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Ettema, T. J. G.

Publications and source records attributed to Ettema, T. J. G..

At least 19 recordsLinked to original sources

Asgard archaeal origin of microtubules

Eukaryotic cells change their shapes, actively segregate their DNA and contain membrane networks, facilitated by a complex cytoskeleton containing actin filaments, microtubules made from tubulin, and other components. These filaments have ancient evolutionary origins since actin- and tubulin-like proteins form prokaryotic cytoskeletons in archaea and bacteria. Bona fide eukaryotic F-actin can be traced back to crenarchaea and Asgard archaea, which are the closest known relatives of eukaryotes. A possible Asgard archaeal origin of microtubules was suggested recently with the discovery of a lokiarchaeon containing AtubAB mini microtubules that share architectural features with their eukaryotic counterparts. Using phylogenetic analyses of metagenomic data, here we report the broad occurrence of tubulins in Asgard archaea. Biochemical and structural analyses showed that one of our newly discovered heimdallarchaeial AtubAB tubulin pairs forms four-protofilament mini-microtubules that show dynamic instability and are inhibited by the tubulin drug maytansine. Our work raises the possibility that microtubule architecture and dynamics evolved in Asgard archaea prior to eukaryogenesis.

cell biology↗

The Escherichia coli replication initiator DnaA is titrated on the chromosome

DNA replication initiation is orchestrated in many prokaryotes by the replication initiator DnaA. Two models for regulation of DnaA activity in Escherichia coli have been proposed: the switch between an active and inactive form of DnaA, and the titration of DnaA on the E. coli chromosome. Although proposed decades ago, experimental evidence of a titration-based control mechanism is still lacking. Here, we first identified a conserved high-density region of binding motifs near the origin of replication, an advantageous trait for titration of DnaA. We then investigated the mobility of DnaA by single-particle tracking microscopy in wild-type and deletion mutants E. coli strains, while monitoring cellular size and DNA content. Our results indicate that the chromosome of E. coli controls the free amount of DnaA in a growth rate-dependent fashion. Finally, we provide insights on the relevance of DnaA titration in stabilising DNA replication by preventing re-initiation events during slow growth.

molecular biology↗

De novo synthesis of fatty acids in Archaea via an archaeal fatty acid synthase complex

Archaea synthesize membranes using isoprenoid-based ether lipids, whereas Bacteria and Eukarya use fatty acid-based ester lipids. While the factors responsible for this "lipid divide" remain unclear, this has important implications for understanding the evolutionary history of eukaryotes, which likely originated from within the Archaea and therefore changed membrane composition from isoprenoid-based to fatty acid-based lipids. Here, using 13C labelling studies, we demonstrate that the archaeal model organisms Sulfolobus acidocaldarius and Haloferax volcanii are capable of de novo fatty acid synthesis. Biochemical characterization and in vitro pathway reconstitution identify the key enzymes of a newly proposed fatty acid synthesis pathway in S. acidocaldarius and show that ketothiolase, ketoacyl-CoA reductase, and hydroxyacyl-CoA dehydratase form a stable assembly mediated by a DUF35 domain protein, which represents the first characterization of an archaeal fatty acid synthase complex. The final step is catalysed by an NADPH-dependent enoyl-CoA reductase. Deletion of the enoyl-CoA reductase demonstrate that this pathway operates in vivo in S. acidocaldarius. The presented results including phylogenetic analysis reveal that the potential to synthesize fatty acids is widespread across archaeal lineages. Collectively, our findings demonstrate that archaea are capable of synthesizing fatty acids, elucidate the molecular mechanisms involved in this process and provide additional insights into the evolutionary histories of fatty acid synthesis in archaea.

