Transcript so difficult to define a “bacterial genome”

Bacterial genomes
Plasmids
Fig.8.5
- usually small (<10 kb), circular DNAs
- independent replication
Main chromosome
(nucleoid structure)
- often present in multiple copies
- carry genes with functions that are
non-essential to bacteria
eg. antibiotic resistance
virulence factors
enzymes to synthesize toxins
Fig.8.3
See Table 8.1
Not all bacteria have single, circular chromosomes…
Table 8.2
Deinococcus radiodurans
2 circular chromosomes (2.6 & 0.4 Mbp),
megaplasmid (177 kb) & plasmid (46 kb)
Borrelia burgdorfei (Lyme disease)
~1.0 Mb linear plus 14-21 small linear &
circular plasmids (ranging in size from
~ 5 – 60 kb, NCBI site)
White Science 286:1571,
1999
… so difficult to define a “bacterial genome”
etc.
Girons Microbiol 140:1803, 1994
If a plasmid carries essential gene(s), consider it part of genome
First bacterial genome sequenced July 1995:
Haemophilus influenza
1.8 Mbp
Small segment of H. influenza genome:
Energy metabolism
Replication
Amino acid biosynthesis
GENOME OF E.coli K12
4639 kb
- coloured blocks above or below line
denote orientation of genes (ie. direction
of transcription)
Further blowup:
Fig.8.6
Genes on opposite strands are
close, but not at exactly same
location
- usually single, circular genomes in bacteria
- tightly packed with genes (rarely introns in bacteria)
- short intergenic spacers
- genes sometimes organized as operons (expressed as single
polycistronic RNA)
~ 600 operons in E.coli, often encode proteins for related
function or pathway (eg lac operon for lactose utilization)
- DNA transposons (IS elements) ~ 20 in E.coli genome
CATEGORIES OF BACTERIAL GENES
Table 8.4
RANGE OF BACTERIAL GENOME SIZES
“Native” genes
Foreign DNA
eg. transposons, IS elements (insertion sequences)
Fig.8.10
DNA transposons in bacteria
Transposons can mediate horizontal gene transfer between bacteria
Fig. 9.17
LATERAL GENE TRANSFER
- movement of genes horizontally from one species to another
(vs. vertical transmission from parent to progeny)
Mediated by bacteriophages,
plasmids, transposons ...
Brown 2d ed Fig. 2.23
And some bacteria have large number of pseudogenes…
Mycobacterium leprae vs. Mycobacterium tuberculosis
Nature 409: 1007, 2001
Massive gene decay in M. leprae
“reductive evolution” in obligate parasites
during colonization of new niche?
3 strains of E.coli compared
Welch PNAS 99:17020, 2002
Venn diagram
All three are very different from each other in gene content!
- recently acquired pathogenicity genes on “islands” in genome
(enable specialized niches?)
- genomic data useful in developing effective drugs?
News release Nov. 13, 2012: “An outbreak of the hospital superbug MRSA has been brought
to an end by UK doctors cracking the bacterium's genetic code”
Lancet Infect Diseases
(published on-line Nov. 14, 2012)
Patient
Hiramatsu Trends Microbiol 9:486,2001
SCBU= special care baby unit
Black boxes: how long in hospital
“After two months without a case and deep
cleaning the ward, another case appeared.
Analysing the DNA showed that it was again
part of the outbreak and attention turned to a
carrier.”
“Tests on 154 members of staff showed that one
[red H in figure] was also carrying MRSA, which
may have been spread to babies in the unit. They
were treated to remove the infection.”
Bacteriophage genomes
Table 9.1
- use as tools in molecular biology (vectors)
- vehicle for movement of genes between bacteria
Genes are tightly packed in bacteriophage & viral genomes
... with some cases of overlapping genes
Gene D (capsid morphogenesis)
Gene E (cell lysis)
Fig. 9.2
- different reading frames are used
Mitochondria (and chloroplasts) originated from
endosymbiotic bacterial ancestors
and many genes were transferred to the host nucleus
But the organelles retained a small number of genes
essential for respiration (mito) and photosynthesis (chl)
see Fig.8.11-813
Timmis Nature Rev Genet 5:123, 2004