Coping with inevitable accidents in metabolism

Abstract

SummaryGenomic studies focus on key metabolites and pathways that, despite their obvious anthropocentric design, keep being ‘predicted’, while this is only finding again what is already known. As increasingly more genomes are sequenced, this lightpost effect may account at least in part for our failure to understand the function of a continuously growing number of genes. Core metabolism often goes astray, accidentally producing a variety of unexpected compounds. Catabolism of these forgotten metabolites makes an essential part of the functions coded in metagenomes. Here, I explore the fate of a limited number of those: compounds resulting from radical reactions and molecules derived from some reactive intermediates produced during normal metabolism. I try both to update investigators with the most recent literature and to uncover old articles that may open up new research avenues in the genome exploration of metabolism. This should allow us to foresee further developments in experimental genomics and genome annotation.

Omnipresent Maxwell's demons orchestrate information management in living cells

“…Another spatial constraint implicates metabolism. To prevent metabolic accidents caused by the mistaken placing of reactive compounds (Danchin, ), metabolism must be channelled into highly specific compartments (de Lorenzo et al ., ). Briefly, the way compartments are created and managed entails creating and managing information, not only plain matter, as Athenians recognized more than two millennia ago when they kept Theseus’ ship afloat despite the weathering of its wood boards [Danchin, 1998, translated in (Danchin, )].…”

Revisiting the methionine salvage pathway and its paralogues

“…It uses both the ( S , S ) and ( R , S ) forms of AdoMet, with a higher affinity for the ( R ,S) diastereomer (Vinci and Clarke, ). This enzyme, and possibly others, will allow the cell to cope with this inevitable accident of metabolism that should be taken into account in biotechnological processes (Danchin, ).…”

Bacteria in the ageing gut: did the taming of fire promote a long human lifespan?

“…While this situation has certainly a large negative impact for organisms with lower rates of metabolism, this cannot be true for high metabolism organisms because they are also those which, generally, have the longest lifespan. Hence, we can argue here that, because of the considerable advantage of flying over being terrestrial in terms of escaping predation and exploring new niches, evolution must have selected efficient ways to cope with the inevitable metabolic accidents deriving from ROS and excess glucose (Danchin, ).…”

“…It happens when an amino acid and a reducing carbohydrate react together, upon heating in particular, producing a series of reactive intermediates. This process, which is commonplace as a metabolic accident (Danchin, ), happens routinely when cooking food that contains a variety of amines and carbonyl groups (Erbersdobler et al ., ). Remarkably, Maillard reaction products (MRPs) are tasty, which suggests a positively selected role in feeding habits, pre‐existing to cooking (as witnessed in apes, as discussed previously).…”