Lectures for 4Y03 (a) Efficiency in Bacterial Cells (b)Codon Usage Bias (c) Mitochondrial Genomes
Bacterial genomes
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Transcript of Bacterial genomes
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