Comparative population genomic analyses of transporters within the Asgard archaeal superphylum

Abstract

Upon discovery of the first archaeal species in the 1970s, life has been subdivided into three domains: Eukarya, Archaea, and Bacteria. However, the organization of the three-domain tree of life has been challenged following the discovery of archaeal lineages such as the TACK and Asgard superphyla. The Asgard Superphylum has emerged as the closest archaeal ancestor to eukaryotes, potentially improving our understanding of the evolution of life forms. We characterized the transportomes and their substrates within four metagenome-assembled genomes (MAGs), that is, Odin-, Thor-, Heimdall- and Loki-archaeota as well as the fully sequenced genome of Candidatus Prometheoarchaeum syntrophicum strain MK-D1 that belongs to the Loki phylum. Using the Transporter Classification Database (TCDB) as reference, candidate transporters encoded within the proteomes were identified based on sequence similarity, alignment coverage, compatibility of hydropathy profiles, TMS topologies and shared domains. Identified transport systems were compared within the Asgard superphylum as well as within dissimilar eukaryotic, archaeal and bacterial organisms. From these analyses, we infer that Asgard organisms rely mostly on the transport of substrates driven by the proton motive force (pmf), the proton electrochemical gradient which then can be used for ATP production and to drive the activities of secondary carriers. The results indicate that Asgard archaea depend heavily on the uptake of organic molecules such as lipid precursors, amino acids and their derivatives, and sugars and their derivatives. Overall, the majority of the transporters identified are more similar to prokaryotic transporters than eukaryotic systems although several instances of the reverse were documented. Taken together, the results support the previous suggestions that the Asgard superphylum includes organisms that are largely mixotrophic and anaerobic but more clearly define their metabolic potential while providing evidence regarding their relatedness to eukaryotes.

Fig 1. Strategy for characterizing transport systems.

To characterize the five Asgard transportomes, candidate single- and multi-component systems were identified in each proteome following the multiple criteria shown in this flow chart. See methods for a detailed description.

Fig 2. Inferred substrates transported by secondary carriers (subclass 2.A) included within the five Asgard transportomes.

The percentage of each substrate type is calculated relative to the total number of substrates transported by secondary carriers per Asgard transportome.

Fig 3. ABC types encoded within the five Asgard proteomes.

The percentages of efflux and uptake ABC transporters are shown for all Asgard proteomes. Note that a) efflux systems predominate in all Asgard proteomes, b) ABC1 efflux systems were not detected in Odin, and c) Loki has the only MAG in which we identified more ABC1 systems than ABC2 or ABC3 systems.

Fig 4. Substrates imported by ABC systems encoded within the five Asgard transportomes.

The percentage of each substrate type was calculated relative to the total number of substrates transported by ABC uptake systems per Asgard transportome.

Fig 5. Conservation of superfamilies within five Asgard proteomes.

TC Subfamilies were selected as the basic unit for counts across all proteomes. Black bars in the first five layers from the center indicate the presence of individual transport subfamilies. The patterns formed by these bars convey the presence or absence of individual subfamilies across proteomes. Blue bars in the sixth layer (Conservation) show the number of proteomes that contain at least one member of a particular subfamily. The outermost layer labels superfamilies as annotated in TCDB. Superfamilies are organized clockwise by decreasing size based on the number of different subfamilies the proteomes contain. Label “Smaller SFs” refers to superfamilies with fewer subfamilies. Label “N/A” denotes subfamilies not yet assigned to any superfamily. This figure was generated using Anvi’o [160, 161].