“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 – Borrelia Plasmids – circular and linear forms

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 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 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)

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

General genome organization

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

Organization of bacterial genomes: coding genes

Organization of bacterial genomes: non-coding genes

Organization of bacterial genomes: repeat sequences

CLUSTERED REGULARLY INTERSPACED SHORT PALINDROMIC SEQUENCES/ CRISPR ASSOCIATED SEQUENCES

“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. This diversity is generated by a variety of mechanisms, including mobile genetic elements and bacteriophages.” Ten years of bacterial genome sequencing: comparative-genomics-based discoveries Binnewies et al. (2006) Funct Integr Genomics (2006) 6: 165–185 Organization of bacterial genomes

Organization of bacterial genomes: mobile elements

Profagos integrados en los genomas de distintas cepas de Salmonella Typhi

Genomic islands (pathogenicity islands)

Organization of bacterial genomes: mobile elements (RNA intermediate) Type II Introns Retrons DGRs: Diversity-generating retroelements

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