A Distinct Abundant Group of Microbial Rhodopsins Discovered Using Functional Metagenomics

Nature. 2018 Jun;558(7711):595-599. doi: 10.1038/s41586-018-0225-9. Epub 2018 Jun 20.

Abstract

Many organisms capture or sense sunlight using rhodopsin pigments1,2, which are integral membrane proteins that bind retinal chromophores. Rhodopsins comprise two distinct protein families 1 , type-1 (microbial rhodopsins) and type-2 (animal rhodopsins). The two families share similar topologies and contain seven transmembrane helices that form a pocket in which retinal is linked covalently as a protonated Schiff base to a lysine at the seventh transmembrane helix2,3. Type-1 and type-2 rhodopsins show little or no sequence similarity to each other, as a consequence of extensive divergence from a common ancestor or convergent evolution of similar structures 1 . Here we report a previously unknown and diverse family of rhodopsins-which we term the heliorhodopsins-that we identified using functional metagenomics and that are distantly related to type-1 rhodopsins. Heliorhodopsins are embedded in the membrane with their N termini facing the cell cytoplasm, an orientation that is opposite to that of type-1 or type-2 rhodopsins. Heliorhodopsins show photocycles that are longer than one second, which is suggestive of light-sensory activity. Heliorhodopsin photocycles accompany retinal isomerization and proton transfer, as in type-1 and type-2 rhodopsins, but protons are never released from the protein, even transiently. Heliorhodopsins are abundant and distributed globally; we detected them in Archaea, Bacteria, Eukarya and their viruses. Our findings reveal a previously unknown family of light-sensing rhodopsins that are widespread in the microbial world.

Publication types

  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Eukaryota / chemistry
  • Evolution, Molecular
  • Metagenomics*
  • Rhodopsin / analysis*
  • Rhodopsin / chemistry
  • Rhodopsin / classification*
  • Rhodopsin / radiation effects
  • Rhodopsins, Microbial / analysis
  • Rhodopsins, Microbial / chemistry
  • Rhodopsins, Microbial / classification
  • Rhodopsins, Microbial / radiation effects

Substances

  • Rhodopsins, Microbial
  • Rhodopsin