title: Topological and phylogenetic analyses of bacterial holin families and superfamilies.
abstract: Holins are small "hole-forming" transmembrane proteins that mediate bacterial cell lysis during programmed cell death or following phage infection. We have identified fifty two families of established or putative holins and have included representative members of these proteins in the Transporter Classification Database (TCDB; www.tcdb.org). We have identified the organismal sources of members of these families, calculated their average protein sizes, estimated their topologies and determined their relative family sizes. Topological analyses suggest that these proteins can have 1, 2, 3 or 4 transmembrane α-helical segments (TMSs), and members of a single family are frequently, but not always, of a single topology. In one case, proteins of a family proved to have either 2 or 4 TMSs, and the latter arose by intragenic duplication of a primordial 2 TMS protein-encoding gene resembling the former. Using established statistical approaches, some of these families have been shown to be related by common descent. Seven superfamilies, including 21 of the 52 recognized families were identified. Conserved motif and Pfam analyses confirmed most superfamily assignments. These results serve to expand upon the scope of channel-forming bacterial holins.
authors.affiliation: Department of Molecular Biology, Division of Biological Sciences, University of California at San Diego, La Jolla, CA 92093-0116, USA; Department of Mathematics and Natural Sciences, College of Letters and Sciences, National University, Ontario, CA 91764, USA.
authors.forename: Bhaskara L
authors.initials: BL
authors.lastname: Reddy
authors.forename: Milton H
authors.initials: MH
authors.lastname: Saier
mesh_terms: D000595:Amino Acid Sequence; D001419:Bacteria / Q000737:chemistry* / Q000145:classification; D001426:Bacterial Proteins / Q000737:chemistry* / Q000145:classification; D008565:Membrane Proteins / Q000737:chemistry* / Q000145:classification; D008969:Molecular Sequence Data; D010802:Phylogeny; D017386:Sequence Homology, Amino Acid
chemical_list: D001426:Bacterial Proteins; D008565:Membrane Proteins
keywords: Autolysin; Holin; Phylogeny; Superfamily; Transmembrane pore; “Hole-forming”