Complex Archaea: Missing link in evolution of Eukaryotes

From early 18^th century to a larger part of 20^th century biologists accepted Darwin’s theory of natural selection which postulated that life on earth evolved from a single cell or pre-cell. The concept described as concept of tree of life believed that diverse species descended from common ancestors. In 1962 an interesting paper submitted by Roger Stainer and C. B. Van Niel categorised living organisms into prokaryotes and Eukaryotes based on cellular organisation.  Later in 1977 Carl Woese and George E Fox experimentally disproved the universally held hypotheses of tree of life. They reported of a third kingdom Archaea bacteria defined as a new urkingdom (domain) distinct from the bacteria and eukaryotes. He redrew the phylogenetic tree with three domains- Bacteria, Archaea and Eucarya. This new hypothesis drew severe criticism from reputed scientists who refused to accept the speculation about an era of rapid evolution where considerable horizontal transfer of genes has occurred.  Often termed as extremophiles, Archaea are anaerobic and can thrive in extreme weather conditions. Now most biologists believe that they are very ancient and could exist in conditions not conducive for normal life. It is predicted that organisms similiar to Archaea could exist in other planets. Eukaryotes and Archaea were considered sister groups for their similarities in genes and metabolic pathways.

In 1996 Woese with his team of scientists published the full genome or blue print of an organism in the domain Archaea and concluded that they are more closely related to Eukaryotes than bacteria. The signature sequence of ribosomal RNA genes found in all organisms was used as a basis to assess the variations or similarities. These studies helped to confirm that Archaea constitute a separate group as it contained hundreds of genes which had no counterparts in either bacteria or eukarya. But the ribosomal proteins of Archaea were similar to those of Eukarya.

Earliest Eukaryotes came into existence 2 billion years ago. The origin of Eukaryotic cell remained a contentious puzzle for biologists for long. While cytologically bacteria and archaea are relatively simple, eukaryotic cell is complex and highly specialised it is hence hard to reconcile the popular hypothesis of prokaryote to eukaryote transition.  One of the prevalent hypotheses about the origin of complex cell is that earliest eukaryotes arose when an archaeon engulfed a bacterium and continued to exist in a symbiotic relationship with it. The engulfed bacterium eventually developed into mitochondria, the power house of cell.  Mitochondria are present in all eukaryotes and its gene sequences are clearly related to Alphaproteobacteria. During the early genomic era, analysis of eukaryotic genome indicated that it was chimaeric in nature containing both bacterial and archaeal genes besides associated eukaryotic genes. While some of the genes could be traced back to alphaproteobacteria the lineage of eukaryotic host remained obscure.

 A scientific article published in Nature by Thijis Ettema of Uppsala University uncovered the mystery of origin of eukaryotic cell. Dr. Ettema and team collected samples from the sea bed of Svalbard, few kilometres from an underwater volcano, Loki’s Castle for a microbial diversity study. A Phylogenetic analyses of Deep Sea Archaeal Group (DSAG) of the Loki Castle region named as Lokiarchaeota is believed to be the missing link between the single-celled organisms to complex living beings. Lokiarchaeota belong to the deeply-branching clade of the archaeal TACK superphylum, sans mitochondria and contains proteins not found in any other archaea but present in Eukaryotes.

Using deep metagenomics technique, 92% of composite gene sequence of Lokiarcheota is assembled. Around 175 predicted microbial proteins were found to be similar to eukaryotes proteins involved in phagocytosis, cell shape formation and membrane remodelling. Archaeal genome contained five actin homologs that are more similar to eukaryote actins than to archaeal actin-like proteins. Nearly 70 homologs of Ras-family small GTPases accounting for 2% of predicted proteins are found in archaea. Gene sequences for ESCRT proteins and proteins involved in intracellular vesicle trafficking mechanisms are also found.  The sheer size of similarities of proteins between Lokiarchaeota and Eukaryotes suggest that these might have been the primitive ancestors of Eukaryotes. They could have paved way for the development of eukaryotes. With proteins needed for phagocytosis they could have started engulfing single celled organisms (one them could have been the alphaproteobacteria). Harboured with basic machinery of cytoskeleton, it might have moved around like amoeba engulfing prey. These set of exciting revelations indicate that probably Lokiarcheaota might have been the missing link between the prokaryotes and Eukaryotes.

A. Spang et al., “Complex archaea that bridge the gap between prokaryotes and eukaryotes,” Nature, doi:10.1038/nature14447, 2015.