Most recent common ancestor of all life may have come from hydrothermal vents

[lpetrich]

Biology Direct | Abstract | Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? (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.

Consistent with the hydrothermal-vent origin-location hypothesis.

Biology Direct | Full text | The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner
Supports the Hartman-Fedorov "chronocyte" hypothesis of a protoeukaryote being a RNA-protein organism that "ate" DNA-genome ones.

The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes. -- redox is reduction-oxidation or electron transfer. This is about the respiratory chain, which chlorophyll photosynthesis originated from. Its parts emerged before the LUCA. Some redox coenzymes, like niacin (NAD) and flavin, likely date back to the RNA world.

Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases. [Biochem Soc Trans. 2002] - PubMed - NCBI
So cytochrome oxidases (oxygen reductases) likely evolved from a nitric-oxide reductase.

Was nitric oxide the first deep electron sink? 10.1016/j.tibs.2008.10.005 : Trends in Biochemical Sciences | ScienceDirect.com
Also concludes that cytochrome oxidases / O2 reductases evolved from a NO reductase -- and evolved more than once (SoxM, SoxB, FixN). This is consistent with O2 being a latecomer.

So some ancestral organisms "breathed" in nitrogen oxides. They were used the way that we use oxygen, as an electron / virtual-hydrogen sink. Some organisms still use nitrogen oxides / nitrites / nitrates in that way.

Some family trees agree with the Eubacteria / Archaea split:

• The respiratory cytochrome bc1 complex / chlorophyll photosynthesizers' cyt b6f complex
• Arsenite (AsO3---) oxidase (to arsenate) -- source of e's, virtual H's

Some family trees are all mixed, suggesting lateral gene transfer:

• Arsenate (AsO4---) reductase (to arsenite) -- sink of e's, virtual H's

Much like phosphite (PO3---) and phosphate (PO4---). Arsenate reductase likely evolved after oxygen became common, oxidizing the arsenite to arsenate.

BMC Evolutionary Biology | Full text | Enzyme Phylogenies as Markers for the Oxidation State of the Environment: the case of the Respiratory Arsenate Reductase and related enzymes

Arsenate reductase is most closely related to polysulfide (Sx--) and thiosulfate (S2O3--) reductases. They accept electrons / virtual H's from quinones, a respiratory coenzyme. Their phylogenies indicate their ancestries:

The sulfur ones have a deep split between Eubacteria and Archaea, meaning that they are likely ancestral. Meaning that some early ancestor liked to "eat" sulfur.

The arsenate one is only present in Proteobacteria and Firmicutes, and is present in mixed-up form among them, pointing to relatively recent origin and lateral gene transfer. Origin from a polysulfide reductase.


Respiratory Transformation of Nitrous Oxide (N2O) to Dinitrogen by Bacteria and Archaea 10.1016/S0065-2911(06)52003-X : Advances in Microbial Physiology | ScienceDirect.com
Like O2 and NO, N2O is used as an electron / virtual-hydrogen sink. The phylogeny of nitrous-oxide reductase has a Eubacteria-Archaea split, indicating that it is ancestral. Meaning another nitrogen oxide that that organism could use. I couldn't find much on nitrite or nitrate reductases, however. NO3- and NO2- are also electron / virtual-hydrogen sinks.


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
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes
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

 

[lpetrich]

Biology Direct | Abstract | Primordial soup or vinaigrette: did the RNA world evolve at acidic pH? (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.

Consistent with the hydrothermal-vent origin-location hypothesis.

Biology Direct | Full text | The Last Universal Common Ancestor: emergence, constitution and genetic legacy of an elusive forerunner
Supports the Hartman-Fedorov "chronocyte" hypothesis of a protoeukaryote being a RNA-protein organism that "ate" DNA-genome ones.

The redox protein construction kit: pre-last universal common ancestor evolution of energy-conserving enzymes. -- redox is reduction-oxidation or electron transfer. This is about the respiratory chain, which chlorophyll photosynthesis originated from. Its parts emerged before the LUCA. Some redox coenzymes, like niacin (NAD) and flavin, likely date back to the RNA world.

Comparison between the nitric oxide reductase family and its aerobic relatives, the cytochrome oxidases. [Biochem Soc Trans. 2002] - PubMed - NCBI
So cytochrome oxidases (oxygen reductases) likely evolved from a nitric-oxide reductase.