microbiology↗

Structure-based inference of eukaryotic complexity in Asgard archaea

Asgard archaea played a key role in the origin of the eukaryotic cell. While previous studies found that Asgard genomes encode diverse eukaryotic signature proteins (ESPs), representing homologs of proteins that play important roles in the complex organization of eukaryotic cells, the cellular characteristics and complexity of the Asgard archaeal ancestor of eukaryotes remain unclear. Here, we used de novo protein structure modeling and sensitive sequence similarity detection algorithms within an expanded Asgard archaeal genomic dataset to build a structural catalogue of the Asgard archaeal pangenome and identify 908 new isomorphic ESPs (iESPs), representing clusters of protein structures most similar to eukaryotic proteins and that likely underwent extensive sequence divergence. While most previously identified ESPs were involved in cellular processes and signaling, iESPs are enriched in information storage and processing functions, with several being potentially implicated in facilitating cellular complexity. By expanding the complement of eukaryotic proteins in Asgard archaea, this study indicates that the archaeal ancestor of eukaryotes was more complex than previously assumed.

evolutionary biology↗

Oxygen metabolism in descendants of the archaeal-eukaryotic ancestor

Asgard archaea were pivotal in the origin of complex cellular life. Hodarchaeales (Asgardarchaeota class Heimdallarchaeia) were recently shown to be the closest relatives of eukaryotes. However, limited sampling of these archaea constrains our understanding of their ecology and evolution1-3, including their anticipated role in eukaryogenesis. Here, we nearly double the number of Asgardarchaeota metagenome-assembled genomes (MAGs) to 869, including 136 new Heimdallarchaeia (49 Hodarchaeales) and several novel lineages. Examining global distribution revealed Hodarcheales are primarily found in coastal marine sediments. Detailed analysis of their metabolic capabilities revealed guilds of Heimdallarchaeia are distinct from other Asgardarchaeota. These archaea encode hallmarks of aerobic eukaryotes, including electron transport chain complexes (III and IV), biosynthesis of heme, and response to reactive oxygen species (ROS). The predicted structural architecture of Heimdallarchaeia membrane-bound hydrogenases includes additional Complex-I-like subunits potentially increasing the proton motive force and ATP synthesis. Heimdallarchaeia genomes encode CoxD, which regulates the electron transport chain (ETC) in eukaryotes. Thus, key hallmarks for aerobic respiration may have been present in the Asgard-eukaryotic ancestor. Moreover, we found that Heimdallarchaeia is present in a variety of oxic marine environments. This expanded diversity reveals these Archaea likely conferred energetic advantages during early stages of eukaryogenesis, fueling cellular complexity.

microbiology↗

RNA-guided RNA silencing by an Asgard archaeal Argonaute

Eukaryotic Argonaute proteins achieve gene repression and defense against viruses and transposons by RNA-guided RNA silencing. By contrast, known prokaryotic Argonautes adopt single-stranded DNA as guides and/or targets, leaving the evolutionary origin of RNA-guided RNA silencing elusive. Here, we show an evolutionary expansion of Asgard archaeal Argonautes (asAgos), including the discovery of HrAgo1 from the Lokiarchaeon Candidatus Harpocratesius repetitus that shares a common origin with eukaryotic PIWI proteins. HrAgo1 exhibits RNA-guided RNA cleavage in vitro and RNA silencing in human cells. The cryo-EM structure of HrAgo1 combined with quantitative single-molecule experiments reveals that HrAgo1 possesses hybrid structural features and target binding modes bridging those of the eukaryotic AGO and PIWI clades. Finally, genomic evidence suggests that eukaryotic Dicer-like processing of double-stranded RNA likely emerged as a mechanism of generating guide RNA for asAgos prior to eukaryogenesis. Our study provides new insights into the evolutionary origin and plasticity of Argonaute-based RNA silencing.

microbiology↗

Morphological and microbial diversity of hydromagnesite microbialites in Lake Salda, A Mars Analog Alkaline Lake

