To the Origin of Life - the Early Evolution of Biosynthesis and Energy Metabolism

[Worldtraveller]

I have to say, reading through all this makes me wish I'd paid more attention to my chemistry classes.

 

[bilby]

So prokaryotedom has a big world of energy metabolism beyond heterotrophy and oxygenic photosynthesis. This is the missing piece of the puzzle, because it enables organisms to be autotrophic without needing to photosynthesize. Indeed, the authors of that recent Nature conclude that the LUCA was an autotroph, making all its biological molecules as a plant does.

As an illustration, I note Bacterial Manganese Reduction and Growth with Manganese Oxide as the Sole Electron Acceptor. That was discovered for Alteromonas putrefaciens MR-1, isolated from lake-bottom sediments. This organism can use a variety of other electron acceptors if they are available: O2, NO3-, NO2-, Fe+++, S2O3--, SO3--, S4O6--, MnO2, glycine, fumarate, trimethylamine-N-oxide. However, it does not use SO4--, MoO4--, CO2.

Now for some troph terminology.

• Autotrophy - making all one's biological molecules.
• Heterotrophy - needing to consume some biological molecules.
• Lithotrophy - living off of inorganic molecules.
• Organotrophy - living off of organic molecules.
• Chemotrophy - getting one's energy from chemical reactions.
• Phototrophy - getting one's energy from light.
• Mixotrophy - mixtures of various modes: auto- and hetero-, litho- and organo-, chemo- and photo-.

... and, of course:
Jules-Rimettrophy - awarded to the winners of the FIFA World Cup until 1970.

 

[lpetrich]

I'd mentioned nitrogen oxides and related compounds earlier, and I've found a paper on early-Earth NOx: Volcanic source for fixed nitrogen in the early Earth's atmosphere

Hot volcanic vents promote the thermal fixation of atmospheric N2 into biologically available forms. The importance of this process for the global nitrogen cycle is poorly understood. At Masaya volcano, Nicaragua, NO and NO2 are intimately associated with volcanic aerosol, such that NOx levels reach as much as an order of magnitude above local background. In-plume HNO3 concentrations are elevated above background to an even greater extent (≤50 μmol·m^(−3)). We estimate the production efficiency of fixed nitrogen at hot vents to be ∼3 × 10^(−8) mol·J^(−1), implying present-day global production of ∼10^(9) mol of fixed N per year. Although conversion efficiency would have been lower in a preoxygenated atmosphere, we suggest that subaerial volcanoes potentially constituted an important source of fixed nitrogen in the early Earth, producing as much as ∼10^(11) mol·yr^(−1) of fixed N during major episodes of volcanism. These fluxes are comparable to estimated nitrogen-fixation rates in the prebiotic Earth from other major sources such as bolide impacts and thunderstorm and volcanic lightning.

This offers a solution to a curious conundrum. Jose Castresana has proposed the "respiration early" hypothesis, that ability to use oxygen is ancestral, and that early organisms could use oxygen produced by breakdown of water by solar ultraviolet light. But a problem is that oxygen produced in that way likely had a very low concentration, since free oxygen started becoming geologically evident only in the Great Oxygenation Event about 2.3 billion years ago.

Respiratory chains in the last common anc... & related info | Mendeley
Respiration in Archaea and Bacteria: Diversity of Prokaryotic Electron ... - Google Books
Evolution of energetic metabolism: the respiration-early hypothesis - ScienceDirect
From the first abstract:

Sequences in current databases show that a number of proteins involved in respiratory processes are homologous in archaeal and bacterial species. In particular, terminal oxidases belonging to oxygen, nitrate, sulfate, and sulfur respiratory pathways have been sequenced in members of both domains. They include cytochrome oxidase, nitrate reductase, adenylylsulfate reductase, sulfite reductase, and polysulfide reductase.

So the LUCA could use O2, NO3-, SO4--, and S as electron acceptors. At least if the enzymes for doing so had not spread by lateral gene transfer.

Was nitric oxide the first deep electron sink? - ScienceDirect Cytochrome oxidase could first have been used for nitric oxide, NO.

A structural and functional perspective on the evolution of the heme–copper oxidases - ScienceDirect -- cytochrome oxidase and similar enzymes.

The heme–copper oxidases (HCOs) catalyze the reduction of O2 to water, and couple the free energy to proton pumping across the membrane. HCOs are divided into three sub-classes, A, B and C, whose order of emergence in evolution has been controversial. Here we have analyzed recent structural and functional data on HCOs and their homologues, the nitric oxide reductases (NORs). We suggest that the C-type oxidases are ancient enzymes that emerged from the NORs. In contrast, the A-type oxidases are the most advanced from both structural and functional viewpoints, which we interpret as evidence for having evolved later.

So our ancestors breathed nitrogen oxides before they breathed oxygen.