Was nitric oxide the first deep electron sink? 10.1016/j.tibs.2008.10.005 : Trends in Biochemical Sciences | ScienceDirect.com
Also concludes that cytochrome oxidases / O2 reductases evolved from a NO reductase -- and evolved more than once (SoxM, SoxB, FixN). This is consistent with O2 being a latecomer.

So some ancestral organisms "breathed" in nitrogen oxides. They were used the way that we use oxygen, as an electron / virtual-hydrogen sink. Some organisms still use nitrogen oxides / nitrites / nitrates in that way.

Some family trees agree with the Eubacteria / Archaea split:

• The respiratory cytochrome bc1 complex / chlorophyll photosynthesizers' cyt b6f complex
• Arsenite (AsO3---) oxidase (to arsenate) -- source of e's, virtual H's

Some family trees are all mixed, suggesting lateral gene transfer:

• Arsenate (AsO4---) reductase (to arsenite) -- sink of e's, virtual H's

Much like phosphite (PO3---) and phosphate (PO4---). Arsenate reductase likely evolved after oxygen became common, oxidizing the arsenite to arsenate.

BMC Evolutionary Biology | Full text | Enzyme Phylogenies as Markers for the Oxidation State of the Environment: the case of the Respiratory Arsenate Reductase and related enzymes

Arsenate reductase is most closely related to polysulfide (Sx--) and thiosulfate (S2O3--) reductases. They accept electrons / virtual H's from quinones, a respiratory coenzyme. Their phylogenies indicate their ancestries:

The sulfur ones have a deep split between Eubacteria and Archaea, meaning that they are likely ancestral. Meaning that some early ancestor liked to "eat" sulfur.

The arsenate one is only present in Proteobacteria and Firmicutes, and is present in mixed-up form among them, pointing to relatively recent origin and lateral gene transfer. Origin from a polysulfide reductase.


Respiratory Transformation of Nitrous Oxide (N2O) to Dinitrogen by Bacteria and Archaea 10.1016/S0065-2911(06)52003-X : Advances in Microbial Physiology | ScienceDirect.com
Like O2 and NO, N2O is used as an electron / virtual-hydrogen sink. The phylogeny of nitrous-oxide reductase has a Eubacteria-Archaea split, indicating that it is ancestral. Meaning another nitrogen oxide that that organism could use. I couldn't find much on nitrite or nitrate reductases, however. NO3- and NO2- are also electron / virtual-hydrogen sinks.


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
Multiple Lateral Transfers of Dissimilatory Sulfite Reductase Genes between Major Lineages of Sulfate-Reducing Prokaryotes
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

 

[lpetrich]

I'll try to sum up what I've posted.

Looking at the two prokaryote domains, we can identify which evolved in each:

• Bacteria only
  • Membrane lipids with fatty acids
  • Chlorophyll photosynthesis: energy and biosynthesis from electron transfer. Uses respiratory-chain parts
• Archaea only
  • Membrane lipids with terpenes
  • Methanogens' production of their eponymous gas: CO2 + 4H2 -> CH4 + 2H2O
  • Bacteriorhodopsin photosynthesis: energy only
• Both
  • DNA-replication complexes

So we get to the LUCA, the Last Universal Common/Cellular Ancestor at least of Bacteria and Archaea. What did it have?

• A cell membrane, with membrane lipids likely with terpenes
• A genome with DNA, but with poorly-developed DNA replication. May have had a DNA-RNA "heteroduplex" genome.
• A respiratory chain, one that can extract energy by electron-transfer (redox) reactions.
  Electron donors:
  • Hydrogen
  • Iron: Fe++ -> Fe+++
  • Arsenic oxides: AsO3--- -> AsO4---
  Electron acceptors:
  • Nitrogen oxides: NO3-, NO2-, NO, N2O -> N2
  • Sulfur: S -> H2S
  • Sulfur oxides: SO4--, S2O3--, SO3-- -> H2S
  Unlike many of its descendants, it could not use oxygen.
• Chemiosmotic energy extraction
• The Krebs cycle
• Protein enzymes
• Gene-to-protein translation apparatus: transfer RNA's and ribosomes
• Complete biosynthesis: nucleotides, amino acids, membrane lipids, coenzymes (molecules that work with enzymes).

