Evolutionary Remodeling of the Cell Envelope in Bacteria of the Planctomycetes Phylum

Abstract

Bacteria of the Planctomycetes phylum have many unique cellular features, such as extensive membrane invaginations and the ability to import macromolecules. These features raise intriguing questions about the composition of their cell envelopes. In this study, we have used microscopy, phylogenomics and proteomics to examine the composition and evolution of cell envelope proteins in Tuwongella immobilis and other members of the Planctomycetes. Cryo electron tomography data indicated a distance of 45 nm between the inner and outer membranes in T. immobilis. Consistent with the wide periplasmic space, our bioinformatics studies showed that the periplasmic segments of outer membrane proteins in type II secretion systems are extended in bacteria of the order Planctomycetales. Homologs of two highly abundant cysteine-rich cell wall proteins in T. immobilis were identified in all members of the Planctomycetales, whereas genes for peptidoglycan biosynthesis and cell elongation have been lost in many members of this bacterial group. The cell wall proteins contain multiple copies of the YTV motif, which is the only domain that is conserved and unique to the Planctomycetales. Earlier diverging taxa in the Planctomycetes phylum contain genes for peptidoglycan biosynthesis but no homologs to the YTV cell wall proteins. The major remodelling of the cell envelope in the ancestor of the Planctomycetales coincided with the emergence of budding and other unique cellular phenotypes. The results have implications for hypotheses about the process whereby complex cellular features evolve in bacteria.

The Subcellular Proteome of a Planctomycetes Bacterium Shows That Newly Evolved Proteins Have Distinct Fractionation Patterns

“…A massspectrometry analysis showed that this membrane layer contained beta barrel proteins, lipoproteins and proteins with cell surface motifs, homologs to which were uniquely identified in the SDS-soluble fraction in T. immobilis. We also observed pores in previous cell wall preparations of T. immobilis (Mahajan et al, 2020a). We therefore favor the hypothesis that the pore-containing membrane corresponds to the outer membrane, an interpretation that has also been suggested by others (Jogler et al, 2019).…”

“…This is consistent with earlier findings showing that neither invaginated membranes nor DNA were observed early in the budding process (Santarella-Mellwig et al, 2013), but only at a later stage (Lee et al, 2009). As in a previous study using cryo electron tomography (Mahajan et al, 2020a), we observed a single, spherical particle of up to 400 nm in diameter in almost every cell. In the reconstructed and another, visually inspected, budding cell, the particle was only present in the mother cell.…”

“…The reconstructed T. immobilis cells showed the presence of a tunnel-like system made by invaginations of the cytoplasmic membrane, which separated the non-compartmentalized cytoplasmic space from the enlarged periplasmic space. These results are consistent with findings of a continuous cytoplasm with invaginations of the cytoplasmic membrane (Santarella-Mellwig et al, 2013;Acehan et al, 2014;Devos, 2014;Boedeker et al, 2017;Mahajan et al, 2020a), but do not support the hypothesis of a nucleus-like structure in either T. immobilis or G. obscuriglobus (Lindsay et al, 2001;Fuerst and Sagulenko, 2011).…”

“…For example, the cell wall has been suggested to be mainly composed of proteins instead of a peptidoglycan (König et al, 1984;Liesack et al, 1986). Consistently, cysteine-rich proteins with YTV domains have been identified in the cell wall preparations of Rhodopirellula baltica (Hieu et al, 2008) and members the Gemmataceae (Sagulenko et al, 2017;Mahajan et al, 2020a). Bioinformatics studies have shown that genes for the YTV domain proteins are solely present in the Planctomycetales, and these genes have not been detected in early diverging species of the phylum nor in other bacteria (Mahajan et al, 2020a).…”

“…Genes for peptidoglycan biosynthesis showed the converse pattern, being present in the early diverging members of the Planctomycetes but notably absent in most species of the Planctomycetales, including the Gemmataceae (van Teeseling et al, 2015;Mahajan et al, 2020a;Wiegand et al, 2020). Furthermore, a strong correlation was observed between the phyletic presence/absence patterns of genes for peptidoglycan biosynthesis and the MreB protein complex involved in cell elongation (Mahajan et al, 2020a). Based on these results, it was suggested that the tight coordination between peptidoglycan biosynthesis, cell elongation and cell division has been lost from many species in the Planctomycetales, thereby enabling invaginations of the inner cytoplasmic membrane (Mahajan et al, 2020a).…”