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 Å3. 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.

A high-quality genome provides insights into the new taxonomic status and genomic characteristics of Cladopus chinensis (Podostemaceae)

“…Functional annotation of the protein-coding genes was carried out by using BLASTP with an E-value ≤ 1e-5 in four integrated protein sequence databases: eggNOG, GO, COG and KEGG. We used InterProScan (version 4.8) 65 and HMMER (version 3.1) 66 to annotate protein domains by searching the INTERPRO (version 32.0) 67 and Pfam (version 27.0) 68 databases. Gene Ontology (GO) terms were produced from the InterPro or Pfam entry 69 .…”

Bacterial Major Vault Protein homologs shed new light on origins of the enigmatic organelle

“…identity to MVP. This event probably has happened before the divergence of major protist groups, animals, plants and fungi (Daly et al, 2013).…”

“…Similar structure of Hyalangium protein could have been acquired convergently or due to a separate lateral gene transfer event. Then sequence of the resulting protein was laterally transmitted from cyanobacteria to early eukaryotes (most likely due to phagotrophic lifestyle of the latter ones (Shaik, 2013)) or due to an endosymbiotic event and w subsequently lost in various lineages possibly including plants and fungi (Daly et al, 2013). Future directions.…”

The Vault Nanoparticle: A Gigantic Ribonucleoprotein Assembly Involved in Diverse Physiological and Pathological Phenomena and an Ideal Nanovector for Drug Delivery and Therapy

“…In this way, they can deliver molecules stored in their interior or take up molecules from the medium, which may be relevant to their physiological functions [17]. Although not ubiquitous, vaults are highly conserved and widespread among animal and possibly plant organisms [18,19] and it is estimated that there are 10 4 to 10 5 particles per cell [4,20]. Nevertheless, their physiological roles and involvement in pathology remain only partially understood, despite extensive investigations being carried out in recent decades.…”