New insights into the evolutionary history of type 1 rhodopsins

J Mol Evol. 2004 Mar;58(3):348-58. doi: 10.1007/s00239-003-2557-8.


Type 1 (archaeal) rhodopsins and related rhodopsin-like proteins had been described in a few halophile archaea, gamma-proteobacteria, a single cyanobacteria, some fungi, and a green alga. In exhaustive database searches, we detected rhodopsin-related sequences derived not only from additional fungal species but also from organisms belonging to three groups in which opsins had hitherto not been described: the alpha-proteobacterium Magnetospirillum magnetotacticum, the cryptomonad alga Guillardia theta, and the dinoflagellate Pyrocystis lunula. Putative plant and human type 1 rhodopsin sequences found in the databases are demonstrated to be contaminants of fungal origin. However, a highly diverged sequence supposedly from the plant Oryza sativa was found that is, together with the Pyrocystis sequence, quite similar to gamma-proteobacterial rhodopsins. These close relationships suggest that at least one horizontal gene transfer event involving rhodopsin genes occurred between prokaryotes and eukaryotes. Alternative hypotheses to explain the current phylogenetic range of type 1 rhodopsins are suggested. The broader phylogenetic range found is compatible with an ancient origin of type 1 rhodopsins, their patchy distribution being caused by losses in multiple lineages. However, the possibility of ancient horizontal transfer events between distant relatives cannot be dismissed.

Publication types

  • Comparative Study
  • Research Support, Non-U.S. Gov't

MeSH terms

  • Amino Acid Sequence
  • Archaea / genetics
  • Bacteria / genetics
  • Chlorophyta / genetics
  • Cluster Analysis
  • Databases, Nucleic Acid
  • Evolution, Molecular*
  • Fungi / genetics
  • Gene Transfer, Horizontal / genetics*
  • Likelihood Functions
  • Models, Genetic
  • Molecular Sequence Data
  • Oryza / genetics
  • Phylogeny*
  • Rhodopsins, Microbial / genetics*
  • Sequence Alignment


  • Rhodopsins, Microbial