The evolution of a living organism, as well as pre-biotic molecular evolution, seems to be inconsistent with the second law of thermodynamics. When a bacterium is compared with some other higher organism, it is clear that all evolution tends to order more and larger molecules into more complex systems. The trick is the radiation of heat from the Earth. The Earth is loosing gravitational energy (～1031Joule) obtained from the accretion of asteroids during its birth 4.55 Gyr ago. Energy loss implies a decrease in entropy which in turn requires ordering of the Earth. As components of the Earth, the lighter elements such as H, C, N, and O at the surface must also evolve to larger molecules and ultimately to living organisms, so that the entire surface of the Earth is now covered by low entropy materials of life.
Thus, the entropy decrease of the Earth is responsible for the evolution of living organisms. The above argument suggests a new scenario for the origin of life as well as its source, biomolecules. The heavy fall of the extraterrestrial objects containing metallic iron into the ocean would produce a reducing atmosphere thus generating a wide variety of organic molecules at about 4.0 Gyr ago. Of these, only hydrophilic and clay-affinitive molecules could have survived the environment of strong UV radiation and weakly oxidation, because they could be immersed in seawater and be adsorbed on clay particles that were finally deposited on the seabed.
A recent shock recovery experiment simulating the heavy fall of meteorite into the ocean supports the scenario of the origin of organic molecules. Various biomolecules has been formed in that experiment. Therefore, the above arguments may be answers for the fundamental questions on the life why living organisms have to evolve and why biomolecules are all hydrophilic and clay-affinitive. A further scenario of pre-biotic molecular evolution can be seen elsewhere.
Arthrobacter sp. (formerly Flavobacterium sp.) KI72 has enzymes which are responsible for the degradation of nylon-6 industry by-products (nylon-oligomer). NylB encoded on plasmid pOAD2 is one of these enzymes and has a specific activity toward the degradation of 6-aminohexanoate-linear dimer (Ald). The plasmid, pOAD2, has also an analogous protein, NylB', which has 88 % homology to NylB but only about 0.5 % of the specific activity. We constructed Hyb24 (a hybrid between the NylB and NylB' with NylB'-level activity), Hyb24DN (with double mutation of G181D and H266N with NylB-level activity) and Hyb24DNA (a mutant of Hyb24DN with an additional mutation of S112A at the active site) proteins and solved the three-dimensional structures by x-ray crystallography. In case of Hyb24DNA, the structure of a complex with substrate, Ald, was determined. The overall structures of three proteins are almost identical with a two-domain structure that is categorized in β-lactamase fold. On the basis of the spatial arrangements of amino acid residues at the active site of Hyb24DN and Hyb24DNA-Ald complex, we conclude that the nylon-oligomer hydrolase has evolved from the ester hydrolysis enzymes, of which essential residue is nucleophilic Ser112, with a β-lactamase fold as an ancestral protein by substitution of two residues G181D and H266N at the active site pocket.
How a mechanism of the subunit exchange in a supra-molecular complex does to be a suitable and reasonable form? It seems like to be existing a simple exchange in a complex. However, there are generally so many restrictions on the tertiary structure of the protein folding, for examples hydrogen bonds, hydrophobic and ionic interactions. A mammalian proteasome has two-types complexes, one is constitutive and other immunologic. The immuno-proteasome has six different subunits than constitutive-proteasome, when living cells are in an immune response. How do exchange occur in the complex particle? How and what characteristics in the tertiary structure of the proteasome are existing. We investigated it that contributions of hydrogen bonds among subunits control and form suitable complex by comparing a bovine liver and yeast proteasome, having immune response and no one, respectively.
Contrary to our expectation, yeast proteasome has much hydrogen bonds even if an incorrect subunit exists, rather than a bovine proteasome. The resultant shows bovine proteasome has strict recognition mechanism for incorrect subunits than yeast ones, which may supply possibilities on exchanges of subunits when the immune response occurs in our living cells.
Discrepancies among phylogenetic trees based on different biopolymers and morphology, as well as diversity of fundamental features in spite of general belief that most fundamental features are common to all forms of life, led us to propose a hypothesis that the major driving force for evolution is information exchanges among different species, rather than divergence of species resulting from accumulation of point mutations. Mutations are mainly responsible for the changes in the biopolymer sequences in different species. Examples of diversity in biochemical features of living things dealt with include such fundamental features as chirality of the membrane lipids, mechanisms to mature mRNAs, synthesis of aminoacyl-tRNAs, synthesis of isoprenoid precursors, coenzymes, etc. Admitting interspecies information exchanges as the driving force for evolution, the life is not necessarily originated from a single ancestor, but the possibilities of multiple ancestors have to be considered. Several hypotheses for the origin of life, which are consistent with multiple ancestors are presented.