Looking for Catalytic Partners Cofactors and Aptamers

The discovery that present-day living cells use RNA catalysts to hydrolyze RNA molecules or to perform the complex reactions of excision, ligation, and cycliza-tion supporting a limited catalytic diversity, raises the question of the respective domains of RNA and protein catalysis. The recent advances in RNA catalysis using the SELEX method make it possible to enhance the catalytic capabilities of RNA with small molecules as catalytic partners. In this way some RNAs may be analogous to protein in catalytic competence.

Purine nucleotides, and in particular those containing adenine, participate in a large variety of cellular biochemical processes (Maurel and Decout, 1999). Their best-known function is that of monomeric precursors of RNAs and DNAs. Nevertheless, derivatives of adenine are universal cofators. They serve in biological systems as source of energy (ATP), allosteric regulators of enzymatic activity and regulation signals (cyclic AMP). They are also found as acceptors during oxidative phosphorylation (ADP), as components of coenzymes (such as in FAD, NAD, NADP, coenzyme A; Fig. 3.6), as transfer agents of methyl groups of S-adenosyl-methionine, as possible precursors of polyprenoids in C5 (adenosylhopane) (Neunlist et al., 1987), and - last but not least - adenine 2451 conserved within the large rRNA in the three kingdoms, would be involved in catalysis during the formation of the peptide bond (Muth et al., 2000, 2001; Green and Lorsch, 2002).

On the other hand, biosynthesis of the amino acid histidine, which would have appeared late in evolution, begins with 5-phosphoribosyl-1-phosphate (PRPP) that forms N'-(5-phosphoribosyl)-ATP by condensation with ATP. This reaction is akin to the initial reaction of purine biosynthesis. Finally, the ease with which purine bases are formed in prebiotic conditions (Oro, 1960) suggests that these bases were probably essential components of an early genetic system. The nucleotides that by post-transcriptional modification can acquire the majority of functional groups present in amino acids possess a great potential diversity that is expressed in the modified bases of tRNAs and rRNAs and also at the level of ribonucleotide coenzymes (several coenzymes derive from AMP; Fig. 3.7). In particular many coenzymes are nucleotide analogs and the role of these cofactors at all steps of the current metabolism, and their distribution within the three kingdoms, suggests that a great variety of nucleotides were present in the last common ancestor. It as been suggested (White, 1976; Tremolieres, 1980) that coenzymes and modified nucleotides that were present before the appearance of the translation machinery may have played a prominent role in primeval catalysis.

Proteins would have appeared only at a later stage, coenzymes and ribozymes being fossil traces of past catalysts. Indeed, in the living cell, only a minority of enzymes function without coenzyme; they are mostly hydrolases, and apart from this group, 70% of the enzymes require a coenzyme. If metal coenzymes involved in catalysis are considered, the number of enzymes that depend on coenzymes increases further. Present-day coenzymes, indispensable cofactors for many proteins, would be living fossils of catalysts of primitive metabolism (Maurel and Haenni, 2005).

Most coenzymes are nucleotides (NAD, NADP, FAD, coenzyme A, ATP, etc.) or contain heterocyclic nitrogen bases that can originate from nucleotides (thiamine pyrophosphate, tetrahydrofolate, pyridoxal phosphate, etc.). Consequently the efficiency of selected ribozymes can be further expanded if coenzymes and/or nucleotide analogs containing functionalities (thiols, amino groups, imidazolyl

Fig. 3.6 Coenzyme structures.
Fig. 3.7 List of coenzymes derived from AMP.

moieties, etc.) are used. Modern selections yield various co-assisted dependent ribozymes, justifying an RNA-based metabolism.

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