 

[lpetrich]

Here are some oxygen alternatives:

Nitrate
HNO3 + H2 -> HNO2 + H2O
Nitrite
HNO2 + (1/2)H2 -> NO + H2O
Nitric oxide
2NO + H2 -> N2O + H2O
Nitrous oxide
N2O + H2 -> N2 + H2O
Nitrogen molecules

Sulfate
H2SO4 + H2 -> H2SO3 + H2O
Sulfite
H2SO3 + 3H2 -> H2S + 3H2O
Hydrogen sulfide

Sulfur
S + H2 -> H2S
Hydrogen sulfide

Enzyme phylogenies as markers for the oxidation state of the environment: The case of respiratory arsenate reductase and related enzymes | BMC Evolutionary Biology | Full Text -- some organisms can use arsenic in their metabolism. This brings to mind the "arsenic bug", but as far as anyone can tell, it is a very arsenic-tolerant organism and not one that substitutes arsenic for phosphorus, however interesting that might be.

Arsenic typically appears in oxidized form:
Arsenite: AsO3--- (more reduced)
Arsenate: AsO4--- (more oxidized)
(like phosphite, PO3--, and phosphate, PO4--)
Redox:
AsO3--- + H2O <-> AsO4--- + 2H+ + 2e
<- reduction oxidation ->

This can be hooked into electron-transfer metabolism with enzymes arsenite oxidase (Aro: supplies electrons) and arsenate reductase (Arr: removed electrons).

Aro they found to be older than the LUCA (Arsenite Oxidase, an Ancient Bioenergetic Enzyme | Molecular Biology and Evolution | Oxford Academic), while Arr has a separate origin that is much more recent. It was found in Proteobacteria and Firmicutes in Bacteria, and not in Archaea, and its family tree did not match the species family tree very well. So it originated relatively recently as a modification of some enzyme related to thiosulfate (S2O3--) /polysulfide (Sx--) reductases, and it was then spread laterally.

Arsenite was the most common form in the early Earth, because it is less oxidized than arsenate, the most common present-day form.

 

[lpetrich]

Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases. - PubMed - NCBI -- also concludes that O2 reductases (cytochrome oxidases) evolved from NO reductase.

Respiratory Transformation of Nitrous Oxide (N2O) to Dinitrogen by Bacteria and Archaea - ScienceDirect -- N2O as an electron sink, giving N2. It likely goes back to the LUCA.

More generally, I've found Microbiology Society Journals | Nitrate reduction and the nitrogen cycle in archaea and Denitrifying genes in bacterial and archaeal genomes, but they do not discuss how far back this sort of metabolism goes. From their phylogenies, it looks like it goes back to the LUCA.


I also researched sulfate (SO4--) and sulfite (SO3--) reductases, and while they are old and likely ancestral, they have some evidence of lateral gene transfer.
Phylogeny of Dissimilatory Sulfite Reductases Supports an Early Origin of Sulfate Respiration | Journal of Bacteriology
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes | Journal of Bacteriology
Microbiology Society Journals | Phylogeny of the alpha and beta subunits of the dissimilatory adenosine-5′-phosphosulfate (APS) reductase from sulfate-reducing prokaryotes – origin and evolution of the dissimilatory sulfate-reduction pathway


I looked for additional stuff on the early evolution of electron-transfer metabolism, and I found this:
The respiratory complex I of bacteria, archaea and eukarya and its module common with membrane‐bound multisubunit hydrogenases It transfers electrons from NAD to quinone, and in Archaea, from "coenzyme F420" to quinone. Coenzyme 420 contains flavin, so it's another member of the riboflavin family.

I couldn't find anything on the early evolution of quinone-to-cytochrome systems, though it may be buried somewhere in some papers.

 

[DrZoidberg]

I have to say, reading through all this makes me wish I'd paid more attention to my chemistry classes.

I agree. It's an incredibly interesting thread. Thanks everybody for contributing.

 

[lpetrich]

The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes. -- a very evocative title.

Genome analyses and the resolution of three-dimensional structures have provided evidence in recent years for hitherto unexpected family relationships between redox proteins of very diverse enzymes involved in bioenergetic electron transport. Many of these enzymes appear in fact to be constructed from only a limited set of building blocks. Phylogenetic analysis of selected units from this "redox enzyme construction kit" indicates an origin for several prominent bioenergetic enzymes that is very early, lying before the divergence of Bacteria and Archaea. Possible scenarios for the early evolution of selected complexes are proposed based on the obtained tree topologies.

...
With the possible exception of photosynthesis and methanogenesis, which have so far only been found in Bacteria and Archaea, respectively, all major energy-conserving electron transport chains are operative in both prokaryotic kingdoms (Castresana & Moreira 1999). Phylogenetic analyses of constituent enzymes in most cases argue against lateral gene transfer of these mechanisms between kingdoms—a notable exception being sulphate reduction where evidence for inter-kingdom lateral transfer has been reported (Klein et al. 2001).

