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.
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 mudﬂat sediments. These genomes from deep anoxic layers suggest the presence of Thorarchaeota with the potential to degrade organic matter, ﬁx inorganic carbon, reduce sulfur/sulfate and produce acetate. In particular, Thorarchaeota may be involved in ethanol production, nitrogen ﬁxation, nitrite reduction, and arsenic detoxiﬁcation. Inter estingly, these Thorarchaeotal genomes are inferred to
contain the tetrahydromethanopterin and tetrahydrofolate Wood–Ljungdahl (WL) pathways for CO2 reduction, 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 Calvin–Benson– Bassham cycle. The existence of eukaryotic selen ocysteine insertion sequences and many genes for proteins previously considered eukaryote-speciﬁc 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.
Here is some of the press that covered the impacts of the storm on my lab, institute, lab members, and family.
New insights into microbial hydrocarbon cycling and metabolic interdependencies in hydrothermal sediments
Congrats Nina and Kiley!
This paper details the genetic diversity of these sediments and describes genomes belonging to a uncultured archaeal group (GoM-Arc1) that contain novel pathways for hydrocarbon cycling, related to ANME (anaerobic methane oxidizers).
In addition to Theionarchaea, this new paper that appears in ISME Journal also details a variety of archaeal genomes there were obtained from the White Oak River Estuary in North Carolina. This digram summarizes the ecological roles we have inferred from these genomes. This is important because NONE of these lineages have been grown in a laboratory, so having their genomes has significantly advanced our understanding of what they do in nature.
Genomic reconstruction of multiple lineages of uncultured benthic archaea suggests distinct biogeochemical roles and ecological niches
Asgard archaea illuminate the origin of eukaryotic cellular complexity
This week our new paper describing the discovery of 4 archaea phyla that are related to eukaryotes was published in Nature. These phyla are belong to the same branch of life and have been named after different Norse gods, Thor, Odin, Heimdall, and Loki. This is a collaboration with Thijs Ettema’s lab in Sweden. Last year we published the discovery of Thorarchaeota in ISME.
Genomic reconstruction of a novel, deeply branched sediment archaeal phylum with pathways for acetogenesis and sulfur reduction
This paper adds 2 additional phyla, Odinarchaeota and Heimdallarchaeota. The focus of this paper is further resolve the phylogenetic position of eukaryotes in this new superphylum. It also examines the presence of several new ESPs or eukaryotic signature proteins. These proteins were mostly thought to exist in eukaryotes, but these genomes contain a variety of them!
Press releases to accompany this study:
UT press release
The Atlantic article by Ed Yong
Uppsala press release
by Rachel Mackelprang & Olivia U. Mason
DNA-SIP metagenomic experimental strategy for the identification and characterization of hydrocarbon-degrading microorgansims from DWH oil spill deep-plume and surface-slick samples.