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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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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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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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DNA-only transposons are called autonomous transposons since they code for the enzyme transposase that is required for the transposition mechanism. Insertion of transposons can alter gene functions in multiple ways. They can mutate the gene, alter gene expression by introducing a novel promoter or insulator sequence, introduce new splice sites, and change the mRNA transcripts produced, or remodel chromatin structure.
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Transposons make up a significant part of genomes of various organisms. Therefore, it is believed that transposition played a major evolutionary role in speciation by changing genome sizes and modifying gene expression patterns. For example, in bacteria, transposition can lead to conferring antibiotic resistance. Movement of transposable elements within the genetic pool of pathogenic bacteria can aid in transfer of antibiotic-resistant genetic elements. In eukaryotes, transposons can carry out...
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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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Las inversiones de ADN intragénico amplían la capacidad de codificación bacteriana

Rachael B Chanin1, Patrick T West1, Jakob Wirbel1

  • 1Department of Medicine, Division of Hematology, Stanford University, Stanford, CA, USA.

Nature
|September 25, 2024
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Resumen

Las bacterias generan diversidad usando inversiones de ADN, un proceso llamado variación de fase. Los investigadores descubrieron nuevos invertones intragénicos dentro de los genes, expandiendo la diversidad de proteínas bacterianas sin aumentar el tamaño del genoma.

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Área de la Ciencia:

  • Microbiología
  • La genómica
  • La bioinformática

Sus antecedentes:

  • Las poblaciones bacterianas exhiben heterogeneidad, no clonalidad estricta, debido a mecanismos como la variación de fase.
  • La variación de fase, a menudo mediada por inversiones de ADN, altera la expresión génica e impacta la aptitud y supervivencia bacteriana.
  • Las inversiones de ADN pueden invertir las orientaciones de los promotores, controlando la transcripción génica.

Objetivo del estudio:

  • Desarrollar una herramienta computacional (PhaVa) para identificar inversiones de ADN en datos de secuenciación de larga lectura.
  • Descubrir y caracterizar una nueva clase de inversiones de ADN, denominadas "invertones intragénicos", ubicadas dentro de los genes.

Principales métodos:

  • Desarrollo de la herramienta computacional PhaVa para la detección de la inversión del ADN.
  • Análisis de conjuntos de datos de secuenciación de larga lectura de aislamientos bacterianos y arqueológicos.
  • Validación experimental de los invertones intragénicos identificados en *Bacteroides thetaiotaomicron*.

Principales resultados:

  • Identificación de 372 nuevos inversionistas intragénicos en diversos genomas bacterianos y arqueos.
  • Demostración de que los invertones intragénicos permiten a los genes codificar múltiples variantes de proteínas al invertir las secuencias internas de ADN.
  • Validación experimental de diez invertones intragénicos y caracterización de uno en el gen *thiC*.

Conclusiones:

  • Los invertones intragénicos representan un descubrimiento significativo, expandiendo la capacidad de codificación de los genomas bacterianos.
  • PhaVa es una herramienta valiosa para identificar las inversiones de ADN, lo que facilita la investigación adicional sobre la dinámica del genoma bacteriano.
  • Este mecanismo proporciona a las bacterias una nueva estrategia para generar diversidad de proteínas y adaptarse a los cambios ambientales.