In addition to their evolutionary sequence divergence, the smaller 30s ribosomal RNAs of each domain, show distinct structural features characteristic of their own domain, but also emphasizing structural links between Bacteria and Archaea on the one hand and Archaea and Eukaryotes on the other, qualitatively confirming the central place of the Archaea in the divergence. Fig 4: Small and large rRNA subunits of the eubacteia Thermus thermophilus and the archaeon Haloarcula marismortui. RNA orange and yellow, protein blue and active site green. (Wikipedia Ribosome) Click either image to see it rotating. The validity of the RNA-era concept and the capacity for RNAs to be both replicating informational and active ribo-enzymes is emphasized by the continuing dependence of the ribosome on rRNA rather than the protein components demonstrated by the 3-dimensional realizations of the two subunits in fig 4, which show that the rRNA molecules are still carrying out the central task of protein assembly with only minor modification due to the chaperoning proteins, despite 3.8 billion years of evolution. Fig 5: Further elaboration of the rRNA tree (Pace 1997) Click to enlarge Norman Pace subsequently enlarged the scope and accuracy of the rRNA tree, including a greater diversity of organisms. This tree has become the basis of several other studies (see e.g. fig 10). Fig 6: Lower right: A third rRNA tree which suggests Archaea lie very close to the root is contrasted with that for the enzyme HMGCoA reductase, which also shows evidence of horizontal transfer to an Archaean (ex Doolittle 2000). The Copernican principle asserts that the Earth is a typical rocky planet in a typical planetary system, located in an unexceptional region of a common barred-spiral galaxy, hence it is probable that the universe teems with complex life. This is supported to a reasonable extent by the discovery of an increasing number of planets including some putative Goldilocks zone planets where water would be liquid and life as we know it could potentially exist. Set against this, the Rare Earth hypothesis argues that the emergence of complex life requires a host of fortuitous circumstances including a galactic habitable zone, a central star and planetary system having the requisite character, the circumstellar habitable zone, the size of the planet, the advantage of a large satellite, conditions needed to assure the planet has a magnetosphere and plate tectonics, the chemistry of the lithosphere, atmosphere, and oceans, the role of evolutionary pumps such as massive glaciation and rare bolide impacts, and whatever led to the still mysterious Cambrian explosion of animal phyla. This might mean that planets able to support a bacterial level of life are not so uncommon, but those supporting complex multicellular life might be. Bringing this question to a pivotal crux in our context, the emergence of mitochondria as endosymbionts has been proposed to be a critical bottleneck which allowed complex life to evolve only once, because, only in this effectively fractal cellular architecture, can the membrane surface areas necessary to support the chemical reactions enabling the vastly larger number of genes in a complex organisms genome to maintain metabolic stability (Lane and Martin). Whether such endo-symbiosis is rare. or a common extreme of parasitic relationships would then determine how likely or unlikely complex life might be. Left: Bacterium Gemmata obscuriglobus with internal nuclear envelope and vaccuoles (Rachel Melwig & Christine Panagiotidis / EMBL). Right: Ultrathin EM section of a mimivirus in amoeba (Jean-Michel Claverie) Inset: Mimivirus infected by sputnik phage. Ocean trawl reveals megavirus Oct 11 Offset against both the uniqueness of the mitochondrial endo-symbiosis and the closely linked, but independent question of the origin of the nucleus and nuclear envelope, has been the discovery of mimiviruses and mamaviruses infecting amoeba (Raoult et, al.) and related very large aquatic viruses such as CroV infecting single celled plankton species, which despite their recent discovery, appear from ocean gene analyses to be potentially ubiquitous and widespread in the oceans and possibly playing a crucial role in regulating the atmospheric-oceanic pathways, such as carbon sequestration (Fisher et. al.). These form an intermediate genetic position between viruses and cells, having the largest genomes, with extensive cellular machinery and larger than the smallest completely autonomous bacterial and archaeal genomes. As an illustration of genes in mimivirus normally appearing only in cellular genomes, the mimivirus has genes for central protein-translation components, including four amino-acyl transfer RNA synthetases, peptide release factor 1, translation elongation factor EF-TU, and translation initiation factor 1. The genome also exhibits six tRNAs. Other notable features include the presence of both type I and type II topoisomerases, components of all DNA repair pathways, many polysaccharide synthesis enzymes, and one intein-containing gene. Inteins are protein-splicing domains encoded by mobile intervening sequences (IVSs). They self-catalyze their excision from the host protein, ligating their former flanks by a peptide bond. They have been found in all domains of life (Eukaria, Archaea, and Eubacteria), but their distribution is highly sporadic. Only a few instances of viral inteins have been described. Self-splicing type I introns are a different type of mobile IVS, self-excising at the mRNA level. They are rare in viruses. Mimivirus exhibits four instances of self-excising intron, all in RNA polymerase genes. Evolutionary diversification of Mimiviruses from nucleocytoplasmic large DNA viruses (Fisher et. al.) and in relation to the three domains of cellular life based on the concatenated sequences of seven universally conserved protein sequences (Raoult et. al.) Mimiviruses also host parasitic virophages, affectionately named sputnik as viral satellites, which piggy back on the metabolism of the large viral factories set up by these giant viral genomes causing the mimiviruses to sicken, and these virophages also contains genes that are linked to viruses infecting each of the three domains of life Eukarya, Archaea and Bacteria (La Scola et. al.). It has thus been suggested that they have a primary role in the establishment of cellular life and that they may have been instrumental in the emergence of the nuclear envelope. Tangled Roots of Horizontal Transfer Despite the division into three domains, further investigations of proteins in the three domains began to reveal a much more confused and complicated picture. Firstly the ribosomal proteins, like the rRNAs show distinct, easily differentiated morphologies with some correspeondences linking one pair of domains and other another pair (Forterre 2006b, Woese 2000). Secondly, the proteins in Eukaryotes appear to have a mixed origin with the informational ones having an evolutionary relationship with Archaea but the metabolic enzymes appearing to have a bacterial origin. This suggests that the Eukaryote genome has either resulted from one, or more symbiotic fusions e.g. an Archaeal and a bacterial genome and/or that there has been a high degree of horizontal gene transfer between bacteria and Eukaryotes. Fig 7: Evolution of iron-sulphur cluster proteins of mitochondria is linked to α-proetobacteria (Emelyanov 2003) The evidence for symbiotic inclusions is clear from the fact that all Eukaryotes, except for a few primitive anaerobic varieties, such as the metamonad human gut parasite Giardia lamblia, all have endosymbiotic respiring mitochondria, which are evolutionarily related to α-proteobacteria such as Rickettsiae (Emelyanov 2003). Plants also have photosynthetic chloroplasts derived from cyanobacteria. α-proteobacteria, including Rickettsiae (and related Wollbachia and Agrocbacterium), obligately live in the cytoplasm of other cells and so are naturally adapted to becoming an endo-symbiont of a glycolytic organism by providing respiring energy to the hosts metabolism resulting in the mitochondrion. Giardia still retains traces of mitochondrial proteins so appears to have lost its respiring organelles, rather than occupying a place in the tree before mitochondria were incorporated into eucarya (Adam 2000).
Posted on: Tue, 19 Nov 2013 20:00:05 +0000