february 11, 2012 seth bordenstein departments of biological sciences & pathology, microbiology,...
TRANSCRIPT
Viral Evolution in Endosymbionts
February 11, 2012
Seth BordensteinDepartments of Biological Sciences &Pathology, Microbiology, and [email protected]
Symbiosis: “The living together of dissimilar organisms” de Bary 1879
Gene loss / Genome reduction
How do bacterial genomes change during symbiosis?
Single nt mutations
Insertions of DNA from foreign sources;Duplications
The Genome Sizes of Life
Rule 1: Genome Size Variation Correlates with Gene Number Variation
Genome Size (Mb)
Prot
ein
Codi
ng G
enes
Rule 2: Bacterial Ecology Alters Genome Evolution
Diagram modified from Mira, A., Ochman, H. & Moran, N.A. 2001. Trends Genet 17, 589-96.
DNA Inflow DNA Outflow
Eukaryotic cell • Mutation bias for
DNA deletions
• Relaxed selection on redundant genes between bacteria and host
• Reduced exposure to novel gene pools
Bacteriophage TransposonPlasmid
Rule 3: Bacterial Mobile DNAs AreThe Agents of Open Source Evolution
Ecology Affects Mobile DNA Abundance
• Exposure to other microbes• Horizontal Gene Transfer• Mobile DNA
• Reduced exposure to other microbes
• Genome Reduction• Genome Stability
Free-living Bacteria Obligate Intracellular Bacteria
Diagram modified from Mira, A., Ochman, H. & Moran, N.A. 2001. Trends Genet 17, 589-96.
DNA Inflow DNA Outflow
Eukaryotic cell
DNA Inflow?Mobile DNA?
Three Questions
• How variable are mobile DNA contents in Bacteria?
• Does this variation statistically associate with phylogeny, genome size, or ecology?
• How do mobile elements survive and flourish in obligate, intracellular bacteria?
The Genomes of LifeBACTERI
A2622
GenomesARCHAEA
147 Genomes
EUCARYA166
Genomes
How variable are mobile DNA contents in Bacteria?
% Transposon % Prophage % PlasmidNewton & Bordenstein 2011
Is Mobile DNA Gene Density Independent
of Phylogeny?
16S rRNA Tree & Mobile DNA %
K statistic
Full dataset, K = 0.0024K > 1 is significant association
Mobile DNA % is scattered randomly across the tree
Newton & Bordenstein 2011
Do Constraints in Ecology Vary with Mobile DNA
Gene Density?
Facultative
Intracellular world
Facultative Extracellular
Free-living world
ObligateIntracellular
Three Bacterial Ecotypes
Facultative Extracellular Obligate0
1
2
3
4
Mo
bil
e D
NA
De
ns
ity
(%
)
> >
P < 0.001
P < 0.005
N = 270N = 74 N = 40
Newton & Bordenstein 2011
FacultativeIntracellular world
Free-living world
Obligate
Facultative Extracellular