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

Abstract

Vaults are large cone-shaped and highly conservative ribonucleoprotein complexes present in the cells of most major eukaryote clades. However, despite their wide distribution, their functions and evolutionary dynamics still remain enigmatic. Several minor functions in modulating signaling cascades and multidrug resistance phenotypes were previously discovered for eukaryotic vaults, yet nothing is known about bacterial homologs of the major vault protein (MVP), a protein that comprises the entirety of vault external surface. Using gene and protein BLAST searches in NCBI and UniProt databases we identified a number of bacterial species in prokaryotic orders Myxococcales, Cytophagales and Oscillatoriales with >50% identity to eukaryotic MVP sequences. Interestingly, all of these species are characterized by one common feature - gliding type of motility. Secondary structures of the identified proteins were predicted using RAPTORX web service and aligned via jFATCAT-flexible algorithm in the RCSB PDB Java Structure Alignment tool to elucidate structural identity. Coiled coil domain at the MVP C-terminus of all studied bacterial species resembled TolA protein of Escherichia coli by both structure and sequence. We also showed that MVP sequences from chemotrophic bacteria Myxococcales and Cytophagales contain a domain homologous to eukaryotic band-7 domain, unlike cyanobacterial and eukaryotic major vault proteins. As expected, maximum-likelihood phylogenetic trees for MVP sequences separate studied taxa into two clades - first clade contains Oscillatoriales (Cyanobacteria) and Eukaryotes and the second one contains chemotrophic bacteria. In addition, binding prediction via RAPTORX showed great multiplicity GMP and CMP nucleoside monophosphate binding pockets in Myxococcales and Cytophagales MVP, unlike eukaryotic and cyanobacterial proteins which had much lower affinity to these substrates. Due to high similarity of eukaryotic and cyanobacterial MVP sequences and a pattern of its phylogenetic distribution, we can speculate that the most likely scenario for vault appearance in eukaryotes is horizontal gene transfer from cyanobacteria. Presence of GMP and CMP binding pockets in MVP could also point to a function in depleting cytosolic nucleotide concentration which would be beneficial, for instance, during a viral infection. Further research is necessary to uncover potential functions of this enigmatic protein in bacteria and to determine its evolutionary patterns. In addition, a correlation between MVP presence and gliding motility in bacteria could also lead to elucidating selective pressures on the early evolution of this protein.