The Compartmentalized Bacteria of the Planctomycetes-Verrucomicrobia-Chlamydiae Superphylum Have Membrane Coat-Like Proteins

Compartmentalized bacteria have proteins that are structurally related to eukaryotic membrane coats, and one of these proteins localizes at the membrane of vesicles formed inside bacterial cells.
The development of the endomembrane system was a major step in eukaryotic evolution. Membrane coats, which exhibit a unique arrangement of β-propeller and α-helical repeat domains, play key roles in shaping eukaryotic membranes. Such proteins are likely to have been present in the ancestral eukaryote but cannot be detected in prokaryotes using sequence-only searches. We have used a structure-based detection protocol to search all proteomes for proteins with this domain architecture. Apart from the eukaryotes, we identified this protein architecture only in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum, many members of which share a compartmentalized cell plan. We determined that one such protein is partly localized at the membranes of vesicles formed inside the cells in the planctomycete Gemmata obscuriglobus. Our results demonstrate similarities between bacterial and eukaryotic compartmentalization machinery, suggesting that the bacterial PVC superphylum contributed significantly to eukaryogenesis.
Author Summary Despite decades of research, the origin of eukaryotic cells remains an unsolved issue. The endomembrane system defines the eukaryotic cell, and its origin is linked to that of eukaryotes. A search was conducted within all known sequences for proteins that are characteristic of the eukaryotic endomembrane system, using a combination of fold types that is uniquely found in the membrane coat proteins. Outside eukaryotes, such proteins were solely found in the Planctomycetes-Verrucomicrobia-Chlamydiae (PVC) bacterial superphylum. By immuno-electron microscopy, one of these bacterial proteins was found to localize adjacent to the membranes of vesicles found within the cells of one member of the PVC superphylum. Thus, there appear to be similarities between bacterial and eukaryotic compartmentalization systems, suggesting that the bacterial PVC superphylum may have contributed significantly to eukaryogenesis.