Meaning that a lot of electron-transfer metabolism is pre-LUCA.


Arsenics as bioenergetic substrates - ScienceDirect -- agrees with the earlier paper that I'd linked to: arsenite oxidase is ancestral, while arsenate reductase is much more recent.

Looking at the paper's diagrams, I notice that the arsenic stays outside of the cell, and interacts with enzymes embedded in the cell membrane. Avoiding arsenic uptake would keep arsenic-using organisms from being poisoned by it. The infamous "arsenic bug" turns out to be an organism with high tolerance for arsenic. ‘Arsenic-life’ bacterium prefers phosphorus after all : Nature News & Comment Most if not all cellular organisms use a transporter protein to bring phosphate ions into their cell interiors (PO4---,  Inorganic phosphate transporter family), and some researchers compared how some such proteins due with arsenate ions (AsO4---, The molecular basis of phosphate discrimination in arsenate-rich environments | Nature). They found that, for several bacteria, phosphate transporters tend to reject arsenic by a factor of at least 500 to 1, and in one case, at least 4,500 to 1. So arsenic-tolerating organisms tolerate arsenic by keeping it outside their cell interiors.

 

[lpetrich]

Acquisition of 1,000 eubacterial genes physiologically transformed a methanogen at the origin of Haloarchaea | PNAS

The 1,089 acquisitions include genes for catabolic carbon metabolism, membrane transporters, menaquinone biosynthesis, and complexes I–IV of the eubacterial respiratory chain that functions in the haloarchaeal membrane consisting of diphytanyl isoprene ether lipids. LGT on a massive scale transformed a strictly anaerobic, chemolithoautotrophic methanogen into the heterotrophic, oxygen-respiring, and bacteriorhodopsin-photosynthetic haloarchaeal common ancestor.

These genes were acquired by the ancestor of Haloarchaea, and in the process, that ancestor lost methanogenesis, and its metabolism changed from anaerobic and autotrophic to aerobic and heterotrophic.

However, the organism's membrane lipids stayed terpenoid rather than become fatty-acid.


Back to that paper on arsenic as bioenergetic substrates, it mentions a relative of arsenate reductase that works on chlorine-containing ions: an enzyme that transfers electrons to chlorate ions (ClO3-), making them chlorite ones (ClO2-). Chlorate reductases were spread laterally, and like arsenate reductases, also likely have relative recent origin. As to where chlorate-reductase possessors might find these ions, chlorates and perchlorates (ClO4-) have been found in arid and hyperarid environments, and also: Perchlorate found on Mars : Nature News.

The recent origin of chlorate reductases, like arsenate ones, suggests that chlorate ions need atmospheric oxygen to form, like arsenate ones.

 

[lpetrich]

The evolution of respiratory O2/NO reductases: an out-of-the-phylogenetic-box perspective -- another attempt to solve this conundrum.

Mentions an organism called Methylomirabilis oxyfera that makes oxygen molecules (O2) for the first step in methane-consuming metabolism. It apparently does so by taking two NO molecules and making N2 and O2 from them. This could resolve the conundrum of apparent evidence for early O2 use -- organisms making O2 by a non-photosynthetic route long before the Great Oxygenation Event from the emergence of cyanobacteria.

In this scenario, high-affinity oxygen reductases like cbb3 in Bacteria and Sox in Archaea would have emerged from NO reductases early as a response to organisms making O2 from NO. High-affinity meaning efficient collection of low-concentration O2. Low-affinity O2 reductases were likely a recent invention, after the GOE, when O2 became more abundant.


The role of geochemistry and energetics in the evolution of modern respiratory complexes from a proton-reducing ancestor - ScienceDirect -- rather complicated to untangle, but it's another paper on the evolution of Complex I. It's found all over Bacteria and Archaea, and thus is likely in the LUCA.

That article mentioned an addition to quinones that some bacteria have: phenazines. They are relatives of riboflavin with a terpenoid chain, much like what biological quinones have. That terpenoid chain anchors the molecule in the cell membrane. Since quinones likely go back to the LUCA, that means that the LUCA could make terpenoids. So we have:

• Terpenoids: LUCA, Bacteria, Archaea
• Fatty acids: Bacteria only

So the LUCA's membrane lipids were likely terpenoids, like Archaea ones, with an early (eu)bacterium inventing fatty acids for itself.

 

[lpetrich]

On the universal core of bioenergetics - ScienceDirect -- updates the "redox construction kit" paper with a lot of detail -- and arcane biochemical detail at that.

In section 3.2, "Ways to overcome endergonic barriers", it discusses how electrons can be pushed uphill in energy, most likely for certain biosynthesis reactions. One way is the chemiosmotic mechanism -- let some proton-expulsion reactions run in reverse, adding energy to electrons. Another way is a more direct coupling of electron transfers, so one electron going lower in energy can drive another electron to higher energy.

