| 1. |
- Eme, Laura, et al.
(författare)
-
Inference and reconstruction of the heimdallarchaeial ancestry of eukaryotes
- 2023
-
Ingår i: Nature. - : Springer Nature. - 0028-0836 .- 1476-4687. ; 618:7967, s. 992-
-
Tidskriftsartikel (refereegranskat)abstract
- 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 part as the closest archaeal relatives of eukaryotes(1). However, the nature and phylogenetic identity of the last common ancestor of Asgard archaea and eukaryotes remain unresolved(2-4). Here we analyse 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 and as a sister lineage to Hodarchaeales, a newly proposed order within Heimdallarchaeia. Using sophisticated gene tree and species tree reconciliation approaches, we show that analogous to the evolution of eukaryotic genomes, genome evolution in Asgard archaea involved significantly more gene duplication and fewer gene loss events compared with other archaea. Finally, we infer that the last common ancestor of Asgard archaea was probably 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 a platform for better understanding the emergence of cellular complexity in eukaryotic cells.
|
|
| 2. |
- Baker, Brett J., et al.
(författare)
-
Genomic inference of the metabolism of cosmopolitan subsurface Archaea, Hadesarchaea
- 2016
-
Ingår i: Nature Microbiology. - 2058-5276. ; 1:3
-
Tidskriftsartikel (refereegranskat)abstract
- The subsurface biosphere is largely unexplored and contains a broad diversity of uncultured microbes(1). Despite being one of the few prokaryotic lineages that is cosmopolitan in both the terrestrial and marine subsurface(2-4), the physiological and ecological roles of SAGMEG (South-African Gold Mine Miscellaneous Euryarchaeal Group) Archaea are unknown. Here, we report the metabolic capabilities of this enigmatic group as inferred from genomic reconstructions. Four high-quality (63-90% complete) genomes were obtained from White Oak River estuary and Yellowstone National Park hot spring sediment metagenomes. Phylogenomic analyses place SAGMEG Archaea as a deeply rooting sister clade of the Thermococci, leading us to propose the name Hadesarchaea for this new Archaeal class. With an estimated genome size of around 1.5 Mbp, the genomes of Hadesarchaea are distinctly streamlined, yet metabolically versatile. They share several physiological mechanisms with strict anaerobic Euryarchaeota. Several metabolic characteristics make them successful in the subsurface, including genes involved in CO and H-2 oxidation (or H-2 production), with potential coupling to nitrite reduction to ammonia (DNRA). This first glimpse into the metabolic capabilities of these cosmopolitan Archaea suggests they are mediating key geochemical processes and are specialized for survival in the subsurface biosphere.
|
|
| 3. |
- Saw, Jimmy H., et al.
(författare)
-
Exploring microbial dark matter to resolve the deep archaeal ancestry of eukaryotes
- 2015
-
Ingår i: Philosophical Transactions of the Royal Society of London. Biological Sciences. - : The Royal Society. - 0962-8436 .- 1471-2970. ; 370:1678
-
Tidskriftsartikel (refereegranskat)abstract
- The origin of eukaryotes represents an enigmatic puzzle, which is still lacking a number of essential pieces. Whereas it is currently accepted that the process of eukaryogenesis involved an interplay between a host cell and an alphaproteo-bacterial endosymbiont, we currently lack detailed information regarding the identity and nature of these players. A number of studies have provided increasing support for the emergence of the eukaryotic host cell from within the archaeal domain of life, displaying a specific affiliation with the archaeal TACK superphylum. Recent studies have shown that genomic exploration of yet-uncultivated archaea, the so-called archaeal 'dark matter', is able to provide unprecedented insights into the process of eukaryogenesis. Here, we provide an overview of state-of-the-art cultivation-independent approaches, and demonstrate how these methods were used to obtain draft genome sequences of several novel members of the TACK superphylum, including Lokiarchaeum, two representatives of the Miscellaneous Crenarchaeotal Group (Bathyarchaeota), and a Korarchaeum-related lineage. The maturation of cultivation-independent genomics approaches, as well as future developments in next-generation sequencing technologies, will revolutionize our current view of microbial evolution and diversity, and provide profound new insights into the early evolution of life, including the enigmatic origin of the eukaryotic cell.
|
|
| 4. |
|
|
| 5. |
- Spang, Anja, et al.
