Before the RNA World?

Sulfur-based metabolism before RNA?

The accumulation of small heritable changes within populations over time.

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Before the RNA World?

#1  Postby lpetrich » Feb 26, 2019 3:49 pm

Remnants of an Ancient Metabolism without Phosphate: Cell - proposes a predecessor to the RNA world: what might be called a sulfur-metabolism world.

The RNA world successfully accounts for several molecular-level features of our biota:
  • DNA as modified RNA
  • Protein-assembly apparatus: messenger, transfer, and ribosomal RNA's
  • RNA enzymes (ribozymes)
  • RNA cofactors (ATP, B vitamins, etc.)
But it has a big problem: the origin of the RNA. It is hard to make RNA prebiotically. It also has the problem that it uses phosphorus. Its backbone is ribose and phosphate in alternation. The paper's authors also note that this element is not very geochemically accessible, thus causing a further problem.

So the authors decided to consider what metabolic pathways do not use phosphate, and they had a surprisingly impressive haul. They found the Krebs cycle (citric-acid cycle, tricarboxylic-acid cycle), biosynthesis pathways for several protein-forming amino acids, and several others.

Some of these reactions use thioesters. A thioester is

R1 - (C = O) - S - R2

where R1 and R2 are the rest of the molecule. Note the sulfur instead of one of the oxygens. A notable thioester is acetyl coenzyme A, an important metabolic intermediate:

CH3 - (C = O) - S - CoA

Another notable feature of these pathways is that they have a lot of enzymes with iron-sulfur groups and metal ions in them, especially zinc ions. This sort of feature is often considered a relic of prebiotic origins, from mineral catalysts causing reactions that were later taken over by enzymes.

All this suggests that the RNA world had a predecessor, a predecessor likely with its own kind of replicator molecule. This replicator could be something like peptide nucleic acid (PNA), but whatever it was, it became displaced by RNA. But this replicator could have been what origin-of-life researchers are looking for: a replicator without a predecessor replicator.
Last edited by lpetrich on Feb 26, 2019 3:52 pm, edited 1 time in total.
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Re: Before the RNA World?

#2  Postby lpetrich » Feb 26, 2019 3:50 pm

The authors used:

KEGG Database

KEGG (Kyoto Encyclopedia of Genes and Genomes) is a database resource that integrates genomic, chemical and systemic functional information. In particular, gene catalogs from completely sequenced genomes are linked to higher-level systemic functions of the cell, the organism and the ecosystem.

LUCApedia

LUCApedia is a unified framework containing multiple datasets related to the Last Universal Common Ancestor (LUCA) and its predecessors. The database can be searched by protein name or Uniprot ID. Text and MySQL datafiles are also available on the download page.

eQuilibrator: The Biochemical Thermodynamics Calculator
One can input reactions like glucose ⇌ 2 ethanol + 2 CO2 , compounds like ATP , and enzymes like rubisco .


This has implications for how common the origin of life might be. It is evident from this research and a lot of other research that Earth life bears the stamp of origin in a hydrothermal vent. It also suggests that RNA may be one of several possible replacements and elaborations that the original replicator might have had.
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