Very complicated, and a long way from the primordial soup/pizza. However, biologists have come up with a remarkable partial solution: the RNA world. In it, RNA would act both as genome and as enzyme, simplifying the problem of its origin. Leaving the RNA world required

• Development of the translation apparatus and protein enzymes. The most important parts of the translation apparatus are RNA: transfer and ribosomal RNA. So they could easily have come out of the RNA world.
• DNA as a modification of RNA. To this day, DNA building blocks are made from RNA ones in two steps: ribose -> deoxyribose and uracil -> thymine.

RNA-world organisms developed some coenzymes to help them, like niacin, flavin, thiamine, and porphyrins (now found in heme, chlorophyll, vitamin B12, etc.). Since the enzymes proper were RNA, amino acids and the first proteins would have served as coenzymes.

The RNA world had ATP as an energy intermediate, and it also had redox metabolism. Did it also have a respiratory chain and chemiosmotic energy extraction? If so, it would also have had a cell membrane.

-

The next question is the origin of the RNA.

One can find plausible prebiotic-synthesis pathways for the bases -- adenine, guanine, uracil, and cytosine -- but it's much more difficult to find one for the ribose. So I've seen speculation that the ribose was replacement of something else. But what? I've seen speculations like amino acids and polycyclic aromatic hydrocarbons.

So from prebiotic chemistry to the RNA world, there's IMO still a gap.

 

[lpetrich]

Then an issue that IMO we need to set the record straight on.

Was the original sort of metabolism fermentation? That's been a common view over the last century, but is that really likely? We've had some success in mapping out early evolution back to the Last Universal Common Ancestor and beyond, and how well does it support fermentation-first?

How did LUCA make a living? Chemiosmosis in the origin of life - Nick Lane, John F. Allen, and William Martin
DOI 10.1002/bies.200900131
BioEssays 9999:1–10, 2010 Wiley Periodicals, Inc

They argue that fermentation was not ancestral, for these reasons:

• Fermentation is more complicated than a simple redox reaction, and it does not release much energy. Embden-Meyerhoff glucose fermentation requires about 12 enzymes.
• "Pure" fermenters are never on the early branches; those branches always have prokaryotes that get energy with the chemiosmotic mechanism.
• All known autotrophs and the majority of heterotrophs use this mechanism for energy metabolism, and many fermenters maintain some of it.
• Chemiosmosis is necessary to power taking in nutrient molecules and moving a flagellum.
• Fermentation enzymes have greatly different sequences and structures across Bacteria and Archaea, suggesting separate origins.

But there is something that's widely present and that was likely present in the LUCA: the respiratory chain, complete with coupling to the chemiosmotic mechanism. Is it possible to have autotrophic metabolism from it? Surprisingly, yes. Some prokaryotes have chemolithotrophic metabolism, and some of them do indeed use the respiratory chain in it.

Energetically, reduction of nitrogen oxides will work, nitrogen oxides including nitrates and nitrites. This reduction needs to be balanced with oxidation of something, and there are several energetically-feasible possibilities: hydrogen, sulfur, arsenic, and iron (ferrous to ferric, Fe++ to Fe+++).

So if an early organism could find nitrogen oxides, it would have no trouble getting the energy it needed.

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.

Even in the absence of nitrogen oxides, an organism could use such alternatives as carbon dioxide.


What a thought. Our ancestors of around 3 to 4 billion years ago lived off of nitrogen oxides, including nitric acid.

 

[rousseau]

The origin of life on earth and abiogenesis was the big bang and the inception of the universe... a bunch of stuff just happened before an inorganic molecule became an organic molecule.

I don't get what you have in mind.

I'm just being annoying and pedantic. Idea is that life is just a part of the chemical evolution of the universe. So the term 'life' in a sense isn't a meaningful distinction from non-life.

 

[lpetrich]

I once found an amusing analogy for the evolution of biosynthesis pathways. It was in Iosif Shklovsky's and Carl Sagan's 1966 book Intelligent Life in the Universe, in one of CS's parts of that book.

Imagine a population of sort-of-human-shaped robots that likes to mine a big old junkyard for parts to repair themselves and to build new robots.

At first, they have no trouble finding parts. But they run out of arms. They then work out how to make arms from legs. But when they run out of legs, they figure out how to make legs from car engines. When they run out of car engines, they figure out how to make the car engines from iron ore. Thus getting

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

Then CS noted that geneticist Norman Horowitz had proposed that biosynthesis pathways had evolved in this fashion also. Checking on  Norman Horowitz, the article labeled this hypothesis "backward evolution". That article linked to On the Evolution of Biochemical Syntheses (PNAS, 1945)

For the simpler biological molecules, it was likely the primordial soup or pizza or whatever foodstuff. For more complicated ones, I've seen the "metabolic leakage" hypothesis, that these may have originated as biosynthesis mistakes.