(författare)
-
Complex archaea that bridge the gap between prokaryotes and eukaryotes
- 2015
-
Ingår i: Nature. - : Springer Science and Business Media LLC. - 0028-0836 .- 1476-4687. ; 521:7551, s. 173-179
-
Tidskriftsartikel (refereegranskat)abstract
- The origin of the eukaryotic cell remains one of the most contentious puzzles in modern biology. Recent studies have provided support for the emergence of the eukaryotic host cell from within the archaeal domain of life, but the identity and nature of the putative archaeal ancestor remain a subject of debate. Here we describe the discovery of 'Lokiarchaeota', a novel candidate archaeal phylum, which forms a monophyletic group with eukaryotes in phylogenomic analyses, and whose genomes encode an expanded repertoire of eukaryotic signature proteins that are suggestive of sophisticated membrane remodelling capabilities. Our results provide strong support for hypotheses in which the eukaryotic host evolved from a bona fide archaeon, and demonstrate that many components that underpin eukaryote-specific features were already present in that ancestor. This provided the host with a rich genomic 'starter-kit' to support the increase in the cellular and genomic complexity that is characteristic of eukaryotes.
|
|
| 6. |
- Zepeda, Vanessa K., et al.
(författare)
-
Terasakiispira papahanaumokuakeensis gen. nov., sp nov., a gammaproteobacterium from Pearl and Hermes Atoll, Northwestern Hawaiian Islands
- 2015
-
Ingår i: International Journal of Systematic and Evolutionary Microbiology. - : Microbiology Society. - 1466-5026 .- 1466-5034. ; 65, s. 3609-3617
-
Tidskriftsartikel (refereegranskat)abstract
- A Gram-negative, helical bacterium designated PH27A(T) was cultivated from an anchialine pool on Pearl and Hermes Atoll, Northwestern Hawaiian Islands. The obligately halophilic strain was motile by bipolar tufts of flagella and grew optimally at pH 7, and microaerobically or aerobically. Closest neighbours based on 16S rRNA gene nucleotide sequence identity are Marinospirillum celere v1c_Sn-red(T) (93.31 %) and M. alkaliphilum Z4(T) (92.10 %) in the family Oceanospirillaceae, class Gammaproteobacteria. PH27A(T) is distinguished phenotypically from members of the genus Marinospirillum by its hydrolysis of gelatin, the absence of growth in media containing <= 1 % (w/v) NaCl and the ranges of temperature (12-40 degrees C) and pH (5-8) for growth. The major compound ubiquinone Q-9 distinguishes the quinone system of strain PH27A(T) from those in members of the genus Marinospirillum and other members of the Oceanospirillaceae, in which the major quinone is Q-8. Major polar lipids in PH27A(T) were phosphatidylethanolamine and phosphatidylglycerol, with moderate amounts of diphosphatidylglycerol and phosphatidylserine. Spermidine and cadaverine dominated the polyamine pattern; large proportions of cadaverine have not been reported in members of the genus Marinospirillum. Genotypic and chemotaxonomic data show that PH27A(T) does not belong in the genus Marinospirillum or other genera of the family Oceanospirillaceae or the Halomonadaceae. We propose a new genus, Terasakiispira gen. nov., be created to accommodate Terasakiispira papahanaumokuakeensis gen. nov., sp. nov. as the type species, with PH27A(T) (=ATCC BAA-995(T)=DSM 16455(T)=DSM 23961(T)) as the type strain.
|
|
