Abstract
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.
Highlights
Outer membrane beta barrels (OMBBs) have a remarkably homogeneous architecture
All known OMBBs in Gram-negative bacteria, save one (Dong et al, 2006), are right-handed, up-down beta barrels with the N and C termini of the barrel remaining on the membrane face from which they are inserted
We compiled a data set of 138 OMBBs at
Summary
All known OMBBs in Gram-negative bacteria, save one (Dong et al, 2006), are right-handed, up-down beta barrels with the N and C termini of the barrel remaining on the membrane face from which they are inserted. These proteins carry out all the functions necessary for the interface between the cell and its environment: adhesion, various specific and nonspecific forms of import and efflux, pilus formation, and proteolysis. The barrel’s girth is a function of strand number. Widening or narrowing the barrel changes the location of the loops, which makes for better adhesion or pilus formation.
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