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Gene Duplication and Divergence02:37

Gene Duplication and Divergence

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The seminal work of Ohno in 1970 popularized the idea of gene duplication and divergence. DNA sequence comparison studies reveal that a large portion of the genes in bacteria, archaebacteria, and eukaryotes was  generated by gene duplication and divergence, indicating its critical role in evolution.
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Gene families consist of groups of genes proposed to have originated from a common ancestor. Typically these arise through events in which a gene or genes are mistakenly duplicated during cell division. Unlike their parent genes (which are subject to selection pressure to maintain function), these gene copies do not need to preserve their sequences and may evolve at a relatively faster rate.
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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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Cis-regulatory sequences are short fragments of non-coding DNA that are present on the same chromosomes as the genes that they regulate. These fragments serve as binding sites for transcriptional regulators, proteins that are responsible for controlling gene transcription and differential gene expression across cell types in eukaryotes. Cis-regulatory sequences can be close to the gene of interest or thousands of bases away in the DNA sequence; however, those sequences that are further away are...
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Detecting functional divergence after gene duplication through evolutionary changes in posttranslational regulatory

Alex N Nguyen Ba1, Bob Strome2, Jun Jie Hua2

  • 1Department of Cell & Systems Biology, University of Toronto, Toronto, Canada; Centre for the Analysis of Genome Evolution and Function, University of Toronto, Toronto, Canada.

Plos Computational Biology
|December 5, 2014
PubMed
Summary
This summary is machine-generated.

Gene duplication drives evolution by altering protein regulation. This study shows changes in short regulatory motifs after duplication contribute to new functions in yeast paralogs.

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Area of Science:

  • Evolutionary biology
  • Molecular biology
  • Genomics

Background:

  • Gene duplication is a key evolutionary process leading to functional divergence in gene copies (paralogs).
  • While accelerated evolution in retained paralogs is observed, the impact on molecular functions, particularly posttranslational regulation, remains unclear.
  • Short linear motifs (SLiMs) are crucial for posttranslational regulation and can evolve rapidly.

Purpose of the Study:

  • To investigate the evolutionary dynamics of SLiMs in retained gene duplicates following whole-genome duplication in budding yeast.
  • To determine if changes in SLiM evolution contribute to functional divergence between paralogs.
  • To explore the role of posttranslational regulatory changes in the evolution of gene function.

Main Methods:

  • Identification of retained gene duplicates from budding yeast whole-genome duplication.
  • Application of a likelihood-ratio test with a non-central chi-squared null distribution to detect relaxed evolutionary constraints on SLiMs.
  • Comparative analysis of SLiM evolutionary constraints in duplicates versus single-copy genes.
  • Experimental validation of predicted regulatory changes in specific paralog pairs (Ace2/Swi5).

Main Results:

  • Retained gene duplicates exhibit a higher likelihood of altered evolutionary constraints on SLiMs compared to single-copy genes.
  • Changes in SLiM constraints correlate with known differences in posttranslational regulation for paralogs like Rck1/Rck2, Fkh1/Fkh2, and Ace2/Swi5.
  • Experimental data confirmed the loss of Cbk1-regulated localization in the SWI5 lineage after duplication.

Conclusions:

  • Changes in posttranslational regulation, mediated by SLiMs, are a significant factor in functional divergence after gene duplication.
  • This study provides evidence for the systematic contribution of SLiM evolution to the emergence of new functions in duplicated genes.
  • The findings highlight the importance of studying regulatory sequence evolution to understand gene functional diversification.