title: Phylogenetic analysis of the formin homology 2 domain.
abstract: Formin proteins are key regulators of eukaryotic actin filament assembly and elongation, and many species possess multiple formin isoforms. A nomenclature system based on fundamental features would be desirable, to aid the rapid identification and characterization of novel formins. In this article, we attempt to systematize the formin family by performing phylogenetic analyses of the formin homology 2 (FH2) domain, an independently folding region common to all formins, which alone can influence actin dynamics. Through database searches, we identify 101 FH2 domains from 26 eukaryotic species, including 15 in mice. Sequence alignments reveal a highly conserved yeast-specific insert in the "knob loop" region of the FH2 domain, with unknown functional consequences. Phylogenetic analysis using minimum evolution (ME), maximum parsimony (MP), and maximum likelihood (ML) algorithms strongly supports the existence of seven metazoan groups. Yeast FH2 domains segregate from all other eukaryotes, including metazoans, other fungi, plants, and protists. Sequence comparisons of non-FH2 regions support relationships between three metazoan groups (Dia, DAAM, and FRL) and examine previously identified coiled-coil and Diaphanous auto-regulatory domain sequences. This analysis allows for a formin nomenclature system based on sequence relationships, as well as suggesting strategies for the determination of biochemical and cellular activities of these proteins.
authors.affiliation: Department of Biochemistry, Dartmouth Medical School, Hanover, NH 03755, USA. henry.n.higgs@dartmouth.edu
authors.forename: Henry N
authors.initials: HN
authors.lastname: Higgs
authors.forename: Kevin J
authors.initials: KJ
authors.lastname: Peterson
mesh_terms: D048868:Adaptor Proteins, Signal Transducing / Q000737:chemistry*; D000465:Algorithms; D000595:Amino Acid Sequence; D000818:Animals; D019295:Computational Biology; D019992:Databases as Topic; D005656:Fungal Proteins / Q000737:chemistry; D006801:Humans; D016013:Likelihood Functions; D008958:Models, Molecular; D008969:Molecular Sequence Data; D009419:Nerve Tissue Proteins / Q000737:chemistry*; D010802:Phylogeny; D011487:Protein Conformation; D017434:Protein Structure, Tertiary; D017386:Sequence Homology, Amino Acid; D009626:Terminology as Topic
chemical_list: D048868:Adaptor Proteins, Signal Transducing; D005656:Fungal Proteins; D009419:Nerve Tissue Proteins