AbstractLake Salda, recognized as a terrestrial analog for the paleolake in Jezero Crater on Mars, hosts modern, sub/fossil and fossil hydromagnesite microbialites. A comprehensive study was conducted to reveal the distribution, and morphological-mineralogical, microbial diversity of the microbialites that are currently growing in the shallow (<1 m) and deeper waters (up to 15 m) of the lake. Six major microbialite forming zones were identified (Zone I-VI) comprising previously unknown morphotypes of the microbialites. These newly identified morphologies include; linked columns and microbial pavements, exhibiting distinct surface textures such as bulbous, mini columnar, knobby, cerebroidal and smooth. The shallow microbialites showed well-preserved radially growing stromatolitic layers in cm-scale, producing cauliflower structures while the deeper samples exhibit mm scale layering within the mini columnar structures. 16S rRNA amplicon data reveal that abundance of major bacterial taxa of the thrombolitic microbialites from deeper regions are distinct than those of the shallow-growing microbialites with stromatolitic structures. Cyanobacteria were found to be generally less abundant (0.01% to 2%) in the thrombolitic microbialites compared to the stromatolitic microbialites with smooth surface. The Anaerolineae class of the phylum Chloroflexi was prominently present in the stromatolitic microbialites with smooth surface. Notably, the lake exhibited a high abundance of the genus Exiguobacterium, particularly in the deep thrombolitic microbialites (e.g., 93%). Microscopy analysis of the deep microbial mats showed the presence of abundant nano and microcrystalline platy/flakey hydrated Mg carbonate crystals that co- existed with mineralized filaments and spherulitic aggregates within abundant exopolymeric substances (EPSs). Moreover, palygorskite mineral was exclusively identified within the deep microbialites. Co-existence of aragonite and hydromagnesite minerals in particular within the deep microbialites that grow under non-evaporative conditions and the abundant presence of entombed biomass (e.g., filamentous) collectively suggest the potential preservation of biosignatures within the hydrated Mg carbonate build-ups in Lake Salda.

ecology↗

Type III-B CRISPR-Cas signaling-based cascade of proteolytic cleavages

Type III CRISPR-Cas systems provide a sequence-specific adaptive immune response that protects prokaryotic hosts against viruses and other foreign genetic invaders. These crRNA-guided Cas effector complexes bind and cleave complementary RNA targets. Specific target binding stimulates the Cas10 subunit to generate cyclic oligoadenylate (cOA) signaling molecules, that in turn allosterically activate proteins carrying cognate sensory domains: CARF or SAVED. Here, we characterize an elaborate set of genes associated with the type III-B CRISPR-Cas system from Haliangium ochraceum, which includes a signal transduction module of a CBASS defense system with two caspase-like proteases, SAVED-CHAT and PCaspase (Prokaryotic Caspase). We show that binding of a 3-nucleotide cOA (cA3) to the SAVED domain of SAVED-CHAT induces its oligomerization into long filaments that activate the proteolytic activity of the CHAT domain. Surprisingly, we find that activated SAVED-CHAT specifically cleaves and activates the second protease, PCaspase. In turn, activated PCaspase cleaves a multitude of other proteins, including a putative sigma factor and a PCaspase-inhibitor. We expressed the type III-B system and its associated genes in E. coli and observed a strong abortive phenotype when offering a complementary target RNA, but only in the presence of both SAVED-CHAT and PCaspase. Together, our findings show an intriguing cascade of proteolytic activities (conceptually similar to eukaryotic caspases) in this bacterial immune system that reveals yet another strategy to effectively defend against mobile genetic elements.

biochemistry↗

Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes

In the ongoing debates about eukaryogenesis, the series of evolutionary events leading to the emergence of the eukaryotic cell from prokaryotic ancestors, members of the Asgard archaea play a key role as the closest archaeal relatives of eukaryotes. However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved. Here, we analyze distinct phylogenetic marker datasets of an expanded genomic sampling of Asgard archaea and evaluate competing evolutionary scenarios using state-of-the-art phylogenomic approaches. We find that eukaryotes are placed, with high confidence, as a well-nested clade within Asgard archaea, as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree/species tree reconciliation approaches, we show that, in analogy to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared to other archaea. Finally, we infer that the last common ancestor of Asgard archaea likely was a thermophilic chemolithotroph, and that the lineage from which eukaryotes evolved adapted to mesophilic conditions and acquired the genetic potential to support a heterotrophic lifestyle. Our work provides key insights into the prokaryote-to-eukaryote transition and the platform for the emergence of cellular complexity in eukaryotic cells.

