title: Mimivirus reveals Mre11/Rad50 fusion proteins with a sporadic distribution in eukaryotes, bacteria, viruses and plasmids.
abstract: BACKGROUND
  The Mre11/Rad50 complex and the homologous SbcD/SbcC complex in bacteria play crucial roles in the metabolism of DNA double-strand breaks, including DNA repair, genome replication, homologous recombination and non-homologous end-joining in cellular life forms and viruses. Here we investigated the amino acid sequence of the Mimivirus R555 gene product, originally annotated as a Rad50 homolog, and later shown to have close homologs in marine microbial metagenomes.
  
  
  RESULTS
  Our bioinformatics analysis revealed that R555 protein sequence is constituted from the fusion of an N-terminal Mre11-like domain with a C-terminal Rad50-like domain. A systematic database search revealed twelve additional cases of Mre11/Rad50 (or SbcD/SbcC) fusions in a wide variety of unrelated organisms including unicellular and multicellular eukaryotes, the megaplasmid of a bacterium associated to deep-sea hydrothermal vents (Deferribacter desulfuricans) and the plasmid of Clostridium kluyveri. We also showed that R555 homologs are abundant in the metagenomes from different aquatic environments and that they most likely belong to aquatic viruses. The observed phyletic distribution of these fusion proteins suggests their recurrent creation and lateral gene transfers across organisms.
  
  
  CONCLUSIONS
  The existence of the fused version of protein sequences is consistent with known functional interactions between Mre11 and Rad50, and the gene fusion probably enhanced the opportunity for lateral transfer. The abundance of the Mre11/Rad50 fusion genes in viral metagenomes and their sporadic phyletic distribution in cellular organisms suggest that viruses, plasmids and transposons played a crucial role in the formation of the fusion proteins and their propagation into cellular genomes.
authors: Structural and Genomic Information Laboratory, CNRS-UPR 2589, Aix-Marseille University, Mediterranean Institute of Microbiology, 163 Avenue de Luminy, Case 934, 13288 Marseille Cedex 9, France.
authors: Takashi
authors: T
authors: Yoshida
authors: Jean-Michel
authors: JM
authors: Claverie
authors: Hiroyuki
authors: H
authors: Ogata
mesh_terms: D017766:Acid Anhydride Hydrolases; D000818:Animals; D059001:Aquatic Organisms / Q000235:genetics*; D019843:Archaeal Proteins / Q000235:genetics; D001419:Bacteria / Q000235:genetics; D001426:Bacterial Proteins / Q000235:genetics; D019295:Computational Biology; D053903:DNA Breaks, Double-Stranded; D004260:DNA Repair; D045643:DNA Repair Enzymes / Q000737:chemistry / Q000235:genetics*; D004268:DNA-Binding Proteins / Q000737:chemistry / Q000235:genetics*; D030541:Databases, Genetic; D003851:Deoxyribonucleases / Q000235:genetics; D004706:Endodeoxyribonucleases / Q000737:chemistry / Q000235:genetics*; D029968:Escherichia coli Proteins / Q000235:genetics; D005090:Exodeoxyribonucleases / Q000737:chemistry / Q000235:genetics*; D005092:Exonucleases / Q000235:genetics; D022761:Gene Transfer, Horizontal; D016679:Genome, Viral; D006801:Humans; D054892:Metagenome; D056186:Metagenomics; D056686:Mimiviridae / Q000737:chemistry / Q000235:genetics*; D010802:Phylogeny; D010957:Plasmids / Q000737:chemistry / Q000235:genetics; D029701:Saccharomyces cerevisiae Proteins / Q000737:chemistry / Q000235:genetics*; D014760:Viral Fusion Proteins / Q000737:chemistry / Q000235:genetics*; D014764:Viral Proteins / Q000737:chemistry / Q000235:genetics*
chemical_list: D019843:Archaeal Proteins; D001426:Bacterial Proteins; D004268:DNA-Binding Proteins; D029968:Escherichia coli Proteins; D029701:Saccharomyces cerevisiae Proteins; C061563:SbcC protein, Bacteria; D014760:Viral Fusion Proteins; D014764:Viral Proteins; D003851:Deoxyribonucleases; D004706:Endodeoxyribonucleases; D005090:Exodeoxyribonucleases; D005092:Exonucleases; C094191:MRE11 protein, S cerevisiae; C081229:sbcD protein, E coli; D017766:Acid Anhydride Hydrolases; C112158:RAD50 protein, human; D045643:DNA Repair Enzymes