Evidence that plant-like genes in Chlamydia species reflect an ancestral relationship between Chlamydiaceae, cyanobacteria, and the chloroplast

Genome Res. 2002 Aug;12(8):1159-67. doi: 10.1101/gr.341802.


An unusually high proportion of proteins encoded in Chlamydia genomes are most similar to plant proteins, leading to proposals that a Chlamydia ancestor obtained genes from a plant or plant-like host organism by horizontal gene transfer. However, during an analysis of bacterial-eukaryotic protein similarities, we found that the vast majority of plant-like sequences in Chlamydia are most similar to plant proteins that are targeted to the chloroplast, an organelle derived from a cyanobacterium. We present further evidence suggesting that plant-like genes in Chlamydia, and other Chlamydiaceae, are likely a reflection of an unappreciated evolutionary relationship between the Chlamydiaceae and the cyanobacteria-chloroplast lineage. Further analyses of bacterial and eukaryotic genomes indicates the importance of evaluating organellar ancestry of eukaryotic proteins when identifying bacteria-eukaryote homologs or horizontal gene transfer and supports the proposal that Chlamydiaceae, which are obligate intracellular bacterial pathogens of animals, are not likely exchanging DNA with their hosts.

Publication types

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

MeSH terms

  • Animals
  • Bacterial Proteins / chemistry
  • Bacterial Proteins / genetics
  • Base Composition / genetics
  • Caenorhabditis elegans Proteins / chemistry
  • Caenorhabditis elegans Proteins / genetics
  • Chlamydia / genetics*
  • Chlamydiaceae / genetics*
  • Chloroplasts / genetics*
  • Computational Biology / methods
  • Cyanobacteria / genetics*
  • Databases, Genetic
  • Databases, Protein
  • Drosophila Proteins / chemistry
  • Drosophila Proteins / genetics
  • Evolution, Molecular*
  • Genes, Bacterial / genetics*
  • Genes, Plant / genetics*
  • Genome, Bacterial
  • Humans
  • Mitochondria / genetics
  • Phylogeny
  • Rickettsia / genetics
  • Saccharomyces cerevisiae Proteins / chemistry
  • Saccharomyces cerevisiae Proteins / genetics
  • Sequence Homology, Amino Acid


  • Bacterial Proteins
  • Caenorhabditis elegans Proteins
  • Drosophila Proteins
  • Saccharomyces cerevisiae Proteins