Systematic comparison of unilamellar vesicles reveals that archaeal core lipid membranes are more permeable than bacterial membranes

Abstract

One of the deepest branches in the tree of life separates the Archaea from the Bacteria. These prokaryotic groups have distinct cellular systems including fundamentally different phospholipid membrane bilayers. This dichotomy has been termed the lipid divide and possibly bestows different biophysical and biochemical characteristics on each cell type. Classic experiments suggest that bacterial membranes (formed from lipids extracted from Escherichia coli, for example) show permeability to key metabolites comparable to archaeal membranes (formed from lipids extracted from Halobacterium salinarum), yet systematic analyses based on direct measurements of membrane permeability are absent. Here, we develop a new approach for assessing the membrane permeability of approximately 10 μm unilamellar vesicles, consisting of an aqueous medium enclosed by a single lipid bilayer. Comparing the permeability of 18 metabolites demonstrates that diether glycerol-1-phosphate lipids with methyl branches, often the most abundant membrane lipids of sampled archaea, are permeable to a wide range of compounds useful for core metabolic networks, including amino acids, sugars, and nucleobases. Permeability is significantly lower in diester glycerol-3-phosphate lipids without methyl branches, the common building block of bacterial membranes. To identify the membrane characteristics that determine permeability, we use this experimental platform to test a variety of lipid forms bearing a diversity of intermediate characteristics. We found that increased membrane permeability is dependent on both the methyl branches on the lipid tails and the ether bond between the tails and the head group, both of which are present on the archaeal phospholipids. These permeability differences must have had profound effects on the cell physiology and proteome evolution of early prokaryotic forms. To explore this further, we compare the abundance and distribution of transmembrane transporter-encoding protein families present on genomes sampled from across the prokaryotic tree of life. These data demonstrate that archaea tend to have a reduced repertoire of transporter gene families, consistent with increased membrane permeation. These results demonstrate that the lipid divide demarcates a clear difference in permeability function with implications for understanding some of the earliest transitions in cell origins and evolution.

Phage-induced efflux down-regulation boosts antibiotic efficacy

“…Moreover, temperate phage activity is known to enhance antibiotic efficacy through depletion of lysogens 32 . Although we found evidence of prophage ΦE125 and ΦE12-2 85,86 , it is unlikely that depletion of ΦE125 or ΦE12-2 lysogens plays a role in our experiments since we did not find evidence of plaque formation in the presence of ciprofloxacin, that is a lysogen activating antibiotic 32 , in the absence of ΦBp-AMP1.…”

“…These bacteria were then introduced in the central channel of the mother machine device from where they reached the lateral channel at an average concentration of one bacterium per channel 84 . Next, the device was mounted on an inverted microscope (IX73 Olympus, Tokyo, Japan) located in a temperature-controlled chamber kept at 37 °C 85 . Fluorinated ethylene propylene tubing (1/32” × 0.008”) was connected to the device as inlet and outlet tubes further connected to a computerised pressure-based flow control system (MFCS-4C, Fluigent) 86 .…”

“…Simultaneously, bright field images of 20 areas of the mother machine, each containing 23 lateral channels were acquired at 2 min intervals via a 60× 1.2 N.A. objective (UPLSAPO60XW, Olympus) and an sCMOS camera with an exposure time of 0.01 s (Zyla 4.2, Andor, Belfast, United Kingdom) controlled via Labview 109,110 . This microfluidics-microscopy platform was also used to quantify the accumulation of ciprofloxacin as previously reported 52,111,112 .…”

Membrane permeability selection drove the stereochemistry of life

“…Here, we expand such comparisons to a range of compounds useful for proto-metabolism and focus on archaeal and hybrid membrane mimics. We focus on these two membrane mimics because our previous experiments show they display the highest permeability [61]. The aim of this work is to test the hypothesis that membrane chemistry imposes permeability selection on enantiomers.…”

Engineering semi-permeable giant liposomes

“…21 Membranes composed of unsaturated lipids are revealed to exhibit enantioselective permeability to sugars, simple carbohydrates, 22 and dipeptides. 23 Modulating the physical properties of the membrane by lipids made of unsaturated chains, 23 short chain length lipids, 24 branched lipids, 25 and single chain amphiphiles 26,27 can also impart permeability to vesicles.…”