Abstract
BackgroundAll cells rely on lipids for key functions. Lipid transfer proteins allow lipids to exit the hydrophobic environment of bilayers, and cross aqueous spaces. One lipid transfer domain fold present in almost all eukaryotes is the TUbular LIPid binding (TULIP) domain. Three TULIP families have been identified in bacteria (P47, OrfX2 and YceB), but their homology to eukaryotic proteins is too low to specify a common origin. Another recently described eukaryotic lipid transfer domain in VPS13 and ATG2 is Chorein-N, which has no known bacterial homologues. There has been no systematic search for bacterial TULIPs or Chorein-N domains.ResultsRemote homology predictions for bacterial TULIP domains using HHsearch identified four new TULIP domains in three bacterial families. DUF4403 is a full length pseudo-dimeric TULIP with a 6 strand β-meander dimer interface like eukaryotic TULIPs. A similar sheet is also present in YceB, suggesting it homo-dimerizes. TULIP domains were also found in DUF2140 and in the C-terminus DUF2993. Remote homology predictions for bacterial Chorein-N domains identified strong hits in the N-termini of AsmA and TamB in diderm bacteria, which are related to Mdm31p in eukaryotic mitochondria. The N-terminus of DUF2993 has a Chorein-N domain adjacent to its TULIP domain.ConclusionsTULIP lipid transfer domains are widespread in bacteria. Chorein-N domains are also found in bacteria, at the N-terminus of multiple proteins in the intermembrane space of diderms (AsmA, TamB and their relatives) and in Mdm31p, a protein that is likely to have evolved from an AsmA/TamB-like protein in the endosymbiotic mitochondrial ancestor. This indicates that both TULIP and Chorein-N lipid transfer domains may have originated in bacteria.
Highlights
All cells rely on lipids for key functions
We found that the strands make a dimerization βmeander similar to that of bactericidal/permeability increasing protein (BPI) (Fig. 2c), potentially allowing dimerization similar to eukaryotic TUbular LIPid binding (TULIP) (Fig. 2d)
The core of the TULIP in DUF2993 is shorter than other TULIPs, even shorter than DUF2140 (Fig. 3f and Additional file 1: Figure S1). These results suggest that TULIP domains are widespread in bacteria, both monoderms and diderms, most being able to dimerize by the same mechanism as BPI, and one having the same pseudodimeric form as BPI
Summary
All cells rely on lipids for key functions. Lipid transfer proteins allow lipids to exit the hydrophobic environment of bilayers, and cross aqueous spaces. One lipid transfer domain fold present in almost all eukaryotes is the TUbular LIPid binding (TULIP) domain. Three TULIP families have been identified in bacteria (P47, OrfX2 and YceB), but their homology to eukaryotic proteins is too low to specify a common origin. Another recently described eukaryotic lipid transfer domain in VPS13 and ATG2 is Chorein-N, which has no known bacterial homologues. There has been no systematic search for bacterial TULIPs or Chorein-N domains Both eukaryotic and bacterial cells require lipids to be distributed away from the site of their synthesis by lipid transfer proteins [1, 2]. Two homologous conical TULIP domains 6 nm long, ≤2.5 nm in diameter dimerize head-to-head to create an elongated cylinder with two hydrophobic pockets (Fig. 1a), Levine BMC Molecular and Cell Biology (2019) 20:43
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