evolutionary biology↗

Genomic diversity and biosynthetic capabilities ofsponge-associated chlamydiae

Sponge microbiomes contribute to host health, nutrition, and defense through the production of secondary metabolites. Chlamydiae, a phylum of obligate intracellular bacteria ranging from animal pathogens to endosymbionts of microbial eukaryotes, are frequently found associated with sponges. However, sponge-associated chlamydial diversity has not yet been investigated at the genomic level and host-interactions remain thus far unexplored. Here, we sequenced the microbiomes of three sponge species and found high, though variable, Chlamydiae relative abundances of up to 21.2% of bacterial diversity. Using genome-resolved metagenomics 18 high-quality sponge-associated chlamydial genomes were reconstructed, covering four chlamydial families. Among these, Sorochlamydiaceae shares a common ancestor with Chlamydiaceae animal pathogens, suggesting long-term co-evolution with animals. Sponge-associated chlamydiae genomes mostly resembled environmental chlamydial endosymbionts, but not pathogens, and encoded genes for degrading diverse compounds associated with sponges, such as taurine. Unexpectedly, we identified widespread genetic potential for secondary metabolite biosynthesis across Chlamydiae, which may represent an explored reservoir of novel natural products. This finding suggests that chlamydiae may partake in defensive symbioses and that secondary metabolites play a wider role in mediating intracellular interactions. Furthermore, sponge-associated chlamydiae relatives were found in other marine invertebrates, pointing towards wider impacts of this phylum on marine ecosystems.

microbiology↗

MAPR origins reveal a new class of prokaryotic cytochrome b5 proteins and possible role in eukaryogenesis

The multiple functions of PGRMC1, the archetypal heme-binding eukaryotic MAPR family member, include steroidogenic regulation, membrane trafficking, and steroid responsiveness. The interrelationships between these functions are currently poorly understood. Previous work has shown that different MAPR subclasses were present early in eukaryotic evolution, and that tyrosine phosphorylated residues appeared in the eumetazoan ancestor, coincident with a gastrulation organizer. Here we show that MAPR proteins are related to a newly recognized class of prokaryotic cytochrome-b5 domain proteins. Our first solved structure of this new class exhibits shared MAPR-like folded architecture and heme-binding orientation. We also report that a protein subgroup from Candidate Phyla Radiation bacteria shares MAPR-like heme-interacting tyrosines. Our results support bacterial origins for both PGRMC1 and CYP51A, that catalyze the meiosis-associated 14-demethylation of the first sterol lanosterol from yeast to humans. We propose that eukaryotic acquisition of a membrane-trafficking function related to sterol metabolism was associated with the appearance of MAPR genes early in eukaryotic evolution.

evolutionary biology↗

A closed Candidatus Odinarchaeum genome exposes Asgard archaeal viruses

Asgard archaea have recently been identified as the closest archaeal relatives of eukaryotes. Their ecology remains enigmatic, and their virome, completely unknown. Here, we describe the closed genome of Ca. Odinarchaeum yellowstonii LCB_4, and, from this, obtain novel CRISPR arrays with spacer targets to several viral contigs. We find related viruses in sequence data from thermophilic environments and in the genomes of diverse prokaryotes, including other Asgard archaea. These novel viruses open research avenues into the ecology and evolution of Asgard archaea.

microbiology↗

The evolutionary origin of host association in an ancient bacterial clade

The evolution of obligate host-association of bacterial symbionts and pathogens remains poorly understood. The Rickettsiales represent an order of obligate alphaproteobacterial endosymbionts and parasites that infect a wide variety of eukaryotic hosts, including humans, livestock, insects and protists. Induced by their host-associated lifestyle, Rickettsiales genomes have undergone reductive evolution, leading to small, AT-rich genomes with limited metabolic capacities. We describe several genomes of deep-branching, environmental alphaproteobacteria that branch basal to previously sampled Rickettsiales, and whose genome content are reminiscent of free-living and biofilm-associated lifestyles. Ancestral genome content reconstruction across the Rickettsiales tree revealed that the free-living to host-association transition of this group occurred more recently than previously anticipated, and likely involved the repurposing of a type IV secretion system. One-Sentence SummaryDeep-branching Rickettsiales provide insights into the evolution of obligate host-associated lifestyle

