Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes

Cunha, Violette Da; Gaïa, Morgan; Gadelle, Danièle; Nasir, Arshan; Forterre, Patrick

doi:10.1371/journal.pgen.1006810

Cited by 137 publications

(179 citation statements)

References 81 publications

(154 reference statements)

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“…However, most analyses support the super‐class Methanomada, which groups Methanococcales with other group I methanogens, i.e., Methanobacteriales and Methanopyrales (Supporting Information Fig. S1; Adam et al ., ; Da Cunha et al ., ).…”

Section: Introductionmentioning

confidence: 97%

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Badel

Erauso

Gomez

et al. 2019

Environmental Microbiology

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Summary Although plasmids play an important role in biological evolution, the number of plasmid families well‐characterized in terms of geographical distribution and evolution remains limited, especially in archaea. Here, we describe the first systematic study of an archaeal plasmid family, the pT26‐2 plasmid family. The in‐depth analysis of the distribution, biogeography and host–plasmid co‐evolution patterns of 26 integrated and 3 extrachromosomal plasmids of this plasmid family shows that they are widespread in Thermococcales and Methanococcales isolated from around the globe but are restricted to these two orders. All members of the family share seven core genes but employ different integration and replication strategies. Phylogenetic analysis of the core genes and CRISPR spacer distribution suggests that plasmids of the pT26‐2 family evolved with their hosts independently in Thermococcales and Methanococcales, despite these hosts exhibiting similar geographic distribution. Remarkably, core genes are conserved even in integrated plasmids that have lost replication genes and/or replication origins suggesting that they may be beneficial for their hosts. We hypothesize that the core proteins encode for a novel type of DNA/protein transfer mechanism, explaining the widespread oceanic distribution of the pT26‐2 plasmid family.

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Section: Introductionmentioning

confidence: 97%

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Badel

Erauso

Gomez

et al. 2019

Environmental Microbiology

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“…The core topology of the tree of life remains contentious, [2][3][4] but evidence amassed over the last decade supports the view that eukaryotes as we presently know them arose from a merger of prokaryotic cells, [5][6][7][8][9] involving an archaeal host [10][11][12] (likely from within the recently described Asgard superphylum) [13,14] and an endosymbiotic [5] bacterium (likely from a lineage within or closely related to the modern Alphaproteobacteria). [15][16][17] If this was the case, eukaryotes likely inherited their membrane lipids from their prokaryotic forebears.…”

Section: Introductionmentioning

confidence: 99%

Why the Lipid Divide? Membrane Proteins as Drivers of the Split between the Lipids of the Three Domains of Life

Sojo

2019

BioEssays

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Recent results from engineered and natural samples show that the starkly different lipids of archaea and bacteria can form stable hybrid membranes. But if the two types can mix, why don't they? That is, why do most bacteria and all eukaryotes have only typically bacterial lipids, and archaea archaeal lipids? It is suggested here that the reason may lie on the other main component of cellular membranes: membrane proteins, and their close adaptation to the lipids. Archaeal lipids in modern bacteria could suggest that the last universal common ancestor (LUCA) had both lipid types. However, this would imply a rather elaborate evolutionary scenario, while negating simpler alternatives. In light of widespread horizontal gene transfer across the prokaryotic domains, hybrid membranes reveal that the lipid divide did not just occur once at the divergence of archaea and bacteria from LUCA. Instead, it continues to occur actively to this day. Also see the video abstract here https://youtu.be/TdKjxoDAtsg.

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“…In the traditional three domain tree of life, eukaryotes are seen as a sister group to archaea [14][15][16] (Fig. 1a).…”

Section: Introductionmentioning

confidence: 99%

Bacterial genes outnumber archaeal genes in eukaryotic genomes

Bruckner

Martin

2019

Preprint

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AbstractThe origin of eukaryotes is one of evolution’s most important transitions, yet it is still poorly understood. Evidence for how it occurred should be preserved in eukaryotic genomes. Based on phylogenetic trees from ribosomal RNA and ribosomal proteins, eukaryotes are typically depicted as branching together with or within archaea. This ribosomal affiliation is widely interpreted as evidence for an archaeal origin of eukaryotes. However, the extent to which the archaeal ancestry of genes for the cytosolic ribosomes of eukaryotic cells is representative for the rest of the eukaryotic genome is unknown. Here we have clustered 19,050,992 protein sequences from 5,443 bacteria and 212 archaea with 3,420,731 protein sequences from 150 eukaryotes spanning six eukaryotic supergroups to identify genes that link eukaryotes exclusively to bacteria and archaea respectively. By downsampling the bacterial sample we obtain estimates for the bacterial and archaeal proportions of genes among 150 eukaryotic genomes. Eukaryotic genomes possess a bacterial majority of genes. On average, eukaryotic genes are 56% bacterial in origin. The majority drops to 53% in eukaryotes that never possessed plastids, and increases to 61% in photosynthetic eukaryotic lineages, where the cyanobacterial ancestor of plastids contributed additional genes to the eukaryotic genome, reaching 67% in higher plants. Intracellular parasites, which undergo reductive evolution in adaptation to the nutrient rich environment of the cells that they infect, relinquish bacterial genes for metabolic processes. In the current sample, this process of adaptive gene loss is most pronounced in the human parasite Encephalitozoon intestinalis with 86% archaeal and 14% bacterial derived genes. The most bacterial eukaryote genome sampled is rice, with 67% bacterial and 33% archaeal genes. The functional dichotomy, initially described for yeast, of archaeal genes being involved in genetic information processing and bacterial genes being involved in metabolic processes is conserved across all eukaryotic supergroups.

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Lokiarchaea are close relatives of Euryarchaeota, not bridging the gap between prokaryotes and eukaryotes

Cited by 137 publications

References 81 publications

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

The global distribution and evolutionary history of the pT26‐2 archaeal plasmid family

Why the Lipid Divide? Membrane Proteins as Drivers of the Split between the Lipids of the Three Domains of Life

Bacterial genes outnumber archaeal genes in eukaryotic genomes

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