Gram-negative outer membrane proteins with multiple β-barrel domains

Abstract

Outer membrane beta barrels (OMBBs) are found in the outer membrane of Gram-negative bacteria and eukaryotic organelles. OMBBs fold as antiparallel β-sheets that close onto themselves, forming pores that traverse the membrane. Currently known structures include only one barrel, of 8-36 strands, per chain. The lack of multi-OMBB chains is surprising, as most OMBBs form oligomers and some function only in this state. Using a combination of sensitive sequence-comparison methods and co-evolutionary analysis tools, we identify many proteins combining multiple beta barrels within a single chain; combinations that include 8-stranded barrels prevail. These multi-barrels seem to be the result of independent, lineage-specific fusion and amplification events. The absence of multi-barrels that are universally conserved in bacteria with an outer membrane, coupled with their frequent de novo genesis suggests that their functions are not essential, but rather beneficial in specific environments. Adjacent barrels of complementary function within the same chain may allow for new functions beyond those of the individual barrels.

Bacterial outer-membrane polysaccharide export (OPX) proteins occupy three structural classes with selective β-barrel porin requirements for polymer secretion

“…The separate yjbEFGH (paralogous to gfcABCD) operon implicated in polysaccharide secretion encodes the GfcD-like protein YjbH (Ferrières et al, 2007). Both GfcD and YjbH are β-barrel proteins, which were recently identified to be part of a novel class of OM proteins (lacking published structures) with two separate β-barrels predicted to be formed by the same polypeptide chain (Solan et al, 2021). Herein, fold-recognition analysis revealed the N-terminal halves to be matches to the β-barrel amyloid transporter FapF from Pseudomonas, whereas the C-terminal halves (GfcDCterβb and YjbHCterβb, respectively) possessed structural homology to the PNAG PgaAβb module described above (Supplementary Fig.…”

Proteins with multiple G protein-coupled receptor domains

“…We recently identified proteins from another class of membrane proteins -multiple outer membrane beta-barrels (OMBBs) -with multi-domain architectures [16]. We discovered more than 30 multi-OMBBs in Gram-negative bacteria, some with up to 11 OMBB domains in one chain.…”

“…If dimerization is necessary for function of certain GPCRs, there may be proteins with two or more GPCR domains concatenated on the same chain. This possibility is supported by our recent discovery of another class of multi-domain membrane proteins -bacterial outer membrane proteins with multiple beta-barrel domains [16]. To discover these bacterial multi-domain proteins, we modeled all structurally characterized outer membrane beta-barrels as hidden Markov models (HMMs) and searched in the UniRef database for proteins with non-overlapping matches to two or more beta-barrel HMMs.…”