Evolutionary pathways of repeat protein topology in bacterial outer membrane proteins

• Main Authors: Meghan Whitney Franklin, Sergey Nepomnyachyi, Ryan Feehan, Nir Ben-Tal, Rachel Kolodny, Joanna SG Slusky
• Format: Article
• Language: English
• Published: eLife Sciences Publications Ltd 2018-11-01
• Series: eLife
• Subjects: outer membrane proteins; beta barrels; repeat proteins; beta hairpin; outer membrane beta barrels
• Online Access: https://elifesciences.org/articles/40308

Outer membrane proteins (OMPs) are the proteins in the surface of Gram-negative bacteria. These proteins have diverse functions but a single topology: the β-barrel. Sequence analysis has suggested that this common fold is a β-hairpin repeat protein, and that amplification of the β-hairpin has resulted in 8–26-stranded barrels. Using an integrated approach that combines sequence and structural analyses, we find events in which non-amplification diversification also increases barrel strand number. Our network-based analysis reveals strand-number-based evolutionary pathways, including one that progresses from a primordial 8-stranded barrel to 16-strands and further, to 18-strands. Among these pathways are mechanisms of strand number accretion without domain duplication, like a loop-to-hairpin transition. These mechanisms illustrate perpetuation of repeat protein topology without genetic duplication, likely induced by the hydrophobic membrane. Finally, we find that the evolutionary trace is particularly prominent in the C-terminal half of OMPs, implicating this region in the nucleation of OMP folding.