microbiology↗

Picozoa are archaeplastids without plastid

The endosymbiotic origin of plastids from cyanobacteria gave eukaryotes photosynthetic capabilities and launched the diversification of countless forms of algae. These primary plastids are found in members of the eukaryotic supergroup Archaeplastida. All known archaeplastids still retain some form of primary plastids, which are widely assumed to have a single origin. Here, we used single-cell genomics from natural samples combined with phylogenomics to infer the evolutionary origin of the phylum Picozoa, a globally distributed but seemingly rare group of marine microbial heterotrophic eukaryotes. Strikingly, the analysis of 43 single-cell genomes shows that Picozoa belong to Archaeplastida, specifically related to red algae and the phagotrophic rhodelphids. These picozoan genomes support the hypothesis that Picozoa lack a plastid, and further reveal no evidence of an early cryptic endosymbiosis with cyanobacteria. These findings change our understanding of plastid evolution as they either represent the first complete plastid loss in a free-living taxon, or indicate that red algae and rhodelphids obtained their plastids independently of other archaeplastids.

evolutionary biology↗

Near-complete Lokiarchaeota genomes from complex environmental samples using long and short read metagenomic analyses

Asgard archaea is a recently proposed superphylum currently comprised of five recognised phyla: Lokiarchaeota, Thorarchaeota, Odinarchaeota, Heimdallarchaeota and Helarchaeota. Members of this group have been identified based on culture-independent approaches with several metagenome-assembled genomes (MAGs) reconstructed to date. However, most of these genomes consist of several relatively small contigs, and, until recently, no complete Asgard archaea genome is yet available. Large scale phylogenetic analyses suggest that Asgard archaea represent the closest archaeal relatives of eukaryotes. In addition, members of this superphylum encode proteins that were originally thought to be specific to eukaryotes, including components of the trafficking machinery, cytoskeleton and endosomal sorting complexes required for transport (ESCRT). Yet, these findings have been questioned on the basis that the genome sequences that underpin them were assembled from metagenomic data, and could have been subjected to contamination and other assembly artefacts. Even though several lines of evidence indicate that the previously reported findings were not affected by these issues, having access to high-quality and preferentially fully closed Asgard archaea genomes is needed to definitively close this debate. Current long-read sequencing technologies such as Oxford Nanopore allow the generation of long reads in a high-throughput manner making them suitable for their use in metagenomics. Although the use of long reads is still limited in this field, recent analyses have shown that it is feasible to obtain complete or near-complete genomes of abundant members of mock communities and metagenomes of various level of complexity. Here, we show that long read metagenomics can be successfully applied to obtain near-complete genomes of low-abundant members of complex communities from sediment samples. We were able to reconstruct six MAGs from different Lokiarchaeota lineages that show high completeness and low fragmentation, with one of them being a near-complete genome only consisting of three contigs. Our analyses confirm that the eukaryote-like features previously associated with Lokiarchaeota are not the result of contamination or assembly artefacts, and can indeed be found in the newly reconstructed genomes.

microbiology↗

An efficient single-cell transcriptomics workflow to assess protist diversity and lifestyle

Most diversity in the eukaryotic tree of life are represented by microbial eukaryotes, which is a polyphyletic group also referred to as protists. Among the protists, currently sequenced genomes and transcriptomes give a biased view of the actual diversity. This biased view is partly caused by the scientific community, which has prioritized certain microbes of biomedical and agricultural importance. Additionally, it is challenging to establish protist cultures, which further influence what has been studied. It is now possible to bypass the time-consuming process of cultivation and directly analyze the gene content of single protist cells. Single-cell genomics was used in the first experiments where individual protists cells were genomically explored. Unfortunately, single-cell genomics for protists are often associated with low genome recovery and the assembly process can be complicated because of repetitive intergenic regions. Sequencing repetitive sequences can be avoided if single-cell transcriptomics is used, which only targets the part of the genome that is transcribed. In this study we test different modifications of Smart-seq2, a single-cell RNA sequencing protocol originally developed for mammalian cells, to establish a robust and more cost-efficient workflow for protists. The diplomonad Giardia intestinalis was used in all experiments and the available genome for this species allowed us to benchmark our results. We could observe increased transcript recovery when freeze-thaw cycles were added as an extra step to the Smart-seq2 protocol. Further we tried reducing the reaction volume and purifying with alternative beads to test different cost-reducing changes of Smart-seq2. Neither improved the procedure, and cutting the volumes by half actually led to significantly fewer genes detected. We also added a 5 biotin modification to our primers and reduced the concentration of oligo-dT, to potentially reduce generation of artifacts. Except adding freeze-thaw cycles and reducing the volume, no other modifications lead to a significant change in gene detection. Therefore, we suggest adding freeze-thaw cycles to Smart-seq2 when working with protists and further consider our other modification described to improve cost and time-efficiency.

