Question 5: On the Chemical Reality of the RNA World

The discovery of catalytic RNA has revolutionised modern molecular biology and bears important implications for the origin of Life research. Catalytic RNA, in particular self-replicating RNA, prompted the hypothesis of an early “RNA world” where RNA molecules played all major roles such information storage and catalysis. The actual role of RNA as primary actor in the origin of life has been under debate for a long time, with a particular emphasis on possible pathways to the prebiotic synthesis of mononucleotides; their polymerization and the possibility of spontaneous emergence of catalytic RNAs synthesised under plausible prebiotic conditions. However, little emphasis has been put on the chemical reality of an RNA world; in particular concerning the chemical constrains that such scenario should have met to be feasible. This paper intends to address those concerns with regard to the achievement of high local RNA molecules concentration and the aetiology of unique sequence under plausible prebiotic conditions. Presented at: International School of Complexity – 4th Course: Basic Questions on the Origins of Life; “Ettore Majorana” Foundation and Centre for Scientific Culture, Erice, Italy, 1–6 October 2006.     

New retention mechanism of mononucleotides with buffer concentrations in ion-suppressing RP-HPLC

HPLC separation of ionic samples tends to be more complicated and difficult to understand than that of non-ionic compounds. On the other hand, band spacing is much more easily manipulated for ionic than for neutral samples. Ion-suppressing RP-HPLC method was used with organic modifier and aqueous buffer solution. In this work, five mononucleotides of cytidine-5-monophosphate (5′-CMP) disodium salt, uridine-5-monophosphate disodium salt (5′-UMP), guanosine-5-monophosphate disodium salt (5′-GMP), inosine-5-monophosphate disodium salt (5′-IMP), and adenosine-5-monophosphate disodium salt (5′-AMP) were examined. Acetic acid and sodium phosphate were used as buffers, and methanol as an organic modifier. A new relationship between the retention factor and the buffer concentration at a fixed modifier content (5% of methanol) could be expressed by fol|lowing:k=(k ₋₁+k ₀ (K _B/K _S)C _B ^a)/(1+(K _B/K _S)C _B ^a), whereC _B was the concentration of buffer. Using this relationship, the calculated values closely matched the experimental data. The derived relationship showed that as the buffer concentration increased, the retention factor approached a certain value, and this was buffer dependent.     

A factor promoting the ejection of deacylated initiator transfer RNA from ribosomes

Experiments in bacterial cell-free extracts show that the deacylated initiator transfer RNA can be specifically discharged from its complex with the ribosome and messenger by addition of GTF and a factor derived from ribosomal salt-washings. This release-factor differs from that for the non-initiating tRNA's in its capability to dissociate the tRNA_f^Met-30 s ribosome-ApUpG complex^‡, in its inability to be inhibited by fusidic acid, and in its Chromatographic mobility on an ion-exchange column.     

Nonenzymatic Template-directed Synthesis of RNA from Monomers

Reviewed are the latest achievements in studying the information transfer mechanisms and the evolutionary significance of prebiotic RNA synthesis, the double helix structures most preferred in this respect, and the possible reasons for the prevalence of particular enantiomeric forms of nucleotides in template-directed synthesis.     

The reactivity of mononucleotides with cholecystokinin/gastrin antisera

Dibutyryl cyclic GMP has been reported to interact with antisera specific for C-terminal tetrapeptide amide common for cholecystokinin (CCK) and gastrin. Moreover, cyclic nucleotides elute by gel chromatography in the same position as the free CCK/gastrin tetrapeptide. Therefore, we have examined the reactivity of 25 mononucleotides with eight CCK and gastrin antisera. The results show that the nucleotides all bind poorly to the antisera (nucleotide concentration required 1 mM). Hence, endogenous cyclic nucleotides, which are present in biological extracts in pM to nM concentrations, do not interfere with immunochemical CCK or gastrin measurements. The antisera displayed highly individual patterns of reactivity without preferential binding of di- or monobutyryl cyclic nucleotides (AMP, GMP or IMP). Thus, the present results do not support the idea of structural resemblance between the C-terminus of CCK/gastrin peptides and butyryl derivatives of cyclic GMP. Enzymatic treatment of the antral tetrapeptide-like immunoreactivity showed that nucleotides do not contribute to this material, which appears exclusively peptidergic.     

The influence of carbon sources and mononucleotides on the production of extracellular alkaline phosphatase by bacillus intermedium

The biosynthesis of extracellular alkaline phosphatase in the streptomycin-resistant strainsBacillus intermedius S3-19 and S7 in the presence in the medium of 5’-nucleoside monophosphates and different sources of carbon—glucose, sodium pyruvate, sodium lactate, or glycerol—was studied. It was established that, in the presence of mononucleotides, the content of extracellular alkaline phosphatase in both strains increased; the maximal effect was caused by 5’-AMP at a concentration of 20μg/ml. In medium with a low orthophosphate content, where active biosynthesis of alkaline phosphatase occurred, 1% glucose and 0.5% pyruvate stimulated this process 2.5–4 times, and 2% sodium lactate and sodium pyruvate, on the contrary, inhibited it by 20–40%. Analysis of the dynamics of growth and accumulation of extracellular phosphatase in the presence of different sources of carbon in the medium gives evidence of an interrelationship between the biosynthesis of alkaline phosphatase and carbon metabolism inBacillus intermedius.