Phylogenetic origin and sequence features of MreB from the wall-less swimming bacteria Spiroplasma

Daichi Takahashi,Ikuko Fujiwara,Makoto Miyata

doi:10.1016/j.bbrc.2020.09.060

Daichi Takahashi, Ikuko Fujiwara + Show 1 more

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https://doi.org/10.1016/j.bbrc.2020.09.060

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Abstract

Spiroplasma are wall-less bacteria which belong to the phylum Tenericutes that evolved from Firmicutes including Bacillus subtilis. Spiroplasma swim by a mechanism unrelated to widespread bacterial motilities, such as flagellar motility, and caused by helicity switching with kinks traveling along the helical cell body. The swimming force is likely generated by five classes of bacterial actin homolog MreBs (SMreBs 1–5) involved in the helical bone structure. We analyzed sequences of SMreBs to clarify their phylogeny and sequence features. The maximum likelihood method based on around 5000 MreB sequences showed that the phylogenetic tree was divided into several radiations. SMreBs formed a clade adjacent to the radiation of MreBH, an MreB isoform of Firmicutes. Sequence comparisons of SMreBs and Bacillus MreBs were also performed to clarify the features of SMreB. Catalytic glutamic acid and threonine were substituted to aspartic acid and lysine, respectively, in SMreB3. In SMreBs 2 and 4, amino acids involved in inter- and intra-protofilament interactions were significantly different from those in Bacillus MreBs. A membrane-binding region was not identified in most SMreBs 1 and 4 unlike many walled-bacterial MreBs. SMreB5 had a significantly longer C-terminal region than the other MreBs, which possibly forms protein-protein interactions. These features may support the functions responsible for the unique mechanism of Spiroplasma swimming.

Highlights

The bacterial phylum Tenericutes that evolved from the phylum Firmicutes is comprised of the class Mollicutes, which includes the genera Spiroplasma and Mycoplasma [1]
Molecular dynamics (MD) simulations suggest that the inter- and intra-protofilament interactions are comprised of four helices, two strands, and three loops (H3, H5, and H8 shown in Fig. 2A and Fig. S3C for inter-protofilament interaction; H9, S12, S13 and loops between S6-H1, S9-S10, and S10-S11 shown in Fig. 2A and Fig. S3D for intra-protofilament interaction) [16]
A previous study reported that many MreBs have two consecutive hydrophobic amino acids for membrane binding in the hydrophobic loops in domain IA, and some MreBs of Gram-negative bacteria have an amphipathic helix at the N-terminus as an additional factor for membrane binding (Fig. 2A) [17]

Summary

Introduction

The bacterial phylum Tenericutes that evolved from the phylum Firmicutes is comprised of the class Mollicutes, which includes the genera Spiroplasma and Mycoplasma [1] Species of these genera are characterized by small genome size, being mostly parasitic or commensal, and absence of peptidoglycan. They cannot equip conventional machineries for bacterial motility, such as flagella or type IV pili, due to the lack of a peptidoglycan layer. MreB is well known as an ATPase like other actin superfamily proteins [14,15] These facts suggest that the MreBs are employed in the Spiroplasma swimming. A previous study reported that many MreBs have two consecutive hydrophobic amino acids for membrane binding in the hydrophobic loops in domain IA, and some MreBs of Gram-negative bacteria have an amphipathic helix at the N-terminus as an additional factor for membrane binding (Fig. 2A) [17]

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