Its final section, 7.3, "Are we there yet?" discusses some implications for what the LUCA was like. I'd previously posted on how NAD-to-quinone goes back to the LUCA, and the authors mention evidence that quinone-to-other-stuff also does so. Like quinone-to-NO and Complex III / cytochrome bc1. Also mentions polysulfide reductase (makes sulfides like hydrogen sulfide) and formate dehydrogenase (breaks formic acid HCOOH down into H2 and CO2).

Having quinones and NO reductases and the like means the ability to live off of nitrogen oxides and oxyanions (nitrite and nitrate), and likely also Fe+++. Thus getting more energy per reaction than with CO2.


Here are some biochemically interesting redox potentials. All the reactions are given in the reduction (electron addition) direction. To get the oxidation (electron subtraction) reaction, go in reverse. They are all in aqueous solution, pH 7 (neutral), 25 C, unless indicated otherwise.

• -0.421 ... 2H+ + 2e -> H2
• -0.320 ... NAD+ + 2H+ + 2e -> NADH + H+ ... has niacin
• -0.022 ... FAD + 2H+ + 2e -> FADH2 ... has riboflavin (another source has +0.031)
• -0.11 ... CO2 + 2H+ + 2e -> HCOOH ... formic acid (example of carbon fixation)
• 0 (definition) ... 2H+ + 2e -> H2 at pH 0 ... strong acidity: lots of H+ ions forces it down
• +0.045 ... ubiquinone + 2H+ + 2e -> ubiquinol
• +0.070 ... cyt b(ox) + e -> cyt b(red) ... Complex III, bc1
• +0.254 ... cyt c(ox) + e -> cyt c(red)
• +0.375 ... NO2- + 2H+ + e -> NO + H2O ... nitrite to nitric oxide
• +0.385 ... cyt a3(ox) + e -> cyt a3(red) ... Complex IV, cytochrome oxidase
• +0.420 ... NO3- + 2H+ + 2e -> NO2- + H2O ... nitrate to nitrite
• +0.56 ... AsO4--- + 2H+ + 2e -> AsO3--- + H2O ... arsenate to arsenite (arsenic)
• +0.77 ... Fe+++ + e -> Fe++
• +1.175 ... 2NO + 2H+ + 2e -> N2O + H2O ... nitric oxide to nitrous oxide
• +1.20 ... ClO4- + 2H+ + 2e -> ClO3 + H2O ... chlorate to chlorite (chlorine)
• +1.229 ... O2 + 4H+ + 4e -> H2O ... for organisms, I find +0.816 (curious discrepancy)
• +1.355 ... N2O + 2H+ + 2e -> N2 + H2O ... nitrous oxide to (di)nitrogen

I couldn't find appropriate numbers for sulfide and sulfate metabolism, but "On the universal core of bioenergetics" has about -0.23 for sulfate and -0.27 for sulfide. It also has -0.25 for CO2-to-CH4 and -0.27 for making acetic acid.

When two of these reactions are coupled, the upper reaction goes backward (oxidation) and the lower reaction goes forward (reduction).

Notice that nitrogen oxides and nitrogen oxyanions are way down there in the tables, along with oxygen. That makes them good oxidizers, just like oxygen itself, and thus good for extracting energy. By comparison, methanogenesis (making methane) and acetogenesis (making acetic acid) are much poorer for that.

So the LUCA likely used NOx whenever it could, falling back on acetogenesis when it had to.

 

[lpetrich]

From Search BioNumbers - The Database of Useful Biological Numbers I get some numbers for these redox reactions:

• -0.29 ... 2CO2 + 8H+ + 8e -> CH3COOH + 2H2O ... CO2 to acetate (BMID 104403)
• -0.26 ... S + 2H+ + 2e -> H2S ... sulfur to sulfide (my interpretation of BMID 104415)
• -0.24 ... CO2 + 8H+ + 8e -> CH4 + 2H2O ... CO2 to methane (BMID 104404)
• -0.22 ... SO4-- + 8H+ + 8e -> S-- + 4H2O ... sulfate to sulfide (BMID 104405)

Most of the other BioNumbers ones agree with my previous ones, though the oxygen-to-water one is +0.8 V, agreeing with the previous post's organism value. So sulfates are poor electron acceptors, and carbon dioxide is also. Meaning that it's hard to get much energy from sulfate or from making methane or acetic acid. From the previous post's table, it is evident that iron and nitrogen oxides are as good as oxygen as electron acceptors, so they are much better.


