title: In silico resurrection of the major vault protein suggests it is ancestral in modern eukaryotes.
abstract: Vaults are very large oligomeric ribonucleoproteins conserved among a variety of species. The rat vault 3D structure shows an ovoid oligomeric particle, consisting of 78 major vault protein monomers, each of approximately 861 amino acids. Vaults are probably the largest ribonucleoprotein structures in eukaryote cells, being approximately 70 nm in length with a diameter of 40 nm--the size of three ribosomes and with a lumen capacity of 50 million Å(3). We use both protein sequences and inferred ancestral sequences for in silico virtual resurrection of tertiary and quaternary structures to search for vaults in a wide variety of eukaryotes. We find that the vault's phylogenetic distribution is widespread in eukaryotes, but is apparently absent in some notable model organisms. Our conclusion from the distribution of vaults is that they were present in the last eukaryote common ancestor but they have apparently been lost from a number of groups including fungi, insects, and probably plants. Our approach of inferring ancestral 3D and quaternary structures is expected to be useful generally.
authors.affiliation: Institute of Fundamental Sciences, Massey University, Palmerston North, New Zealand. t.daly1@massey.ac.nz
authors.forename: Toni K
authors.initials: TK
authors.lastname: Daly
authors.forename: Andrew J
authors.initials: AJ
authors.lastname: Sutherland-Smith
authors.forename: David
authors.initials: D
authors.lastname: Penny
mesh_terms: D056893:Alveolata / Q000737:chemistry; D000595:Amino Acid Sequence; D056894:Amoebozoa / Q000737:chemistry; D000818:Animals; D001426:Bacterial Proteins / Q000737:chemistry; D056897:Choanoflagellata / Q000737:chemistry; D003198:Computer Simulation; D056890:Eukaryota / Q000737:chemistry / Q000235:genetics*; D005658:Fungi / Q000737:chemistry; D017343:Genes, Plant; D008958:Models, Molecular; D008969:Molecular Sequence Data; D010802:Phylogeny; D010940:Plant Proteins / Q000737:chemistry; D020836:Protein Structure, Quaternary; D017434:Protein Structure, Tertiary; D051381:Rats; D016415:Sequence Alignment; D020394:Vault Ribonucleoprotein Particles / Q000737:chemistry* / Q000235:genetics; D000099187:Major Vault Protein
chemical_list: D001426:Bacterial Proteins; D010940:Plant Proteins; D020394:Vault Ribonucleoprotein Particles; D000099187:Major Vault Protein
keywords: BLAST; I-TASSER; RosettaDock; ancestral reconstruction (ASR); last eukaryotic common ancestor; vault ribonucleoprotein