“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
– 1x linear
• 2x plasmids, circular
3Mb
2Mb
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 – 5Mb
generalist species
– broad metabolic potential, few organic growth
requirements (E. coli)
• > 5Mb
species 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
Organization of bacterial genomes
“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: 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