One step beyond a ribosome: The ancient anaerobic core - ScienceDirect -- agrees with the previously-mentioned Nature paper that the LUCA had done CO2 + H2 -> acetate. About NO and O2 reductases, the authors claimed that they were spread by lateral gene transfer and that the LUCA did not have quinones and cytochromes. I don't find that very convincing. I like the argument of the authors of "On the universal core of bioenergetics" that a low-yield reaction would not be very suitable for an early organism. A high-yield one, like with nitrogen oxides or iron, has much more margin of error.


As to where the hydrogen came from in the early Earth, there is a chemical reaction called serpentinization. In hot rocks, water can oxidize them, releasing hydrogen:
2FeO + H2O -> Fe2O3 + H2
Fe II (Fe++) -> Fe III (Fe+++)

When serpentinized rock is brought upward by geological processes, organisms can use its Fe+++ as an electron acceptor for its energy metabolism.

Serpentinization and the Formation of H2 and CH4 on Celestial Bodies (Planets, Moons, Comets) -- this process can make nonbiological methane along with hydrogen.

 

[lpetrich]

Protein Domain Structure Uncovers the Origin of Aerobic Metabolism and the Rise of Planetary Oxygen: Structure

Uses protein-fold (F) families (FF) and superfamilies (FSF) to attempt to find the relative ages of different proteins, and thus different sorts of metabolism. With their method, they find that ATP-using proteins are the oldest. This is consistent with the "cofactor-selection" theory of protein origins, that proteins originated as RNA-world cofactors. Eventually the proteins became the main enzymes, and then RNA became cofactors and disappeared outright.

Amino-acid biosynthesis enzymes appeared in the order that their amino acids appeared in the genetic code as determined by other arguments. That is the codon-to-amino-acid translation table, where a codon is a triplet of RNA nucleotides.

Secondary metabolites appear late. "The functions of these secondary metabolites are associated with antibiotic (streptomycin, clavulanic acid), UV-radiation protection (flavonoids), defense (tropane, piperidine and pyridine alkaloids and isoquinoline alkaloids), and antioxidant (ascorbate) activities."

The oldest (di)oxygen-using biosynthesis reaction is for pyridoxal phosphate, a relative of pyridoxine (vitamin B6). It is older than the Great Oxygenation Event (GOE), and it may have originally used oxygen from nitric oxide (2NO -> N2 + O2) if not NO itself.

Metabolism of sulfite and sulfate appeared after the GOE, with metabolism of sulfur and sulfide appearing early.

The origin of modern metabolic networks inferred from phylogenomic analysis of protein architecture | PNAS -- more of this work.

Finds that purines (two-ring nucleobases) come first, then pyrimidines (one-ring nucleobases), then porphyrins (ring of four rings).


I think that the RNA world would have had to do at least some biosynthesis, and that its biosynthesis was gradually taken over by proteins as they emerged. So these arguments apply to when proteins took over each sort of biosynthesis. Secondary metabolites, however, are mostly well after the protein takeover.

 

[lpetrich]

Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? | Biology Direct | Full Text (Vinaigrette: mixture of vinegar and olive oil)

We propose that RNA is well suited for a world evolving at acidic pH. This is supported by the enhanced stability at acidic pH of not only the RNA phosphodiester bond but also of the aminoacyl-(t)RNA and peptide bonds. Examples of in vitro-selected ribozymes with activities at acid pH have recently been documented. The subsequent transition to a DNA genome could have been partly driven by the gradual rise in ocean pH, since DNA has greater stability than RNA at alkaline pH, but not at acidic pH.

Origin of life: Transitioning to DNA genomes in an RNA world | eLife -- "The unexpected ability of an RNA polymerase ribozyme to copy RNA into DNA has ramifications for understanding how DNA genomes evolved."

Meaning that DNA may have emerged in the RNA world without needing proteins.

The lost language of the RNA World | Science Signaling

The discovery of numerous riboswitch classes reveals that many of these RNA structures regulate gene expression in response to the selective binding of coenzymes and signaling molecules derived from RNA monomers or their precursors. It has been proposed that many coenzymes might be of ancient origin, based on their universal distribution in biology and their RNA-like chemical composition. In this Review, which includes four figures and 103 references, we discuss the findings that support the hypothesis that common RNA-derived signaling compounds are ancient and speculate on the possible complexity of the chemical language that might have been used by life-forms long before proteins emerged.

Life | Free Full-Text | How Amino Acids and Peptides Shaped the RNA World -- "We argue that an RNA world completely independent of amino acids never existed."

Life | Free Full-Text | tRNA Core Hypothesis for the Transition from the RNA World to the Ribonucleoprotein World | HTML -- arguing that transfer RNA's came before protein genes and ribosomes.

