title: A phylogenetic analysis of the globins in fungi.
abstract: BACKGROUND
  All globins belong to one of three families: the F (flavohemoglobin) and S (sensor) families that exhibit the canonical 3/3 α-helical fold, and the T (truncated 3/3 fold) globins characterized by a shortened 2/2 α-helical fold. All eukaryote 3/3 hemoglobins are related to the bacterial single domain F globins. It is known that Fungi contain flavohemoglobins and single domain S globins. Our aims are to provide a census of fungal globins and to examine their relationships to bacterial globins.
  
  
  RESULTS
  Examination of 165 genomes revealed that globins are present in >90% of Ascomycota and ~60% of Basidiomycota genomes. The S globins occur in Blastocladiomycota and Chytridiomycota in addition to the phyla that have FHbs. Unexpectedly, group 1 T globins were found in one Blastocladiomycota and one Chytridiomycota genome. Phylogenetic analyses were carried out on the fungal globins, alone and aligned with representative bacterial globins. The Saccharomycetes and Sordariomycetes with two FHbs form two widely divergent clusters separated by the remaining fungal sequences. One of the Saccharomycete groups represents a new subfamily of FHbs, comprising a previously unknown N-terminal and a FHb missing the C-terminal moiety of its reductase domain. The two Saccharomycete groups also form two clusters in the presence of bacterial FHbs; the surrounding bacterial sequences are dominated by Proteobacteria and Bacilli (Firmicutes). The remaining fungal FHbs cluster with Proteobacteria and Actinobacteria. The Sgbs cluster separately from their bacterial counterparts, except for the intercalation of two Planctomycetes and a Proteobacterium between the Fungi incertae sedis and the Blastocladiomycota and Chytridiomycota.
  
  
  CONCLUSIONS
  Our results are compatible with a model of globin evolution put forward earlier, which proposed that eukaryote F, S and T globins originated via horizontal gene transfer of their bacterial counterparts to the eukaryote ancestor, resulting from the endosymbiotic events responsible for the origin of mitochondria and chloroplasts.
authors.affiliation: Institute of Physiology and Zürich Center for Integrative Human Physiology, University of Zürich, Zürich, Switzerland. david.hoogewijs@access.uzh.ch
authors.forename: David
authors.initials: D
authors.lastname: Hoogewijs
authors.forename: Sylvia
authors.initials: S
authors.lastname: Dewilde
authors.forename: Andy
authors.initials: A
authors.lastname: Vierstraete
authors.forename: Luc
authors.initials: L
authors.lastname: Moens
authors.forename: Serge N
authors.initials: SN
authors.lastname: Vinogradov
mesh_terms: D001419:Bacteria / Q000235:genetics; D001499:Bayes Theorem; D002175:Candida / Q000235:genetics; D019295:Computational Biology / Q000379:methods; D019143:Evolution, Molecular; D005658:Fungi / Q000235:genetics / Q000378:metabolism*; D015966:Gene Expression Regulation, Fungal; D016678:Genome; D016681:Genome, Fungal; D005914:Globins / Q000737:chemistry*; D009491:Neurospora / Q000235:genetics; D010802:Phylogeny; D017434:Protein Structure, Tertiary; D012441:Saccharomyces cerevisiae / Q000235:genetics; D016415:Sequence Alignment; D017422:Sequence Analysis, DNA; D013045:Species Specificity
chemical_list: D005914:Globins