Abstract
Abstract The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution. In fact, the exhaustion of the prebiotic supply of amino acids and other compounds that were likely present on the primordial Earth imposed an important selective pressure, favoring those primordial heterotrophic cells that became able to synthesize those molecules. Thus, the emergence of metabolic pathways allowed primitive organisms to become increasingly less dependent on exogenous sources of organic compounds. Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria, and Eukarya reveal that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the emergence of new metabolic abilities. Among these gene elongations, gene and operon duplications played a crucial role since they can lead to the (immediate) appearance of new genetic material that, in turn, might undergo evolutionary divergence, giving rise to new genes coding for new metabolic abilities. Concerning the mechanisms of pathway assembly, both the analysis of completely sequenced genomes and directed evolution experiments strongly support the patchwork hypothesis, according to which metabolic pathways have been assembled through the recruitment of primitive enzymes that could react with a wide range of chemically related substrates. However, the analysis of the structure and organization of genes belonging to ancient metabolic pathways, such as histidine biosynthesis, suggests that other different hypothesis, i.e., the retrograde hypothesis, may account for the evolution of some steps within metabolic pathways.
Highlights
The emergence and evolution of metabolic pathways represented a crucial step in molecular and cellular evolution
Data obtained in the last decade clearly indicate that a very large proportion of the gene set of differentorganisms is the outcome of more or less ancient gene duplication events predating or following the appearance of the Last Universal Common Ancestor (LUCA) and involving ancestral genes, referred to as the starter types, a term first coined by Lazcano and Miller (1994), that underwent duplications
The first attempt to explain in detail the origin of metabolic pathways was made by Horowitz (1945), who suggested that biosynthetic enzymes had been acquired via gene duplication that took place in the reverse order found in current pathways
Summary
In each moment of cell life, billions of molecules are transformed into different ones through reactions that are accelerated (catalyzed) by the so-called enzymes, most of which are represented by proteins. This, in turn, implies that they should possess much simpler genomes, constituted very likely by a few hundreds of genes If this is so, the question is: why and how did primordial cells assemble and evolve their metabolic pathways? It is commonly assumed that early organisms arose and inhabited aquatic environments (oceans, rivers, ponds, etc.) rich in organic compounds spontaneously formed in the prebiotic world This heterotrophic origin of life is generally assumed and is frequently referred to as the Oparin–Haldane theory (Oparin 1924; Lazcano and Miller 1996). The origin and the evolution of basic metabolic pathways represented a crucial step in molecular and cellular evolution since it rendered the primordial cells less dependent on exogenous sources of nutrients (Fig. 4)
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