Inferring Cases of Lineage-Specific Adaptive Evolution in Genomes of

Planctomycete Bacteria

Olga K Kamneva

Contributed Talk

Co-Authors: David Liberles; Naomi Ward

Organisms of the bacterial phylum Planctomycetes exhibit features

atypical for bacteria. They lack cell wall peptidoglycans, reproduce by
budding, and have a unique cell organization. The planctomycete
Gemmata obscuriglobus has an especially unusual cell plan, featuring
an intracellular compartment surrounded by a double-layered
membrane, and containing condensed genomic DNA. Here we report
an investigation into the evolutionary history of the phylum
Planctomycetes and the species G. obscuriglobus. Our central
hypothesis is that if genes responsible for
Planctomycetes/G.obscuriglobus-specific morphological and
physiological features are present in other bacteria lacking these
features they should be different in copy number and/or sequence
(including both substitutions and indels). We tested this hypothesis
through comparative analysis of all currently available planctomycete
genomes and reference genomes from other bacterial phyla, using
several approaches. We identified and characterized genes containing
insertions or deletions on Planctomycetes/G.obscuriglobus lineages.
Insertions were found in genes plausibly connected to the unique cell
plans found in Planctomycetes in general, and G. obscuriglobus in
particular and were characterized in terms of lineage-specific rate and
length distribution. Some examples include insertions on the
Planctomycetes lineage in genes orthologous to those involved in
peptidoglycan biosynthesis and remodeling. Given that
planctomycetes lack cell wall peptidoglycans, this suggests that
insertions in these genes may have facilitated evolution of new
enzymatic function. The substrate and specific biochemical activity of
the encoded proteins remains undetermined, but could plausibly be
connected to the unique planctomycete cell plan. We also examined
gene family expansion on Planctomycetes/ G.obscuriglobus lineages.
Our results indicate that the number of G. obscuriglobus genes
belonging to multi-copy gene families is greater than would be
expected based on genome size alone. We are currently engaged in
further characterization of these lineage-specific gene family
expansions.