The Polygonal Cell Shape and Surface Protein Layer of Anaerobic Methane-Oxidizing Methylomirabilislanthanidiphila Bacteria

Abstract

Methylomirabilis bacteria perform anaerobic methane oxidation coupled to nitrite reduction via an intra-aerobic pathway, producing carbon dioxide and dinitrogen gas. These diderm bacteria possess an unusual polygonal cell shape with sharp ridges that run along the cell body. Previously, a putative surface protein layer (S-layer) was observed as the outermost cell layer of these bacteria. We hypothesized that this S-layer is the determining factor for their polygonal cell shape. Therefore, we enriched the S-layer from M. lanthanidiphila cells and through LC-MS/MS identified a 31 kDa candidate S-layer protein, mela_00855, which had no homology to any other known protein. Antibodies were generated against a synthesized peptide derived from the mela_00855 protein sequence and used in immunogold localization to verify its identity and location. Both on thin sections of M. lanthanidiphila cells and in negative-stained enriched S-layer patches, the immunogold localization identified mela_00855 as the S-layer protein. Using electron cryo-tomography and sub-tomogram averaging of S-layer patches, we observed that the S-layer has a hexagonal symmetry. Cryo-tomography of whole cells showed that the S-layer and the outer membrane, but not the peptidoglycan layer and the cytoplasmic membrane, exhibited the polygonal shape. Moreover, the S-layer consisted of multiple rigid sheets that partially overlapped, most likely giving rise to the unique polygonal cell shape. These characteristics make the S-layer of M. lanthanidiphila a distinctive and intriguing case to study.

Punctuated and continuous structural diversity of S-layers across the prokaryotic tree of life

“…Among these assemblies, the S-layers of prokaryotes are notable for their highly organised, paracrystalline 2D lattices that envelop entire cells (3,(5)(6)(7). S-layers, composed of repeating units of S-layer proteins (SLPs) (8,9), are found across archaea (10)(11)(12) and both Gram-negative (diderm) (13) and Gram-positive (monoderm) bacteria (14)(15)(16)(17). Remarkably, SLPs are often the proteins with the highest copy number in these cells (3), leading to the proposition that SLPs are among the most abundant classes of proteins in nature (3,18).…”