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“Classical” view of bacteria genome

“Classical” view of bacteria genome. Single chromosome May have plasmids and phage Simple gene structure Genes have recognisable phenotype. Vibrio y Bacteriodes. Bacterial genomes come in different conformations. Circular chromosomes the traditional view: E . coli Linear chromosomes

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“Classical” view of bacteria genome

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  1. “Classical” view of bacteria genome • Single chromosome • May have plasmids and phage • Simple gene structure • Genes have recognisable phenotype Vibrio y Bacteriodes

  2. Bacterial genomes come in different conformations • Circular chromosomes • the traditional view: E. coli • Linear chromosomes • Borrelia • Plasmids • circular and linear forms

  3. Bacterial genomes can have several chromosomes • “Chromosomes must harbour some essential genes” • ribosomal RNA (rrn) • “Plasmids should not be required for viability” • only encode supplementary functions • can be very large (1-2 Mb)

  4. Bacterial genomes • Most species have one chromosome • eg E. coli • 1x circular chromosome with rrn, housekeeping genes • Some species have 2 chromosomes (a few 3) • eg Agrobacterium tumefaciens • 2x chromosomes each with rrn and housekeeping genes • 1x circular 3Mb • 1x linear 2Mb • 2x plasmids, circular 200kb, 450kb

  5. Bacterial genomes come in many different sizes • Range 0.6Mb – 9Mb • Bigger genomes encode more genes • < 2Mb specialist species • restricted ecological niche (Mycoplasma) • fastidious growth (Haemophilus influenzae) • obligate intracellular parasites (Chlamidia) • 3 – 5Mb generalist species • broad metabolic potential, few organic growth requirements (E. coli) • > 5Mb species with developmental cycles • (Streptomyces: mycelial growth, spores, complex bioactive compounds)

  6. Burkholderiaxenovorans LB400 (>20 PCBs) (recuèrada de suelo contaminado en Nueva York)

  7. General genome organization

  8. E. coli genome • Packed coding genes. Sequencing has identified 4390 protein coding genes in E. coli K-12 genome (4,6 Mb)

  9. Organization of bacterialgenomes: coding genes

  10. Organization of bacterialgenomes: non-coding genes

  11. Organization of bacterialgenomes: repeatsequences

  12. CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC SEQUENCES/ CRISPR ASSOCIATED SEQUENCES

  13. Organization of bacterialgenomes “Perhaps one of the most important lessons has been that genetic diversity, at the level of large-scale variation amongst even genomes of the same species, is far greater than was thought. The classical textbook view of evolution relying on the relatively Slow accumulation of mutational events at the level of individual bases scattered throughout the genome has changed. Thisdiversityisgeneratedby a variety of mechanisms, including mobile genetic elementsand bacteriophages.” Ten years of bacterial genome sequencing: comparative-genomics-baseddiscoveries Binnewies et al. (2006) FunctIntegrGenomics (2006) 6: 165–185

  14. Organization of bacterialgenomes: mobileelements

  15. Profagos integrados en los genomas de distintas cepas de Salmonella Typhi

  16. Genomicislands (pathogenicityislands)

  17. Organization of bacterial genomes: mobileelements (RNA intermediate) Type II Introns Retrons DGRs: Diversity-generating retroelements

  18. Coros et al. (2009) Mol Cell, 34: 250-6

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