History of the ribosome and the origin of translation | PNAS -- proposes a detailed model:

We present a molecular-level model for the origin and evolution of the translation system, using a 3D comparative method. In this model, the ribosome evolved by accretion, recursively adding expansion segments, iteratively growing, subsuming, and freezing the rRNA. Functions of expansion segments in the ancestral ribosome are assigned by correspondence with their functions in the extant ribosome. The model explains the evolution of the large ribosomal subunit, the small ribosomal subunit, tRNA, and mRNA. Prokaryotic ribosomes evolved in six phases, sequentially acquiring capabilities for RNA folding, catalysis, subunit association, correlated evolution, decoding, energy-driven translocation, and surface proteinization. Two additional phases exclusive to eukaryotes led to tentacle-like rRNA expansions. In this model, ribosomal proteinization was a driving force for the broad adoption of proteins in other biological processes. The exit tunnel was clearly a central theme of all phases of ribosomal evolution and was continuously extended and rigidified. In the primitive noncoding ribosome, proto-mRNA and the small ribosomal subunit acted as cofactors, positioning the activated ends of tRNAs within the peptidyl transferase center. This association linked the evolution of the large and small ribosomal subunits, proto-mRNA, and tRNA.

The RNA world and the origin of metabolic enzymes | Biochemical Society Transactions

Interestingly, considering a metal-catalysed origin of metabolism gives rise to an attractive hypothesis about how the first enzymes could have formed: simple RNA or (poly)peptide molecules could have bound the metal ions, and thus increased their solubility, concentration and accessibility. In a second step, this would have allowed substrate specificity to evolve.

The Ribosome Challenge to the RNA World | SpringerLink
Does the Ribosome Challenge our Understanding of the RNA World? | SpringerLink

But much of this discussion is awfully speculative.

 

[lpetrich]

More on the origin and early evolution of ribosomes:

The origin and evolution of the ribosome | Biology Direct | Full Text (2008)
Origin and Evolution of the Ribosome (Cold Spring Harb Perspect Biol, 2010)
The ribosome as a missing link in the evolution of life - ScienceDirect (2015)
History of the ribosome and the origin of translation | PNAS (2015)

They agree on proposing that ribosomes were initially RNA-only, and that their proteins were later additions to that RNA core.

The RNA world and the origin of metabolic enzymes. - PubMed - NCBI -- proposes that they originated as taking over from nonbiological catalysts, like metal ions.

 

[lpetrich]

Turning to work from the opposite direction, one can make a variety of organic compounds in nonbiological fashion, but it has been hard to get much further than that. For instance, one can make spheres of thermal proteins or proteinoids, essentially randomly assembled proteins, but they are not exactly organisms.

Robert Freitas in his book "Xenology" has a chapter, 7.3.1 - Prebiotic Synthesis, noting all these ways of doing such synthesis:

• Heat
• Ultraviolet light
• Ionizing radiation: X-rays, gamma rays, alpha particles (He-4 nuclei), beta particles (electrons), and accelerated protons
• Electrical discharges (lightning)
• Shock waves (impacts)

Such synthesis efforts also make a difficult-to-analyze goo that Carl Sagan and Bishun Khare have named  Tholin.

Prebiotic synthesis is often described as making a primordial soup, but in its strict form, it is nowadays considered an implausible kind of location for the origin of life. That has led to the primordial-pizza hypothesis, origin on solid surfaces. That makes it much easier for molecules to get together and react, and metal ions in rocks can catalyze their reactions. The hydrothermal-vent hypothesis is a version of primordial pizza.


Miller-Urey and Beyond: What Have We Learned About Prebiotic Organic Synthesis Reactions in the Past 60 Years? | Annual Review of Earth and Planetary Sciences

The synthesis of amino acids in the Miller-Urey spark-discharge experiments in the early 1950s inspired a strong interest in experimental studies of prebiotic organic chemistry that continues today. Over the years, many of the basic building blocks of life as we know it have been synthesized in the laboratory from simple ingredients, including amino acids, sugars, nucleobases, and membrane-forming lipids. Questions remain, however, concerning whether the conditions that allow synthesis of these compounds in the laboratory accurately simulate those that might have been present on the early Earth, and a closer convergence between plausible prebiotic conditions and laboratory simulations remains a challenge for experimentalists.

Not just the Earth, but also elsewhere in the Universe, like early Mars and the interiors of he larger icy moons of the outer planets.

