What is known about major events of pre-LUCA evolution?

Question

All organisms share many common biochemical features (including 20 amino acid genetic code) and are believed to have a common ancestor (so-called LUCA). According to wikipedia article, this common ancestor was quite complex organism with advanced biochemistry. Are there an knowledge about evolutionary events occurred during pre-LUCA era? Namely, which of biochemical pathways already present in LUCA were evolved earlier than anothers?

Answer 1

There is an awful lot of literature and debate about what happened before LUCA consequently here are some key words to read more about, first on Wikipedia, then on review papers and then on the many papers...

• According to the Oparin-Haldane hypothesis life formed from an abiotic primoridal soup.
• These abiotic building blocks were formed by lightning, meteorites, UV or other processes (see Miller–Urey experiment and the Murchison meteorite)
• Not all metabolites we know today existed and many that do not have a use today existed (non-proteogenic amino acids on Wikipedia is an article/list on the topic).
• The genetic code is a frozen accident (Crick), but many believe it went in waves and was rather promiscuous (e.g. 3rd position pairs came later) and may have included ornithine and norleucine, which were "usurped".
• Ignoring the temperature/location aspect, from a chemical point of view, life arises from a hypercycle process and requires gradients.
• DNA did not form as is. The ribose may have been glycol and the nucleobase glycine: many metabolites in nucleotide metabolism are able to base pair.
• The RNA world came first, then DNA with chromosomes came later. This has an odd effect in that early enzymes had to be highly multifunctional.
• To have evolution, you need compartmentalisation.
• Tar is gloop that forms easily abiotically. Tarrification is a threat to early life, but could have helped with compartmentalisation.
• Montmorillonite clay can act as a scaffold for DNA polymerisation.
• Ribozymes are RNA enzymes. The most core cellular processes is still RNA operated: the ribosome and tRNAs.
• Many cofactors are primordial and are attached to riboses, e.g. NADH, FADH and arguably cobalamins.
• Proteins came later, but still today the catalytic power of protein comes from their cofactors or from a single amino acid (e.g. cysteine as a nucleophile).
• Once you have potentially RNA-encoded proto-enzymes you can start building more of the useful compounds that were available in the primordial soup but were depleted. Most pathways will therefore form by retrograde pathway evolution.
• Enzyme activities can only be evolved if there is a pre-existing activity to select. Luckily accidental activities happen, called promiscuous activities (this term a century ago had no sexual meaning and used mean "being muddled").
• Modern enzyme are highly specific and evolved to work at a high turnover (fast) and work at physiological substrate concentrations. But still have promiscuous activities because the substrate chemistry is similar. If the enzyme has never see a given compound the enzyme will not be evolved to not act on it and maybe the activity has no detrimental effect (neutral). When an enzyme evolves into a new activity an intermediate form is seem with higher promiscuity. These are often argued to be primordial-like.
• Many pathways have a common origin, for example the Krebs cycle and the branched chain amino acid pathways and actually experiments in E. coli have found that the enzymes can rescue "deficiency" (auxotrophies) in the other pathway albeit slowly. Therefore, as enzymes could act on different similar substrates a set of overlapping pathways arose (patchwork hypothesis).
• LUCA is the last common ancestor. It was likely thermophilic and lived in thermal vents as seen in every documentary. If life started there is debated.
• Early enzyme were like very unstable, very very slow and may have often broken good metabolites in a futile manner. Given the problem of segregating with a chromosome and the need for high promiscuity, they had to be multifunctional. Not to mention that similar-ish amino acids were used interchangeably —isoleucine and valine say are hard to tell apart to modern tRNA synthases, go figure for the early ones.
• Enzymes generally fall under a few families, which share a common ancestor. Rossmann fold enzymes for example bind NADH. TIM barrels are a ubiquitous fold.

So to answer your question, between the RNA world and LUCA, enzymes were slow and were selected upon to remake the more complex metabolites in the soup and then the simpler ones and thanks to their poor selectivity a patchwork of pathways arose. Once simple core pathways started and all metabolites could be made, more complex compounds that cannot arise abiotically such as the amino acids tryptophan and arginine were made. The enzymes became more selective and stuff like straight chain hydrophobic amino acids were selected against and the genetic code was fixed. Then you can make stuff like chromosomes and everything happens fast and efficiently.

Caveat. Early life was messy, really not efficient (it had no competition) and happened a long time ago. As time machines are physically impossible, all this is conjecture (sensu Popper), but the words theory and hypothesis are used happily in the field of origin of life.