 

[Loren Pechtel]

I once found an amusing analogy for the evolution of biosynthesis pathways. It was in Iosif Shklovsky's and Carl Sagan's 1966 book Intelligent Life in the Universe, in one of CS's parts of that book.

Imagine a population of sort-of-human-shaped robots that likes to mine a big old junkyard for parts to repair themselves and to build new robots.

At first, they have no trouble finding parts. But they run out of arms. They then work out how to make arms from legs. But when they run out of legs, they figure out how to make legs from car engines. When they run out of car engines, they figure out how to make the car engines from iron ore. Thus getting

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

Then CS noted that geneticist Norman Horowitz had proposed that biosynthesis pathways had evolved in this fashion also. Checking on  Norman Horowitz, the article labeled this hypothesis "backward evolution". That article linked to On the Evolution of Biochemical Syntheses (PNAS, 1945)

For the simpler biological molecules, it was likely the primordial soup or pizza or whatever foodstuff. For more complicated ones, I've seen the "metabolic leakage" hypothesis, that these may have originated as biosynthesis mistakes.

I find it hard to imagine evolution working any other way.

 

[bilby]

I once found an amusing analogy for the evolution of biosynthesis pathways. It was in Iosif Shklovsky's and Carl Sagan's 1966 book Intelligent Life in the Universe, in one of CS's parts of that book.

Imagine a population of sort-of-human-shaped robots that likes to mine a big old junkyard for parts to repair themselves and to build new robots.

At first, they have no trouble finding parts. But they run out of arms. They then work out how to make arms from legs. But when they run out of legs, they figure out how to make legs from car engines. When they run out of car engines, they figure out how to make the car engines from iron ore. Thus getting

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

Then CS noted that geneticist Norman Horowitz had proposed that biosynthesis pathways had evolved in this fashion also. Checking on  Norman Horowitz, the article labeled this hypothesis "backward evolution". That article linked to On the Evolution of Biochemical Syntheses (PNAS, 1945)

For the simpler biological molecules, it was likely the primordial soup or pizza or whatever foodstuff. For more complicated ones, I've seen the "metabolic leakage" hypothesis, that these may have originated as biosynthesis mistakes.

I find it hard to imagine evolution working any other way.

I agree; In the absence of living things to consume them, all kinds of random organic compounds are likely to have existed in the early oceans. These days, if anything useful comes along - say a simple sugar like ribose - then some bacterium will gobble it up and use it for fuel. But in a pre-biotic environment, there's really nothing out there to rapidly break down such molecules (assuming that there is a mechanism by which they arise spontaneously in the environment), and they could exist for a long time before being broken down, ultimately rising to useful concentrations (perhaps only in particularly favourable locations and conditions). Of course as soon as metabolism (life) starts, these building blocks will rapidly be used up, and new pathways to synthesize them will be under enormous pressure to evolve, as the ability to do so would be a massive competitive advantage.

 

[fromderinside]

I find it hard to imagine evolution working any other way.

I agree; In the absence of living things to consume them, all kinds of random organic compounds are likely to have existed in the early oceans. These days, if anything useful comes along - say a simple sugar like ribose - then some bacterium will gobble it up and use it for fuel. But in a pre-biotic environment, there's really nothing out there to rapidly break down such molecules (assuming that there is a mechanism by which they arise spontaneously in the environment), and they could exist for a long time before being broken down, ultimately rising to useful concentrations (perhaps only in particularly favourable locations and conditions). Of course as soon as metabolism (life) starts, these building blocks will rapidly be used up, and new pathways to synthesize them will be under enormous pressure to evolve, as the ability to do so would be a massive competitive advantage.

Gee. Isn't this exactly what is proposed in this article wtithout all the step by step personal narraitive? A New Physics Theory of Life http://www.scientificamerican.com/article/a-new-physics-theory-of-life/

Actually I just wanted to get the theory back out there before we begin trying to reverse engineer process that might have been involved in arriving as a life solution. I mean if the mechanism is known and testable why go through all the 'well if this then that' stuff.