Prebiotic organic synthesis under hydrothermal conditions: an overview - ScienceDirect

Organic compounds which are obviously synthesized from inorganic precursors (e.g., CO) by hydrothermal activity are currently a research topic in prebiotic chemistry leading to the origin of life. However, such de novo products would be overwhelmed in present Earth environments, by an excess of thermal alteration (pyrolysis) products formed from contemporary life (e.g., hydrocarbons, alkanoic acids, etc.). Thus, organic syntheses must be demonstrated and distinguished from organic matter alteration initially in the laboratory and then in the field. Organic synthesis under hydrothermal conditions is theoretically possible and various established industrial processes are used to synthesize organic compounds from inorganic substrates with the aid of catalysts. A set of Strecker-type synthesis experiments has been carried out under hydrothermal conditions (150 °C), producing various amino acids. The formation of lipid compounds during an aqueous organic synthesis (Fischer–Tropsch-type) reaction was reported, using solutions of oxalic acid (also formic acid) as the carbon and hydrogen sources, and heating at discrete temperatures (50° intervals) from 100 to 400 °C. The maximum lipid yield, especially for oxygenated compounds was in the window of 150–250 °C. The compounds range from C6 to >C33, including n-alkanols, n-alkanoic acids, n-alkyl formates, n-alkanones, and n-alkanes, all with no carbon number preferences. These lipid compounds, especially the acids, can form lipid bilayers or micelles, potential precursors for membranes. Reductive condensation (i.e., dehydration) reactions also occur under simulated hydrothermal conditions and form amide, nitrile and ester bonds. The chemistry and kinetics of the condensation reactions are under further study and have the potential for oligomerization of acid-amides in aqueous medium. Abiotic organic compounds are not biomarkers per se because they do not originate from biosynthesis. Thus, they should be regarded as a distinctly separate group, termed prebiotic or synthetic organic compounds, in explorations for evidence of life.

So hydrothermal vents are good places for prebiotic synthesis.

A Reassessment of Prebiotic Organic Synthesis in Neutral Planetary Atmospheres | SpringerLink

The action of an electric discharge on reduced gas mixtures such as H2O, CH4 and NH3 (or N2) results in the production of several biologically important organic compounds including amino acids. However, it is now generally held that the early Earth’s atmosphere was likely not reducing, but was dominated by N2 and CO2. The synthesis of organic compounds by the action of electric discharges on neutral gas mixtures has been shown to be much less efficient. We show here that contrary to previous reports, significant amounts of amino acids are produced from neutral gas mixtures. The low yields previously reported appear to be the outcome of oxidation of the organic compounds during hydrolytic workup by nitrite and nitrate produced in the reactions. The yield of amino acids is greatly increased when oxidation inhibitors, such as ferrous iron, are added prior to hydrolysis. Organic synthesis from neutral atmospheres may have depended on the oceanic availability of oxidation inhibitors as well as on the nature of the primitive atmosphere itself. The results reported here suggest that endogenous synthesis from neutral atmospheres may be more important than previously thought.

Ferrous iron: Fe++ or Fe II.
Ferric iron: Fe+++ or Fe III.

So the bulk of the Earth's oceans may be poor sites for prebiotic synthesis unless they have enough dissolved Fe++ to consume the nitrogen-oxygen acids (nitrite / nitrous acid ... nitrate / nitric acid). But even if they are poor sites for that reason, that reason is good news for the hydrothermal-vent hypothesis, because it means that the vents' contents have something oxidized to react with. It is also consistent with the hypothesis that the LUCA consumed nitrogen oxides and nitrogen-oxygen acids: NOx.

 

[Kharakov]

Here is the  Citric acid cycle. Biochemists often like to use -ate instead of -ic acid in the names of acids. Thus, acetate instead of acetic acid.

That's a reasonable position to take in the context of biochemistry, which mostly occurs in highly impure aqueous solutions where multiple anions (and cations) are present. When the cation is the important group, as is invariably the case when discussing acids (H⁺ being the most common and least interesting of the possible anions in an acid solution, by definition), and several anions are present in solution (most biological contexts have plenty of K⁺, Na⁺ and often Mg²⁺ and Ca²⁺ present as well as the ubiquitous H⁺), there is no good reason to specify the anion, and the use of the '-ic acid' suffix might be taken as implying that it is specifically and exclusively H⁺.

Biochemists and organic chemists have a habit of ignoring H⁺ ions, and even covalently bonded H, as it is just assumed to be there by default if no other group or anion is specified.

They just call H₂ hate. It's horrible, and racist.

 

[lpetrich]

Reduction of nitrogen oxides to molecular nitrogen is called  Denitrification.

Looking for LUCA, the Last Universal Common Ancestor | News | Astrobiology -- discusses some of what I've posted about in a rather nontechnical way. Also has a nice overview of hydrothermal vents and their chemistry.

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.

 

[lpetrich]

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.

 

[lpetrich]

Phylogenetic Analysis of Nitrite, Nitric Oxide, and Nitrous Oxide Respiratory Enzymes Reveal a Complex Evolutionary History for Denitrification | Molecular Biology and Evolution | Oxford Academic
From 2008, a bit after some of the other papers on this subject that I'd mentioned.

"Although HGT cannot be ruled out as a factor in the evolution of denitrification genes, our analysis suggests that other phenomena, such gene duplication/divergence and lineage sorting, may have differently influenced the evolution of each denitrification gene."

Suspecting that it is largely inherited, meaning that it likely goes back to the LUCA.


