From chemical metabolism to life: the origin of the genetic coding process

Abstract

Looking for origins is so much rooted in ideology that most studies reflect opinions that fail to explore the first realistic scenarios. To be sure, trying to understand the origins of life should be based on what we know of current chemistry in the solar system and beyond. There, amino acids and very small compounds such as carbon dioxide, dihydrogen or dinitrogen and their immediate derivatives are ubiquitous. Surface-based chemical metabolism using these basic chemicals is the most likely beginning in which amino acids, coenzymes and phosphate-based small carbon molecules were built up. Nucleotides, and of course RNAs, must have come to being much later. As a consequence, the key question to account for life is to understand how chemical metabolism that began with amino acids progressively shaped into a coding process involving RNAs. Here I explore the role of building up complementarity rules as the first information-based process that allowed for the genetic code to emerge, after RNAs were substituted to surfaces to carry over the basic metabolic pathways that drive the pursuit of life.

One‐carbon metabolism, folate, zinc and translation

“…Methionine and AdoMet are the main output of folic acid‐mediated 1‐C metabolism. This is consistent with folate metabolism being primaeval, parallel with purine, flavin and pterin biosyntheses in a general GARD‐like process that created an opportunity for nitrogen fixation (Danchin, 2017a; Lancet et al , 2018). The way we appraise metabolism will heavily depend on preconceived ideas about the nature of the first cells.…”

“…An interesting variant scenario makes use of iron–sulfur‐rich clay environments containing phosphates, where thioester‐based metabolism is the rule (Hartman and Smith, 2019). In this family of scenarios, a thioester swinging arm, such as 4‐phosphopantetheine, would be involved in the polymerization of relevant metabolites, such as those generated today in non‐ribosomal peptide synthesis, polyketide synthesis or fatty acid synthesis (Lipmann, 1971), resulting in the synthesis of coenzymes, pterins in particular (Danchin, 2017a). While this latter view may appear far‐fetched, extant metabolism has identified in at least one case a bacterium displaying an explicit link between non‐ribosomal peptide synthesis and pteridine synthesis (Park et al , 2017).…”

Systems protobiology: origin of life in lipid catalytic networks

“…In other words, how could reproducing composomes discover the new laws of strand complementarity? As lucidly pointed out by Danchin [ 228 ], molecular complementarity is a much broader phenomenon than polynucleotide strand recognition and is seen, for example, in the self-reproduction of the tubulin structures of the centriole. Likewise, at the basis of GARD assembly reproduction are diverse events of inter-lipid molecular complementarity, mediated by chemically diverse headgroups, and underlying mutual catalysis.…”

Cell Communications among Microorganisms, Plants, and Animals: Origin, Evolution and Interplays

“…The origin of the inter-cellular communications becomes merged with the origin of the cells themselves. It has been proposed that Life could have arisen initially not as cellular organisms, but as simple genetic or chemical replicators [199][200][201][202]. Even if life could have begun as a system of such RNA and polypeptide replicators, chemically occurring membranes must have played a primary role in the very first steps of Life on Earth.…”