Spontaneous generation

[lpetrich]

An earlier thread I'd created: To the Origin of Life - the Early Evolution of Biosynthesis and Energy Metabolism

I went into a lot of detail in that one.

The LUCA was, as I'd mentioned, a full-scale prokaryote. Let's see what it had.

• It was a thermophile, liking temperatures around 80 C.
• It had a full-scale DNA-RNA-protein apparatus: a DNA genome, messenger, transfer, and ribosomal RNA's, and RNA-protein ribsomes for making proteins.
• DNA replication may not have been very well-developed in it, at least by the standards of the two independently-elaborated systems, the Bacteria one, and the Archaea-Eukarya one.
• It was autotrophic, meaning that it made al its biological molecules, like a plant.
• It was anaerobic, growing without O2 and being poisoned by it.
• It did carbon fixing (from CO2) and nitrogen fixing (from N2).
• It used a lot of transition metals and iron-sulfur clusters in its enzymes.
• It had electron-transfer metabolism.
• It had electron donors like H2 and Fe++.
• It had a variety of "terminal electron acceptors", doing
  • NOx (N2O, NO, NO2, NO2-, NO3-) to N2,
  • SO4--, S to H2S
• It had post-transcriptional modification of some bits of RNA, like in transfer RNA.
• It had lots of enzyme cofactors, like the B vitamins: modified nucleobases, porphyrin and porphyrin-like rings, etc.

Quite a lot.

 

[lpetrich]

From the RNA world to the LUCA was a lot of evolution:

• DNA as modified RNA
• Protein synthesis with ribosomes and transfer RNA's
• Replacement of nearly all ribozymes (RNA as enzyme) with protein enzymes

The RNA world had:

• RNA as genome and enzyme
• Post-transcriptional modification
• Several cofactors, including B vitamins B1 (thiamine), B2 (riboflavin), B3 (niacin), B5 (pantothenate), B6 (pyridoxal).

Modern Metabolism as a Palimpsest of the RNA World - PubMed - the RNA world also had porphyrin rings and terpenes.

This means that of the two kinds membrane lipids in cell membranes, terpene ones came first. Archaea still have that kind, but Bacteria replaced terpenes with fatty acids there, and Eukarya likely got fatty-acid membrane lipids from Bacteria, even though its informational systems come from Archaea.

 

[lpetrich]

I've seen an amusing analogy for the evolution of biosynthesis. In "Intelligent Life in the Universe", Iosif Shklovskii and Carl Sagan make the analogy of robots that mine garbage dumps for parts to build new ones with. They first find lots of arms, but when they run out of arms, they start making arms from legs, because they can find lots of legs. When legs run out, then they make legs from car engines. When engines run out, they make engines from iron ore and other such raw materials. So they end up with:

Iron ore -> car engines -> legs -> arms

That book is online at Intelligent Life in the Universe : Carl Sagan : Free Download, Borrow, and Streaming : Internet Archive


One would expect most biosynthesis pathways to be pre-LUCA, and we indeed find only one per molecular building block in most cases. But there are some variations.

Ribonucleotide reductases: essential enzymes for bacterial life - they make DNA building blocks from RNA ones, though the uracil ones require an additional step to turn them into thymine ones. There are three different kinds, but it is hard for me to recognize patterns in their distribution, and many organisms have more than one kind of them.


Terpenes / terpenoids / isoprenoids are polymers of isoprene: CH2=C(CH3)CH=CH2 It has this odd feature: Isoprenoid biosynthesis: The evolution of two ancient and distinct pathways across genomes | PNAS They have a simple distribution across prokaryotes:

• Bacteria: deoxyxylulose 5-phosphate (DXP)
• Archaea: mevalonate (MVA) pathway

This makes it difficult to tell what the LUCA used.

Eukaryotes are a mixture that reflects their multiple ancestry. Animals and fungi use MVA, a clear inheritance from Archaea. Plants and algae have both, with MVA for steroids, found in cell membranes, and DXP for everything else, like in quinones, used in energy metabolism in chloroplasts. So DXP came over in chloroplasts but not in mitochondria.

 

[lpetrich]

Porphyrins may be prebiotic:
Possible origin for porphin derivatives in prebiotic chemistry--a computational study. [Orig Life Evol Biosph. 2005] - PubMed - NCBI
Prebiotic Porphyrin Genesis: Porphyrins from Electric Discharge in Methane, Ammonia, and Water Vapor -- PNAS

Their biosynthesis occurs in two ways: C5 and Shemin. Most prokaryotes have C5, and the LUCA likely had it also. Alpha-proteobacteria have Shemin, and that pathway likely originated in some alpha-proteobacterium, an organism that was far from the LUCA. Among eukaryotes, nonphotosynthetic ones use Shemin, and photosynthetic ones C5. So Shemin came over with the mitochondria, and C5 with the chloroplasts.


The amino acid lysine has two pathways, the diaminopimelate (DAP) one and the alpha-aminoadipate (AAA) one.

Methanococci Use the Diaminopimelate Aminotransferase (DapL) Pathway for Lysine Biosynthesis - PubMed
Evolution of Lysine Biosynthesis in the Phylum Deinococcus-Thermus - PubMed
The Evolutionary History of Lysine Biosynthesis Pathways Within Eukaryotes - PubMed
Lysine and Arginine Biosyntheses Mediated by a Common Carrier Protein in Sulfolobus - PubMed
Lysine Biosynthesis of Thermococcus Kodakarensis With the Capacity to Function as an Ornithine Biosynthetic System - PubMed

Most eubacteria, algae, and plants use DAP, while fungi us AAA. But some eubacteria use AAA, like the Deinococcus-Thermus ones, and some archaebacteria are also known to use it, like Sulfolobus.

Seems like lysine is much like isoprene - two main biosynthesis pathways, one for each of the two prokaryote domains.