title: Horizontal gene transfer and genome evolution in Methanosarcina.
abstract: BACKGROUND
  Genomes of Methanosarcina spp. are among the largest archaeal genomes. One suggested reason for that is massive horizontal gene transfer (HGT) from bacteria. Genes of bacterial origin may be involved in the central metabolism and solute transport, in particular sugar synthesis, sulfur metabolism, phosphate metabolism, DNA repair, transport of small molecules etc. Horizontally transferred (HT) genes are considered to play the key role in the ability of Methanosarcina spp. to inhabit diverse environments. At the moment, genomes of three Methanosarcina spp. have been sequenced, and while these genomes vary in length and number of protein-coding genes, they all have been shown to accumulate HT genes. However, previous estimates had been made when fewer archaeal genomes were known. Moreover, several Methanosarcinaceae genomes from other genera have been sequenced recently. Here, we revise the census of genes of bacterial origin in Methanosarcinaceae.
  
  
  RESULTS
  About 5% of Methanosarcina genes have been shown to be horizontally transferred from various bacterial groups to the last common ancestor either of Methanosarcinaceae, or Methanosarcina, or later in the evolution. Simulation of the composition of the NCBI protein non-redundant database for different years demonstrates that the estimates of the HGT rate have decreased drastically since 2002, the year of publication of the first Methanosarcina genome. The phylogenetic distribution of HT gene donors is non-uniform. Most HT genes were transferred from Firmicutes and Proteobacteria, while no HGT events from Actinobacteria to the common ancestor of Methanosarcinaceae were found. About 50% of HT genes are involved in metabolism. Horizontal transfer of transcription factors is not common, while 46% of horizontally transferred genes have demonstrated differential expression in a variety of conditions. HGT of complete operons is relatively infrequent and half of HT genes do not belong to operons.
  
  
  CONCLUSIONS
  While genes of bacterial origin are still more frequent in Methanosarcinaceae than in other Archaea, most HGT events described earlier as Methanosarcina-specific seem to have occurred before the divergence of Methanosarcinaceae. Genes horizontally transferred from bacteria to archaea neither tend to be transferred with their regulators, nor in long operons.
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia. garushyants@iitp.ru.
authors.forename: Sofya K
authors.initials: SK
authors.lastname: Garushyants
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia. mkazanov@gmail.com.
authors.forename: Marat D
authors.initials: MD
authors.lastname: Kazanov
authors.affiliation: A.A. Kharkevich Institute for Information Transmission Problems, RAS, Bolshoi Karetny per. 19, build.1, Moscow, 127051, Russia. gelfand@iitp.ru.|Faculty of Bioengineering and Bioinformatics, M.V. Lomonosov Moscow State University, Vorobievy Gory 1-73, Moscow, 119991, Russia. gelfand@iitp.ru.
authors.forename: Mikhail S
authors.initials: MS
authors.lastname: Gelfand
mesh_terms: D001105:Archaea / Q000145:classification / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D030541:Databases, Genetic; D019143:Evolution, Molecular; D022761:Gene Transfer, Horizontal; D020745:Genome, Archaeal; D017020:Methanosarcina / Q000235:genetics*; D009876:Operon; D010802:Phylogeny