Olga Smbe 2009 Talk

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.