genomics↗

Marine sediments illuminate Chlamydiae diversity and evolution

The bacterial phylum Chlamydiae, which is so far comprised of obligate symbionts of eukaryotic hosts, are well-known as human and animal pathogens1-3. However, the Chlamydiae also include so-called environmental lineages4-6 that primarily infect microbial eukaryotes7. Studying environmental chlamydiae, whose genomes display extended metabolic capabilities compared to their pathogenic relatives8-10 has provided first insights into the evolution of the pathogenic and obligate intracellular lifestyle that is characteristic for this phylum. Here, we report an unprecedented relative abundance and diversity of novel lineages of the Chlamydiae phylum, representing previously undetected, yet potentially important, community members in deep marine sediments. We discovered that chlamydial lineages dominate the microbial communities in the Arctic Mid-Ocean Ridge11, which revealed the dominance of chlamydial lineages at anoxic depths, reaching relative abundances of up to 43% of the bacterial community, and a maximum diversity of 163 different species-level taxonomic unit. Using genome-resolved metagenomics, we reconstructed 24 draft chlamydial genomes, thereby dramatically expanding known interspecies genomic diversity in this phylum. Phylogenomic and comparative analyses revealed several deep-branching Chlamydiae clades, including a sister clade of the pathogenic Chlamydiaceae. Altogether, our study provides new insights into the diversity, evolution and environmental distribution of the Chlamydiae.

microbiology↗

Virus genomes from deep sea sediments expand the ocean megavirome and support independent origins of viral gigantism

The Nucleocytoplasmic Large DNA Viruses (NCLDV) of eukaryotes (proposed order \"Megavirales\") include the families Poxviridae, Asfarviridae, Iridoviridae, Ascoviridae, Phycodnaviridae, Marseilleviridae, and Mimiviridae, as well as still unclassified Pithoviruses, Pandoraviruses, Molliviruses and Faustoviruses. Several of these virus groups include giant viruses, with genome and particle sizes exceeding those of many bacterial and archaeal cells. We explored the diversity of the NCLDV in deep-sea sediments from the Lokis Castle hydrothermal vent area. Using metagenomics, we reconstructed 23 high quality genomic bins of novel NCLDV, 15 of which are closest related to Pithoviruses, 5 to Marseilleviruses, 1 to Iridoviruses, and 2 to Klosneuviruses. Some of the identified Pitho-like and Marseille-like genomes belong to deep branches in the phylogenetic tree of core NCLDV genes, substantially expanding the diversity and phylogenetic depth of the respective groups. The discovered viruses have a broad range of apparent genome sizes including putative giant members of the family Marseilleviridae, in agreement with multiple, independent origins of gigantism in different branches of the NCLDV. Phylogenomic analysis reaffirms the monophyly of the Pitho-Irido-Marseille branch of NCLDV. Similarly to other giant viruses, the Pitho-like viruses from Lokis Castle encode translation systems components. Phylogenetic analysis of these genes indicates a greater bacterial contribution than detected previously. Genome comparison suggests extensive gene exchange between members of the Pitho-like viruses and Mimiviridae. Further exploration of the genomic diversity of \"Megavirales\" in additional sediment samples is expected to yield new insights into the evolution of giant viruses and the composition of the ocean megavirome.\n\nImportanceGenomics and evolution of giant viruses is one of the most vigorously developing areas of virus research. Lately, metagenomics has become the main source of new virus genomes. Here we describe a metagenomic analysis of the genomes of large and giant viruses from deep sea sediments. The assembled new virus genomes substantially expand the known diveristy of the Nucleo-Cytoplasmic Large DNA Viruses of eukaryotes. The results support the concept of independent evolution of giant viruses from smaller ancestors in different virus branches.

microbiology↗