, nonsynonymous, or nonsense mutations in 21 endogenous genes.
  • Measured relative fitness in rich medium and analyzed mRNA expression levels.
  • Assessed fitness variations across different environmental conditions.

Main Results:

  • Three-quarters of synonymous mutations caused a significant fitness reduction in yeast.
  • Both synonymous and nonsynonymous mutations frequently altered mRNA expression levels, partially predicting fitness effects.
  • Nonsynonymous mutations showed greater fitness variation across environments than synonymous mutations.

Conclusions:

  • Synonymous mutations are frequently non-neutral, impacting gene fitness and mRNA expression.
  • The non-neutrality of synonymous mutations may explain observed differences in substitution rates between synonymous and nonsynonymous mutations.
  • The findings challenge the neutrality assumption for synonymous mutations, requiring re-examination of evolutionary and disease models.