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Eukaryotic cells, with complex features such as membrane-bound nuclei, evolved from prokaryotic cells that lack these components. A newly identified prokaryotic group reveals intermediate steps in eukaryotic-cell evolution. See Article p.353 Although the origin of eukaryotic cells from prokaryotic ancestors remains an enigma, it has become clear that the root of eukaryotes lies among a group of prokaryotes known as archaea. The recent identification of newly described archaea belonging to the Asgard superphylum, including Lokiarchaeota and Thorarchaeota, revealed a group of prokaryotes containing many proteins and genetic sequences that are otherwise found only in eukaryotes. Thijs Ettema and colleagues extend the search for eukaryotic roots by describing further additions to the Asgard superphylum: the Odinarchaeota and Heimdallarchaeota. The new Asgard genomes encode homologues of several components of eukaryotic membrane-trafficking machineries, suggesting that the archaeal ancestor of eukaryotes was well equipped to evolve the complex cellular features that are characteristic of eukaryotic cells.

Accumulating evidence that the eukaryotic nuclear lineage originated from within the Archaea provides support for a tree containing only two primary domains of life—the Achaea and Bacteria—over the currently accepted ‘three-domains tree’. Ever since the discovery in 1977 of a group of microorganisms called the Archaea, researchers have generally assumed that all life on Earth can be arranged into three domains: the Bacteria and Archaea, both lacking nuclei but clearly different from one another, and the eukaryotes, which have nucleated cells. But stimulated by the discovery of lineages of environmental Archaea containing genes previously thought specific to eukaryotes, there has been increasing support for a two-domain model of life, in which the eukaryotes evolved from within the Archaea. In this Review, Martin Embley and colleagues conclude that increasing knowledge of archaeal diversity, together with improvements in reconstructing long-sundered phylogenies, now favour the two-domain view. The discovery of the Archaea and the proposal of the three-domains ‘universal’ tree, based on ribosomal RNA and core genes mainly involved in protein translation, catalysed new ideas for cellular evolution and eukaryotic origins. However, accumulating evidence suggests that the three-domains tree may be incorrect: evolutionary trees made using newer methods place eukaryotic core genes within the Archaea, supporting hypotheses in which an archaeon participated in eukaryotic origins by founding the host lineage for the mitochondrial endosymbiont. These results provide support for only two primary domains of life—Archaea and Bacteria—because eukaryotes arose through partnership between them.

The breadth of genomic diversity found among organisms in nature allows populations to adapt to diverse environments1,2. However, genomic diversity is difficult to generate in the laboratory and new phenotypes do not easily arise on practical timescales3. Although in vitro and directed evolution methods4–9 have created genetic variants with usefully altered phenotypes, these methods are limited to laborious and serial manipulation of single genes and are not used for parallel and continuous directed evolution of gene networks or genomes. Here, we describe multiplex automated genome engineering (MAGE) for large-scale programming and evolution of cells. MAGE simultaneously targets many locations on the chromosome for modification in a single cell or across a population of cells, thus producing combinatorial genomic diversity. Because the process is cyclical and scalable, we constructed prototype devices that automate the MAGE technology to facilitate rapid and continuous generation of a diverse set of genetic changes (mismatches, insertions, deletions). We applied MAGE to optimize the 1-deoxy-d-xylulose-5-phosphate (DXP) biosynthesis pathway in Escherichia coli to overproduce the industrially important isoprenoid lycopene. Twenty-four genetic components in the DXP pathway were modified simultaneously using a complex pool of synthetic DNA, creating over 4.3 billion combinatorial genomic variants per day. We isolated variants with more than fivefold increase in lycopene production within 3 days, a significant improvement over existing metabolic engineering techniques. Our multiplex approach embraces engineering in the context of evolution by expediting the design and evolution of organisms with new and improved properties.

THERE has been a great deal written in recent years on evolutionary relationships between prokaryotes and eukaryotes1,2, and the possible origin of photosynthesis in eukaryotic cells by endosymbiosis of a cyanobacterium2,3. Molecular methods have been used in an attempt to elucidate the principal events in Precambrian cellular evolution. For example primary structures of plastocyanin4, cytochrome f5, and ferredoxin6,7 have been published. These sequences have been compared to primary structures of functionally analogous macromolecules from eukaryotes. Before conclusions on the evolutionary relationships between prokaryotic cyanobacteria and eukaryotic algae and plants can be made from one representative amino acid sequence, it is necessary to evaluate the amount of amino acid sequence variation in proteins isolated from a wide range of cyanobacteria. In this study the amount of variation in plastocyanins and in cytochromes f was investigated. The results from complete and partial amino acid sequence determinations on these proteins from a number of cyanobacteria, suggest that the rate of evolution of the proteins in oxygenic photosynthetic prokaryotes is much less than the rates of evolution of corresponding proteins in eukaryotic algae and higher plants.