Cell surface architecture of the cultivated DPANN archaeonNanobdella aerobiophila

Abstract

The DPANN archaeal clade includes obligately ectosymbiotic species. Their cell surfaces potentially play an important role in the symbiotic interaction between the ectosymbionts and their hosts. However, little is known about the mechanism of the ectosymbiosis. Here, we show cell surface structures of the cultivated DPANN archaeonNanobdella aerobiophilastrain MJ1Tand its hostMetallosphaera sedulastrain MJ1HA, using a variety of electron microscopy techniques, i.e., negative-staining transmission electron microscopy (TEM), quick-freeze deep-etch (QFDE) TEM, and 3D electron tomography. The thickness, unit size, and lattice symmetry of the S-layer of strain MJ1Twere different from those of the host archaeon strain MJ1HA. Genomic and transcriptomic analyses highlighted the most highly expressed MJ1Tgene for a putative S-layer protein with multiple glycosylation sites and immunoglobulin-like folds, which has no sequence homology to known S-layer proteins. In addition, genes for putative pectin lyase- or lectin-like extracellular proteins, which are potentially involved in symbiotic interaction, were found in the MJ1T genome based on in silico 3D protein structure prediction. Live cell imaging at the optimum growth temperature of 65°C indicated that cell complexes of strains MJ1Tand MJ1HA were motile, but sole MJ1Tcells were not. Taken together, we propose a model of the symbiotic interaction and cell cycle ofNanobdella aerobiophila.ImportanceDPANN archaea are widely distributed in a variety of natural and artificial environments, and may play a considerable role in the microbial ecosystem. All of the cultivated DPANN archaea so far need host organisms for their growth, i.e., obligately ectosymbiotic. However, the mechanism of the ectosymbiosis by DPANN archaea is largely unknown. To this end, we performed a comprehensive analysis of the cultivated DPANN archaeon,Nanobdella aerobiophila, using electron microscopy, live cell imaging, transcriptomics, and genomics including 3D protein structure prediction. Based on the results, we propose a reasonable model of the symbiotic interaction and cell cycle ofNanobdella aerobiophila, which will enhance our understanding of the enigmatic physiology and ecological significance of DPANN archaea.

A large attachment organelle mediates interaction between a novel Nanobdellota archaeon YN1 and its host

“…1D) imply that YN1 has the capability to undergo cell division away from the host cell. Homologous genes for the recently suggested putative S-layer proteins of Nanobdellota 12 were found in the YN1 genome (YN1_5000 and YN1_2560), suggesting that these genes may be involved in S-layer formation. The presence of genes involved in archaellum formation 32 (FlaBDEHIJF) and the observation of archaellum-like structures in our micrographs suggest the potential for motility in YN1 (Supplementary Fig.…”

“…The nature of DPANN biology and lifecycle is enigmatic. Based on the information of their reduced genome, DPANNs must require external resources to proliferate, but how they obtain resources and utilise them remains underexplored due to the limited number of co-culture systems established to date 6,10,12,[28][29][30] . Previous work has shown that some DPANNs may opt for a parasitic lifestyle, instead of an ectosymbiotic relationship 28 .…”

“…were encoded in the YN1 genome. Kato et al recently revealed the cell surface structure of N. aerobiophila MJ1HA T , and suggested it has putative S-layer proteins (MJ1_0160 and MJ1_0707) 12 . The YN1 genome also encoded these proteins (YN1_5000 and YN1_2560) with high amino acid sequence similarity to MJ1_0160 (69.5%) and MJ1_0707 (61.7%), respectively.…”

“…A significant hurdle in the study of DPANNs lies in the formidable difficulty of isolating and establishing new DPANN co-culture systems. Consequently, very few DPANN co-cultures systems have been cultured and investigated to date 6,7,[12][13][14][15] .…”