Biology subjects

Hamm, J. N.

Publications and source records attributed to Hamm, J. N..

4 recordsLinked to original sources

bioRxiv2026

Emergence of histone-based chromatin complexity in Asgard archaea

The emergence of the eukaryotes coincided with the diversification of histone proteins and their post-translational modifications by enzymes that constitute the core of eukaryotic chromatin. Yet the evolutionary origins of this regulatory machinery are unknown. Here, we show that the key molecular components of histone-based chromatin regulation are present in the Asgard archaea, the closest prokaryotic relatives of eukaryotes. Asgard histones are abundant and have extended N-terminal tails rich in lysine residues that can be post-translationally modified, all of which are features shared with eukaryotic histones. In line with these findings, we identify enzymes from Asgard archaea that deposit or remove lysine acetylation on histone tails in vitro. Moreover, Asgard sirtuin deacetylases (SIR2 proteins) restore chromatin silencing in yeast, demonstrating the functional compatibility of Asgard enzymes with eukaryotic histone substrates. Our findings establish that the foundations of histone-based chromatin predate eukaryogenesis and place Asgard archaea as an evolutionary intermediate in the emergence of eukaryotic chromatin.

evolutionary biology↗

bioRxiv2025

Caliditerrarchaeota, a new sister to Nanohaloarchaeota, provides insights into the evolution of DPANN halophily

The Nanohaloarchaeota are a clade of halophilic symbionts with small cells and genomes. Originally placed within the Euryarchaeota, they are now widely thought to belong to the DPANN archaea. However, the evolution of this clade and its phylogenetic placement within DPANN remain poorly understood. We applied phylogenetic and comparative genomic analyses to assess the evolutionary relationship and genome evolution of the Nanohaloarchaeota and related DPANN lineages. Our phylogenetic analyses resolve Nanohaloarchaeota as a sister group to a phylum-level lineage referred to as EX4484-52, together forming a clade with Aenigmatarchaeota. Representatives of EX4484-52, for which we propose the name Caliditerrarchaeota, have an anaerobic, thermophilic lifestyle but do not appear to be adapted to high salt concentrations. Using gene tree-species tree reconciliations, we investigated the origin of halophily across these archaeal lineages revealing that adaptations to high-salt appear to have evolved on the branch to Nanohaloarchaeota after their divergence from Aenigmatarchaeota and Caliditerrarchaeota. In agreement with recent work, we also identify hallmarks of halophily in another order-level lineage within the Aenigmatarchaeota (Haloaenigmatarchaeaceae) which appears to represent a second independent adaptation of a DPANN clade to halophily. The two halophilic DPANN lineages are inferred to have distinct sets of proteins that enable them to live in environments with high salt levels. Notably, phylogenetic analyses reveal a dominant signal of gene transfers between Haloaenigmatarchaeaceae and Halarchaeoplasmatales, indicating a potential host-symbiont relationship. This work provides the first detailed investigation of the enigmatic Caliditerrarchaeota, and new insights into the evolution of halophilic lifestyles within DPANN.

evolutionary biology↗

bioRxiv2023

Selective lipid recruitment by an archaeal DPANN symbiont from its host

The symbiont Ca. Nanohaloarchaeum antarcticus is obligately dependent on its host Halorubrum lacusprofundi for lipids and other metabolites due to its lack of certain biosynthetic genes. However, it remains unclear which specific lipids or metabolites are acquired from its host, and how the host responds to infection. Here, we explored the lipidome dynamics of the Ca. Nha. antarcticus - Hrr. lacusprofundi symbiotic relationship during co-cultivation. By using a comprehensive untargeted lipidomic methodology, our study reveals that Ca. Nha. antarcticus selectively recruits 110 lipid species from its host, i.e. nearly two-thirds of the total number of host lipids. Lipid profiles of co-cultures displayed shifts in abundances of bacterioruberins and menaquinones and changes in degree of bilayer-forming glycerolipid unsaturation. This likely results in increased membrane fluidity and improved resistance to membrane disruptions, consistent with compensation for higher metabolic load and mechanical stress on host membranes when in contact with Ca. Nha. antarcticus cells. Notably, our findings differ from previous observations of other DPANN symbiont-host systems, where no differences in lipidome composition were reported. Altogether, our work emphasizes the strength of employing untargeted lipidomics approaches to provide details into the dynamics underlying a DPANN symbiont-host system.

microbiology↗

bioRxiv2023

The intracellular lifestyle of an archaeal symbiont

DPANN Archaea are a diverse group of organisms typically characterised by small cells and reduced genomes. To date, all cultivated DPANN Archaea are ectosymbionts that require direct cell contact with an archaeal host species for proliferation. However, the dynamics of DPANN - host interactions and the impacts of these interactions on the host species are poorly understood. Here, we show that one DPANN archaeon (Candidatus Nanohaloarchaeum antarcticus) engages in parasitic interactions with its host (Halorubrum lacusprofundi) that result in host cell lysis. Our data also suggest that these interactions involve invasion of the host cell by the nanohaloarchaeon. This is the first reported instance of such a predatory-like lifestyle amongst Archaea and indicates that some DPANN Archaea may interact with host populations in a manner similar to viruses.

microbiology↗