New paper in Nature Microbiology describing the symbiotic metabolisms that led to the first eukaryotic cells

Proposal of the reverse flow model for the origin of the eukaryotic cell based on comparative analyses of Asgard archaeal metabolism

Our new paper in collaboration with Thijs Ettema’s lab describes a new model for the partnership that led to the origin of eukaryotes.

Summary

The origin of eukaryotes represents an unresolved puzzle in evolutionary biology. Current research suggests that eukaryotes evolved from a merger between a host of archaeal descent and an alphaproteobacterial endosymbiont. The discovery of the Asgard archaea, a proposed archaeal superphylum that includes Lokiarchaeota, Thorarchaeota, Odinarchaeota and Heimdallarchaeota suggested to comprise the closest archaeal relatives of eukaryotes, has helped to elucidate the identity of the putative archaeal host. Whereas Lokiarchaeota are assumed to employ a hydrogen-dependent metabolism, little is known about the metabolic potential of other members of the Asgard superphylum. We infer the central metabolic pathways of Asgard archaea using comparative genomics and phylogenetics to be able to refine current models for the origin of eukaryotes. Our analyses indicate that Thorarchaeota and Lokiarchaeota encode proteins necessary for carbon fixation via the Wood–Ljungdahl pathway and for obtaining reducing equivalents from organic substrates. By contrast, Heimdallarchaeum LC2 and LC3 genomes encode enzymes potentially enabling the oxidation of organic substrates using nitrate or oxygen as electron acceptors. The gene repertoire of Heimdallarchaeum AB125 and Odinarchaeumindicates that these organisms can ferment organic substrates and conserve energy by coupling ferredoxin reoxidation to respiratory proton reduction. Altogether, our genome analyses suggest that Asgard representatives are primarily organoheterotrophs with variable capacity for hydrogen consumption and production. On this basis, we propose the ‘reverse flow model’, an updated symbiogenetic model for the origin of eukaryotes that involves electron or hydrogen flow from an organoheterotrophic archaeal host to a bacterial symbiont.

UT press release

New paper on the metabolic biodiversity of hydrothermal sediments in the Guaymas Basin

Expansive microbial metabolic versatility and biodiversity in dynamic Guaymas Basin hydrothermal sediments

UT press release

Microbes in Guaymas Basin (Gulf of California) hydrothermal sediments thrive on hydrocarbons and sulfur and experience steep, fluctuating temperature and chemical gradients. The functional capacities of communities inhabiting this dynamic habitat are largely unknown. Here, we reconstructed 551 genomes from hydrothermally influenced, and nearby cold sediments belonging to 56 phyla (40 uncultured). These genomes comprise 22 unique lineages, including five new candidate phyla. In contrast to findings from cold hydrocarbon seeps, hydrothermal-associated communities are more diverse and archaea dominate over bacteria. Genome-based metabolic inferences provide first insights into the ecological niches of these uncultured microbes, including methane cycling in new Crenarchaeota and alkane utilization in ANME-1. These communities are shaped by a high biodiversity, partitioning among nitrogen and sulfur pathways and redundancy in core carbon-processing pathways. The dynamic sediments select for distinctive microbial communities that stand out by expansive biodiversity, and open up new physiological perspectives into hydrothermal ecosystem function.

New publication detailing the evolution of elongation factors in archaea and eukaryotes.

 

Complex evolutionary history of translation Elongation Factor 2 and diphthamide biosynthesis in Archaea and parabasalids

Diphthamide is a modified histidine residue which is uniquely present in archaeal and eukaryotic elongation factor 2 (EF-2), an essential GTPase responsible for catalyzing the coordinated translocation of tRNA and mRNA through the ribosome. In part due to the role of diphthamide in maintaining translational fidelity, it was previously assumed that diphthamide biosynthesis genes (dph) are conserved across all eukaryotes and archaea. Here, comparative analysis of new and existing genomes reveals that some archaea (i.e., members of the Asgard superphylum, Geoarchaea, and Korarchaeota) and eukaryotes (i.e., parabasalids) lack dph. In addition, while EF-2 was thought to exist as a single copy in archaea, many of these dph-lacking archaeal genomes encode a second EF-2 paralog missing key-residues required for diphthamide modification and for normal translocase function, perhaps suggesting functional divergence linked to loss of diphthamide biosynthesis. Interestingly, some Heimdallarchaeota previously suggested to be most closely related to the eukaryotic ancestor maintain dph genes and a single gene encoding canonical EF-2. Our findings reveal that the ability to produce diphthamide, once thought to be a universal feature in archaea and eukaryotes, has been lost multiple times during evolution, and suggest that anticipated compensatory mechanisms evolved independently.

New paper on the metabolic diversity of Thorarchaeota

Comparative genomic inference suggests mixotrophic lifestyle for Thorarchaeota

Thorarchaeota are a new archaeal phylum within the Asg ard superphylum, whose ancestors have been proposed to play possible ecological roles in cellular evolution. However, little is known about the lifestyles of these uncultured archaea. To
provide a better resolution of the ecological roles and metabolic capacity of Thorarchaeota, we obtained Thorarchaeota genomes reconstructed from metagenomes of different depth layers in mangrove and mudat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, x inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen xation, nitrite reduction, and arsenic detoxication. Inter estingly, these Thorarchaeotal genomes are inferred to
contain the tetrahydromethanopterin and tetrahydrofolate WoodLjungdahl (WL) pathways for COreduction, and the latter WL pathway appears to have originated from bacteria. These archaea are predicted to be able to use various inorganic and organic carbon sources, possessing genes inferred to encode ribulose bisph osphate carboxy lase-like proteins (normally without RuBisCO activity) and a near-complete CalvinBensonBassham cycle. The existence of eukaryotic selen ocysteine insertion sequences and many genes for proteins previously considered eukaryote-specic in Thorarchaeota genomes provide new insights into their evolutionary roles in the origin of eukaryo tic cellular complexity. Resolving the metabolic capacities of these enigmatic archaea and their origins will enhance our understanding of the origins of eukaryotes and their
roles in ecosystems.