The ineluctable requirement for the trans-iron elements molybdenum and/or tungsten in the origin of life | Scientific Reports
ineluctable = inescapable, unable to be avoided

An evolutionary tree of key enzymes from the Complex-Iron-Sulfur-Molybdoenzyme (CISM) superfamily distinguishes “ancient” members, i.e. enzymes present already in the last universal common ancestor (LUCA) of prokaryotes, from more recently evolved subfamilies. The majority of the presented subfamilies and, as a consequence, the Molybdo-enzyme superfamily as a whole, appear to have existed in LUCA. The results are discussed with respect to the nature of bioenergetic substrates available to early life and to problems arising from the low solubility of molybdenum under conditions of the primordial Earth.

Iron-sulfur groups likely go back to the origin of life, while copper use likely only goes back to the presence of atmospheric oxygen, starting around 2.5 billion years ago.

Arsenate reductases are only in Bacteria and their phylogeny differs from the SSU-rRNA phylogeny. So they are relatively recent and spread by horizontal gene transfer, as I'd mentioned earlier in this thread. They do
AsO4--- -> AsO3---

Also mentions an enzyme that does dimethyl sulfoxide to dimethyl sulfide. It is also relatively recent.

But there are several Mo-containing enzymes whose family trees follow those of SSU-rRNA, which have a prominent Bacteria-Archaea split, and whose roots lie at the base of that split. That means that the LUCA must have had them.

Formate dehydrogenase:
HCOOH -> CO2 + H2
though likely run in reverse

Polysulfide reductase:
Sn -> H2S

Arsenite oxidase:
AsO3--- -> AsO4---

Nitrate reductase:
NO3- -> NO2-
The first step in denitrification

What then of the availability of these two transition metals? W occurs in both acid and alkaline solutions and was thus available to emerging life, whereas Mo is relatively insoluble in reduced and neutral waters, but does occur in mixed valence sulfide and selenide and/or oxide complexes in alkaline solutions. Mo's insolubility at neutral pH values, exacerbated by an anoxic atmosphere, suggested a low bioavailability of this element for early life. Mo-isotope analyses on samples from the Archaean era indeed show substantially lower levels than during Phanerozoic times. Two scenarios can reconcile the results of molecular phylogeny and paleogeochemistry. (i) The ancestral CISM enzyme exclusively used W which was later replaced by Mo. (ii) CISM-catalyzed reactions in early life used Mo supplied by alkaline hydrothermal vents, proposed as cradles for life. The exclusiveness for Mo of many CISM-members as well as findings that primary productivity involving Mo has been comparable to the present since the geological record began at 3.8 Ga lead us to favor the second scenario.

CISM = Complex-Iron-Sulfur-Molybdoenzyme

Mo (molybdenum) and W (tungsten) are both made by dying low-mass stars and merging neutron stars.

 

[Swammerdami]

Investigations into an unusual type of bacterial life are back in the news. These microbes live in saline fracture water deep underground or under the sea floor. This life may represent a significant portion of the Earth's total biomass, and has been proposed as a possible type of life on Mars.

The energy source for these microbes is radioactive decay of minerals like uranium. A metabolic chain begins with alpha- or gamma-particles triggering the reaction 2H₂O --> H₂ + H₂O₂.

Although these life forms may be very ancient and do harness free energy directly — the earliest life could not have used sophisticated mechanisms like photosynthesis — AFAIK they are not proposed as Earth's original life. But the reconstructed LUCA with ribosomes was already very complex: Could there have been earlier stages?

There are many papers on this topic, some linked in the Quanta article linked above. But I don't see much detail about the bacteria beyond a few genus names: Desulfosporosinus, Halothiobacillus, Pseudomonas.

Water radiolysis continuously produces H₂ and oxidized chemicals in wet sediment and rock. Radiolytic H₂ has been identified as the primary electron donor (food) for microorganisms in continental aquifers kilometers below Earth’s surface. Radiolytic products may also be significant for sustaining life in subseafloor sediment and subsurface environments of other planets. However, the extent to which most subsurface ecosystems rely on radiolytic products has been poorly constrained, due to incomplete understanding of radiolytic chemical yields in natural environments. Here we show that all common marine sediment types catalyse radiolytic H₂ production, amplifying yields by up to 27X relative to pure water. In electron equivalents, the global rate of radiolytic H₂ production in marine sediment appears to be 1-2% of the global organic flux to the seafloor. However, most organic matter is consumed at or near the seafloor, whereas radiolytic H₂ is produced at all sediment depths. Comparison of radiolytic H₂ consumption rates to organic oxidation rates suggests that water radiolysis is the principal source of biologically accessible energy for microbial communities in marine sediment older than a few million years. Where water permeates similarly catalytic material on other worlds, life may also be sustained by water radiolysis.