Fig 1.
Cation diffusion facilitators comparison.
(A) Multiple sequence alignment of MamB and MamM CTDs from the Alphaproteobacteria (MSR-1 and QH-2) and Deltaproteobacteria BW-1. Secondary structure representative, base on MamMMSR-1 structure (PDB code 3W5Y). The blue and red frames highlight conserved sequences. (B) Structural overlay of MamBBW-1, MamMBW-1 and MamBQH-2 CTD apo-form structures (PDB codes: 6QFJ, 6QEK, and 5HO5, respectively). Residues that are suggested to participate in the central metal ion-binding site represented as sticks. (C) Structural overlay of MamBBW-1 and MamMMSR-1 CTD structures (PDB codes: 6QFJ and 3W5Y, respectively) Residues that hypothetically participate in central and peripheral metal ion-binding sites represented as sticks.
Fig 2.
Comparison of MamB-MamM crystal structures.
Structural overlay of MamB and MamM CTD monomer apo-form structures from Alphaproteobacteria and Deltaproteobacteria species (PDB codes: 6QFJ (blue), 6QEK (green), 5HO5 (purple) and 3W5Y (yellow)). Root-mean-square deviation (RMSD) values calculated for monomers and dimers respectively, using Swiss-PDB-Viewer [35]. Overall, MamMBW-1 and MamMMSR-1 share the highest structural similarities with RMSD of 0.66 Å over 77 common backbone atoms.
Fig 3.
MamBBW-1 and MamMBW-1 CTD structures and dimerization interface.
(A) MamBBW-1 folded to a metallochaperone-like fold to create a V-shaped dimer. Overlap of the MamMBW-1 monomers on MamBBW-1 V-dimer structure (PDB codes: 6QFJ (Green), 6QEK (blue). (B) MamBBW-1 may create a stable V-shape dimer while the parallel S-shaped typical backbone structure, revealed in the dimerization interface after overlapping the monomers on MamMBW-1 dimer. Hydrophobic interactions between Val235-Pro231 and Ile233-Thr234 from each monomer may hold the dimer. (C) MamMBW-1 presents a stable dimerization interface located at the bottom of the V-shaped dimer. Dimerization interface stability rests on symmetrical backbone interaction between Pro278-Val283 and Ser280-Ile282.
Fig 4.
Proteins CTDs electrostatic potential map.
Alphaproteobacteria and Deltaproteobacteria MamB and MamM CTDs crystal structures, electrostatic potential maps based on the PDB codes: 3HO5, 3W5Y, 6QFJ, and 6QEK. Top of the structures has hydrophobic and positive patches that may fit the interaction model between the CTD-TMD and CTD-magnetosome membrane. Hydrophobic and negative electrostatic charge distribution located at the bottom of the structures. The Central V-shaped dimer cavity showed negative-charge patches found in correlation with the central metal-binding site. MamM structures present an additional negative-charge patch in the periphery above the V-bottom that correlated with the peripheral metal-binding site.
Fig 5.
Phylogenetic tree showing the evolutionary relationships between magnetotactic bacteria and other non-magnetotactic Proteobacteria species.
The tree was built using the Maximum-Likelihood method implemented in IQ-TREE and the concatenation of 53 ribosomal proteins. 500 replicates of a non-parametric bootstrap approach were conducted to test the robustness of the tree topology. Internal branches with support superior to 95% are annotated with a circle. Support values superior to 70% are associated with a grey circle while those below that value are not shown. Magnetotactic species names are in bold. The branch length represents the number of substitutions per site.
Fig 6.
Maximum-likelihood tree showing the evolutionary relationships between MamM and MamB proteins involved in magnetite biomineralization within magnetotactic Proteobacteria strains.
The tree was built using the Maximum-Likelihood method implemented in IQ-TREE and the trimmed alignment of FieF, MamB and MamM sequences detected in the 6 strains. Color of the names of the strains correspond to their affiliation given in the species tree (Fig 5): Alphaproteobacteria (blue), Ca. Etaproteobacteria (brown) and Deltaproteobacteria (Purple). The branch length represents the number of substitutions per site. The robustness of the tree topology was tested with 500 replicates of a non-parametric bootstrap approach (black values). The posterior probability of each clade was also inferred with a Bayesian approach implemented in MrBayes (red values).