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Related Concept Videos

Gene Evolution - Fast or Slow?02:05

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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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While every living organism has a genome of some kind (be it RNA, or DNA), there is considerable variation in the sizes of these blueprints. One major factor that impacts genome size is whether the organism is prokaryotic or eukaryotic. In prokaryotes, the genome contains little to no non-coding sequence, such that genes are tightly clustered in groups or operons sequentially along the chromosome. Conversely, the genes in eukaryotes are punctuated by long stretches of non-coding sequence.
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The evolution of new genes is critical for speciation. Exon recombination, also known as exon shuffling or domain shuffling, is an important means of new gene formation. It is observed across vertebrates, invertebrates, and in some plants such as potatoes and sunflowers. During exon recombination, exons from the same or different genes recombine and produce new exon-intron combinations, which might evolve into new genes. 
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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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Because the DNA segments are cut and reorganized in a direction-specific manner, site-specific recombination has emerged as an efficient genetic engineering technique. Flippase and Cyclization recombinases or Flp and Cre, respectively, are two members of the tyrosine recombinase family derived from bacteriophages, that are used to mediate site-specific DNA insertions, deletions, and targeted expression of proteins in mammalian cell lines.
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Directed Evolution Method in Saccharomyces cerevisiae: Mutant Library Creation and Screening
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Rapid continuous evolution of gene libraries towards arbitrary functions.

Alexander Olek Pisera, Alireza Tanoori, Chang C Liu

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    Summary
    This summary is machine-generated.

    Researchers developed OrthoRep Assisted Continuous Library Evolution (ORACLE) to rapidly evolve new gene functions. This system enables the discovery of novel gene variants with cellular functions in under 100 generations.

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    Area of Science:

    • Evolutionary Biology
    • Synthetic Biology
    • Molecular Biology

    Background:

    • The emergence of new gene functions is crucial for biological innovation but lacks experimental tools for prospective study.
    • Existing directed evolution systems often focus on single genes and functions, unlike natural evolution's complex, multi-gene approach.
    • Mimicking natural gene evolution in the lab is essential for understanding and harnessing biological innovation.

    Purpose of the Study:

    • To introduce a novel experimental system, OrthoRep Assisted Continuous Library Evolution (ORACLE), for rapid, large-scale evolution of gene functions.
    • To enable the observation and study of new gene function emergence under complex selective pressures.
    • To discover novel gene variants with new cellular functions and explore mechanisms of gene innovation.

    Main Methods:

    • Utilizing high-diversity, function-agnostic gene libraries (yeast, bacteria, plant, human).
    • Encoding libraries onto OrthoRep's p1 plasmid in yeast for rapid, durable mutation (up to 1 million times faster than the host genome).
    • Applying complex in vivo selective pressures to drive the evolution of new gene functions.

    Main Results:

    • Discovered numerous novel gene variants conferring new cellular functions within ~100 generations (<1 month).
    • Observed rapid evolution of genes into transcription factors, chaperones, and target inhibitors from initially non-phenotypic states.
    • Demonstrated the ease with which existing genetic material can acquire new functions through selection.

    Conclusions:

    • ORACLE effectively accelerates the observation of gene function evolution and innovation.
    • The system facilitates the discovery of bespoke biomolecules for various applications.
    • Provides a powerful platform for exploring fundamental mechanisms of gene innovation in vivo.