Seth Bordenstein
Departments of Biological Sciences &
Pathology, Microbiology, and Immunology
s.bordenstein@vanderbilt.edu
February 11, 2012
How do bacterial genomes change during symbiosis?
Insertions of
DNA from
foreign sources;
Duplications
Single nt
mutations
Gene loss / Genome reduction
The Genome Sizes of Life
Protein Coding Genes
Rule 1: Genome Size Variation
Correlates with Gene Number
Variation
Genome Size (Mb)
Rule 2: Bacterial Ecology Alters
Genome Evolution
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
Diagram modified from Mira, A., Ochman, H. & Moran, N.A. 2001.
Trends Genet 17, 589-96.
Rule 3: Bacterial Mobile DNAs Are
The Agents of Open Source Evolution
Plasmid
Bacteriophage
Transposon
Ecology Affects Mobile DNA Abundance
Free-living Bacteria
• Exposure to other microbes
• Horizontal Gene Transfer
• Mobile DNA
Obligate Intracellular Bacteria
• Reduced exposure to other
microbes
• Genome Reduction
• Genome Stability
DNA Inflow
DNA Outflow
Eukaryotic
cell
DNA Inflow?
Mobile DNA?
Diagram modified from Mira, A., Ochman, H. & Moran, N.A. 2001.
Trends Genet 17, 589-96.
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 Life
How variable are mobile DNA contents in Bacteria?
% Transposon
% Prophage
% Plasmid
Newton & Bordenstein 2011
Is Mobile DNA Gene
Density Independent
of Phylogeny?
16S rRNA Tree &
Mobile DNA %
K statistic
Full dataset, K = 0.0024
K > 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?
Three Bacterial Ecotypes
Facultative
Extracellular
Free-living world
Intracellular world
Facultative
Obligate
Intracellular
Newton & Bordenstein 2011
Extracellular
Facultative
Free-living world
Intracellular world
Facultative
Mobile DNA Density (%)
4
Obligate
P < 0.005
3
P < 0.001
2
1
N = 74
N = 270
N = 40
0
Facultative
>
Extracellular
>
Obligate