How the archaea got their lipids

At first glance, bacteria and archaea look very much alike. But these prokaryotes are actually quite different. One striking difference is the composition of lipids in their cell membranes. This has raised the question of which lipids were present in the last common ancestor of Bacteria and Archaea. University of Groningen microbiologists, and their colleagues from Sichuan University, China, have discovered a clue which sheds light on how evolution created the ‘lipid divide’. The results were published on 29 September in the journal Cell Research.

The archaea, prokaryotes that are usually found in extreme environments such as volcanic hot springs or salt lakes, were first classified as a kind of primitive bacteria and called ‘archaebacteria’. But in 1977 they were classified as a separate kingdom of life and renamed Archaea, alongside Bacteria and Eukarya.

The evolutionary history of Archaea is complicated, and one thing that has puzzled microbiologists is why the lipid composition of the cell membrane differs between Bacteria and Archaea. Both have a membrane that is composed of glycerol phosphate phospholipids, but Bacteria make this from glycerol-1-phosphate, while Archaea use glycerol-3-phosphate. This results in phospholipids that are each other’s mirror image. Furthermore, the hydrophobic tails attached to the glycerol phosphate heads are of a different chemical composition.

Unique

‘Bacteria and Archaea produce their membrane lipids through pathways that are similar, but use very different enzymes’, explains University of Groningen Professor of Molecular Microbiology Arnold Driessen. The first three steps, in which long tails are attached to the glycerol phosphate head, are mediated by enzymes unique to either Bacteria or Archaea. The enzymes that subsequently modify the membrane lipids are exchangeable between the two kingdoms.

Driessen: ‘The first two enzymes have been described. They appear totally unrelated, even though they perform a very similar role.’ Some time ago, Driessen’s group identified the third enzyme, CDP-archaeol synthase (CarS). Now, with the assistance of scientists from Sichuan University, they have elucidated the 3D structure of this enzyme. ‘The amino acid sequence is again totally different from the equivalent bacterial enzyme. Yet the structure reveals quite a few similarities, for example in binding sites.’ This suggests that the enzymes in Bacteria and Archaea do share a common lineage.

Selective

‘We think that the common ancestor of Bacteria and Archaea had enzymes which were not very selective’, explains Driessen. The membrane of the last common ancestor must therefore have been composed of two different types of lipid, based on both glycerol-1-phosphate and glycerol-3-phosphate. After the two kingdoms split, these enzymes evolved a higher specificity in a parallel fashion, but for different substrates. This resulted in two different and uniform membranes. ‘So the evolution of more specific enzymes created the “lipid divide” between Bacteria and Archaea.’

Reference: Sixue Ren, Antonella Caforio, Qin Yang, Bo Sun, Feng Yu, Xiaofeng Zhu, Jinjing Wang, Chao Dou, Qiuyu Fu, Niu Huang, Qiu Sun, Chunlai Nie, Shiqian Qi, Xinqi Gong, Jianhua He, Yuquan Wei, Arnold JM Driessen & Wei Cheng: Structural and mechanistic insights into the biosynthesis of CDP-archaeol in membranes. Cell Research 29 September 2017, DOI: 10.1038/cr.2017.122