Prokaryote vs. Eukaryote cells: Koonin opines (Introduction)

by David Turell , Thursday, October 15, 2015, 14:15 (3119 days ago) @ David Turell

Eugene Koonin's new think piece on how eukaryotes arrived:-http://www.biomedcentral.com/1741-7007/13/84-"The origin of eukaryotes is one of the hardest problems in evolutionary biology and sometimes raises the ominous specter of irreducible complexity. Reconstruction of the gene repertoire of the last eukaryotic common ancestor (LECA) has revealed a highly complex organism with a variety of advanced features but no detectable evolutionary intermediates to explain their origin. Recently, however, genome analysis of diverse archaea led to the discovery of apparent ancestral versions of several signature eukaryotic systems, such as the actin cytoskeleton and the ubiquitin network, that are scattered among archaea. These findings inspired the hypothesis that the archaeal ancestor of eukaryotes was an unusually complex form with an elaborate intracellular organization. The latest striking discovery made by deep metagenomic sequencing vindicates this hypothesis by showing that in phylogenetic trees eukaryotes fall within a newly identified archaeal group, the Lokiarchaeota, which combine several eukaryotic signatures previously identified in different archaea. The discovery of complex archaea that are the closest living relatives of eukaryotes is most compatible with the symbiogenetic scenario for eukaryogenesis.-***-"A eukaryotic cell is a strikingly complex macromolecular aggregate by any account, but specifically when compared with archaeal and bacterial cells. To begin with, a typical eukaryotic cell has a three to four orders of magnitude larger volume than most bacteria and archaea [3]-[5]. This size difference translates into a difference in the physical principles of cell functioning: unlike most bacteria and archaea in which proteins, nucleic acids and small molecules diffuse more or less freely, the intracellular space in eukaryotes is fully compartmentalized so that molecules are distributed through specialized transport mechanisms [6], [7]. The compartmentalization and transport are supported by the elaborate system of intracellular membranes which includes the membrane of the eponymous eukaryotic organelle, the nucleus, and by an advanced cytoskeleton that consists of actin filaments and tubulin microtubules and includes numerous additional, dedicated proteins. Crucially, the great majority of eukaryotes possess the power-producing organelles, the mitochondria or their derivatives, that are now commonly accepted to have evolved from ?-proteobacteria by endosymbiosis [8], [9]. Although some unicellular eukaryotes lack mitochondria, evolutionary reconstructions clearly point to secondary loss in all amitochondrial groups [10], [11]. -"Thus, eukaryotes show a qualitatively different level of cellular organization from that of archaea and bacteria, and there are no detectable evolutionary intermediates. Comparative analysis of eukaryotic cells and genomes indicates that the signature advanced functional systems of the eukaryotic cells were already present in the last eukaryotic common ancestor (LECA). These ancestral features include the actin and tubulin-based forms of cytoskeleton, the nuclear pore, the spliceosome, and the ubiquitin signaling network, to mention only several aspects of the inherent organizational complexity of eukaryotic cells [12]-[16]. The emergence of these fundamental facets of advanced cellular organization presents a challenge of such scale that Darwin's famous scenario for the evolution of the eye looks like a straightforward solution to an easy problem. To some, the enigma of eukaryogenesis can appear so perplexing that the infamous concept of ‘irreducible complexity' has sneaked into the scientific mainstream [17], although debunking of these ideas has not been long in coming [18]. Below I discuss the recent advances in evolutionary genomics that make the origin of eukaryotes much less mysterious than it appeared even recently." (my bold)-Comment: Lots of hope to save Darwin in his writings:-"What next? Does Loki bridge archaea and eukaryotes as stated in the title of the article by Ettema and colleagues? I think this is still only a halfway bridge. A lot of difficult work remains to be done to join the two banks. First, Loki certainly is not the archaeal ancestor of eukaryotes: that life form existed over a billion years ago. It is entirely possible and actually likely that even closer relatives of eukaryotic ancestors may be discovered, perhaps with an even greater organizational complexity. Loki is only the beginning of the quest for those ancestors, by no means the end. However, further, even possibly exhaustive characterization of archaeal (and bacterial) diversity by methods of metagenomics and single cell genomics is the easy part of the deal. The challenge lies in the investigation of the biology of these organisms. Although we can never know what precisely happened more than a billion years ago, to me, demonstration of the archaeal-bacterial endosymbiosis in the laboratory would mean the completion of the bridge."