Structure prediction of magnetosome-associated proteins

Raz Zarivach,Hila Nudelman

doi:10.3389/fmicb.2014.00009

Abstract

Magnetotactic bacteria (MTB) are Gram-negative bacteria that can navigate along geomagnetic fields. This ability is a result of a unique intracellular organelle, the magnetosome. These organelles are composed of membrane-enclosed magnetite (Fe3O4) or greigite (Fe3S4) crystals ordered into chains along the cell. Magnetosome formation, assembly, and magnetic nano-crystal biomineralization are controlled by magnetosome-associated proteins (MAPs). Most MAP-encoding genes are located in a conserved genomic region – the magnetosome island (MAI). The MAI appears to be conserved in all MTB that were analyzed so far, although the MAI size and organization differs between species. It was shown that MAI deletion leads to a non-magnetic phenotype, further highlighting its important role in magnetosome formation. Today, about 28 proteins are known to be involved in magnetosome formation, but the structures and functions of most MAPs are unknown. To reveal the structure–function relationship of MAPs we used bioinformatics tools in order to build homology models as a way to understand their possible role in magnetosome formation. Here we present a predicted 3D structural models’ overview for all known Magnetospirillum gryphiswaldense strain MSR-1 MAPs.

Highlights

Magnetotactic bacteria (MTB) are a group of Gram-negative aquatic prokaryotes that can synthesize a unique prokaryotic organelle, called a magnetosome (Bazylinski et al, 2004)
By searching for homologous proteins or conserved domains with the BLAST server we found similarities to a conserved domain in the Major Facilitator Superfamily (MFS), members of which are known to function as membrane transporters (Pao et al, 1998; MarchlerBauer et al, 2011; Raschdorf et al, 2013)
In this paper we looked at the magnetosome-associated proteins (MAPs), which are encoded in the M. gryphiswaldense MSR-1 magnetosome island (MAI) region

Summary

INTRODUCTION

Magnetotactic bacteria (MTB) are a group of Gram-negative aquatic prokaryotes that can synthesize a unique prokaryotic organelle, called a magnetosome (Bazylinski et al, 2004). Point mutations in the MamM membranal putative metal binding site (Y46H, Y46D, D50A, H155A, and D159A) lead to changes in crystal size and morphology, which may be the result of a reduction in iron transport rates into the magnetosome vesicles or of the nucleation of magnetite crystals (Uebe et al, 2011). In MamM CTD we found that the amino acids that are involved in zinc binding in FieF are different and create a negative pocket that may be involved in ion binding We cannot find such a negative pocket in the MSR-1 MamB 3D model structure that may indicate different activity for MamB (Figure 5). The MmsF N-terminal is located in the cytoplasmic side whilst the C-terminal faces the magnetite crystals (Figure 6; Murat et al, 2012)

CONCLUSION

Findings

METHODS