Classical view of bacteria genome
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“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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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

Bacterial genomes come in different conformations

  • Circular chromosomes

    • the traditional view: E. coli

  • Linear chromosomes

    • Borrelia

  • Plasmids

    • circular and linear forms


Bacterial genomes can have several chromosomes

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)


Bacterial genomes

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


Bacterial genomes come in many different sizes

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 – 5Mbgeneralist species

    • broad metabolic potential, few organic growth requirements (E. coli)

  • > 5Mbspecies with developmental cycles

    • (Streptomyces: mycelial growth, spores, complex bioactive compounds)


Classical view of bacteria genome

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


Classical view of bacteria genome

General genome

organization


E coli genome

E. coli genome

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


Classical view of bacteria genome

Organization of bacterialgenomes: coding genes


Classical view of bacteria genome

Organization of bacterialgenomes: non-coding genes


Classical view of bacteria genome

Organization of bacterialgenomes: repeatsequences


Classical view of bacteria genome

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC SEQUENCES/

CRISPR ASSOCIATED SEQUENCES


Classical view of bacteria genome

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


Classical view of bacteria genome

Organization of bacterialgenomes: mobileelements


Classical view of bacteria genome

Profagos integrados en los genomas de distintas cepas de

Salmonella Typhi


Classical view of bacteria genome

Genomicislands (pathogenicityislands)


Classical view of bacteria genome

Organization of bacterial

genomes: mobileelements

(RNA intermediate)

Type II Introns

Retrons

DGRs: Diversity-generating

retroelements


Classical view of bacteria genome

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


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