On the Archaeal Origins of Eukaryotes and the Challenges of Inferring Phenotype from Genotype

Abstract

If eukaryotes arose through a merger between archaea and bacteria, what did the first true eukaryotic cell look like? A major step toward an answer came with the discovery of Lokiarchaeum, an archaeon whose genome encodes small GTPases related to those used by eukaryotes to regulate membrane traffic. Although ‘Loki’ cells have yet to be seen, their existence has prompted the suggestion that the archaeal ancestor of eukaryotes engulfed the future mitochondrion by phagocytosis. We propose instead that the archaeal ancestor was a relatively simple cell, and that eukaryotic cellular organization arose as the result of a gradual transfer of bacterial genes and membranes driven by an ever-closer symbiotic partnership between a bacterium and an archaeon.

Debating Eukaryogenesis—Part 1: Does Eukaryogenesis Presuppose Symbiosis Before Uptake?

“…The Asgard GTPases miss canonical recognition sequences for the attachment of the hydrophobic groups and the metagenomes do not encode the necessary enzymes either. [ 25 ] Asgard metagenomes miss other endocytosis components, mediating inward membrane curvature as well as the enzymes capable of membrane scission: dynamins. These seem to be of (mitochondrial) endosymbiont origin as well.…”

“…Burns and co-workers, analyzing trophic mode predictive gene sets, conclude that these archaea are not phagocytic, [16] Dey et al convincingly show that even claiming a "primitive" form is premature at best. [25] Such claims are based on the genomes encoding small GTPases, resembling those involved in vesicle transport, as well as COP (vesicle coat proteins) and TRAnsport protein particle (TRAPP) homologues. First of all: "homologous genes" do not automatically have "homologous functions" (see also Part 2).…”

Taking the technical microbiome into the next decade

“…Phenotypic differentiation, often related to environmental fluctuations, using the same genotype as basis can be observed across the domains of life (West-Eberhard, 1989;Kussell and Leibler, 2005;Fusco and Minelli, 2010;Dey et al, 2016). Phenotypic heterogeneity is often a strategy of microorganisms to sustain their activity in dynamic environments (Ackermann, 2015).…”

The role of archaea in the origin of eukaryotes

“…Однако роль этих ферментов у архей остается неясной. Уста-новлено, что ГТФазы Lokiarchaeum не ассоциированы с внутриклеточными мембранами (в отличие от эука-риот) и, по-видимому, не участвуют в их ремоделиро-вании [36] Кроме рассмотренных выше клеточных систем, не-которым группам архей свойственны и другие сходные с эука риотами черты, которые, очевидно, уже функциони-ровали в LECA. В частности, у Euryarchaeota обнаружены элементы системы интерференции РНК (iRNA) [39,40], включая семейство белков-аргонавтов, защищающих клетки от вирусов и транспозонов.…”