Bacterial genomes

Fig.8.5

Fig.8.3

Main chromosome (nucleoid structure)

Plasmids

- usually small (<10 kb), circular DNAs

- often present in multiple copies

- carry genes with functions that are non-essential to bacteria

- independent replication

eg. antibiotic resistance

virulence factors

enzymes to synthesize toxins

See Table 8.1

Borrelia burgdorfei (Lyme disease)~1.0 Mb linear plus 14-21 small linear & circular plasmids (ranging in size from ~ 5 – 60 kb, NCBI site)

Table 8.2

Not all bacteria have single, circular chromosomes…

… so difficult to define a “bacterial genome”

If a plasmid carries essential gene(s), consider it part of genome

Girons Microbiol 140:1803, 1994

Deinococcus radiodurans 2 circular chromosomes (2.6 & 0.4 Mbp), megaplasmid (177 kb) & plasmid (46 kb)

White Science 286:1571, 1999

etc.

Small segment of H. influenza genome:

Energy metabolism

Replication

Amino acid biosynthesis

1.8 Mbp

First bacterial genome sequenced July 1995:

Haemophilus influenza

Fig.8.6

GENOME OF E.coli K12

- coloured blocks above or below line denote orientation of genes (ie. direction of transcription)

- tightly packed with genes (rarely introns in bacteria)

- genes sometimes organized as operons

- DNA transposons (IS elements)

- usually single, circular genomes in bacteria

~ 600 operons in E.coli, often encode proteins for relatedfunction or pathway (eg lac operon for lactose utilization)

(expressed as single polycistronic RNA)

- short intergenic spacers

Further blowup:

Genes on opposite strands are close, but not at exactly same location

4639 kb

~ 20 in E.coli genome

Table 8.4

CATEGORIES OF BACTERIAL GENES

Fig.8.10

RANGE OF BACTERIAL GENOME SIZES

“Native” genes Foreign DNA

eg. transposons, IS elements (insertion sequences)

DNA transposons in bacteria

Fig. 9.17

Transposons can mediate horizontal gene transfer between bacteria

Brown 2d ed Fig. 2.23

LATERAL GENE TRANSFER- movement of genes horizontally from one species to another

(vs. vertical transmission from parent to progeny)

Mediated by bacteriophages, plasmids, transposons ...

Mycobacterium leprae vs. Mycobacterium tuberculosis

Nature 409: 1007, 2001

Massive gene decay in M. leprae

And some bacteria have large number of pseudogenes…

“reductive evolution” in obligate parasites during colonization of new niche?

Welch PNAS 99:17020, 20023 strains of E.coli compared

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?

Venn diagram

Lancet Infect Diseases (published on-line Nov. 14, 2012)

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”

Hiramatsu Trends Microbiol 9:486,2001

“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.”

SCBU= special care baby unitBlack boxes: how long in hospital

Patient

Table 9.1

- vehicle for movement of genes between bacteria - use as tools in molecular biology (vectors)

Bacteriophage genomes

... with some cases of overlapping genesGenes are tightly packed in bacteriophage & viral genomes

Fig. 9.2

Gene D (capsid morphogenesis)Gene E (cell lysis)

- different reading frames are used

Mitochondria (and chloroplasts) originated from endosymbiotic bacterial ancestors

and many genes were transferred to the host nucleus

Timmis Nature Rev Genet 5:123, 2004

But the organelles retained a small number of genes essential for respiration (mito) and photosynthesis (chl)

see Fig.8.11-813