Formamide-based prebiotic chemistry

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https://en.wikipedia.org/wiki/Formamide-based_prebiotic_chemistry 

Formamide-based prebiotic chemistry is a reconstruction of the beginnings of life on Earth, assuming that formamide could accumulate in sufficiently high amounts to serve as the building block and reaction medium for the synthesis of the first biogenic molecules.

Formamide (NH₂CHO), the simplest naturally occurring amide, contains all the elements (hydrogen, carbon, oxygen, and nitrogen), which are required for the synthesis of biomolecules, and is a ubiquitous molecule in the universe. Formamide has been detected in galactic centers, star-forming regions of dense molecular clouds, high-mass young stellar objects, the interstellar medium, comets, and satellites. In particular, dense clouds containing formamide, with sizes on the order of kiloparsecs, have been observed in the vicinity of the Solar System.

Formamide forms under a variety of conditions, corresponding to both terrestrial environments and interstellar media: e.g., on high-energy particle irradiation of binary mixtures of ammonia (NH₃) and carbon monoxide (CO), or from the reaction between formic acid (HCOOH) with NH₃. It has been suggested that in hydrothermal pores formamide may accumulate in sufficiently high concentrations to enable synthesis of biogenic molecules. Ab initio molecular dynamics simulations suggest that formamide could be a key intermediate of the Miller-Urey experiment as well.

The combinatorial power of carbon is manifested in the composition of the molecular populations detected in circum- and interstellar media (see the Astrochemistry.net web site). The number and the complexity of carbon-containing molecules are significantly higher than those of inorganic compounds, presumably all over the universe. One of the most abundant C-containing three-atoms molecule observed in space is hydrogen cyanide (HCN). The chemistry of HCN has thus attracted attention in origin of life studies since the earliest times, and the laboratory synthesis of adenine from HCN under presumptive prebiotic conditions was reported as early as 1961. The intrinsic limit of HCN stems from its high reactivity, which leads in turn, to instability and the difficulty associated with its concentration and accumulation in unreacted form. The “Warm Little Pond” in which life is supposed to have started, as imagined by Charles Darwin and re-elaborated by Alexander Oparin, had most likely to reach sufficiently high concentrations to start creating the next levels of complexity. Hence the necessity of a derivative of HCN that is sufficiently stable to survive for time periods extended enough to allow its concentration in the actual physico-chemical settings, but that is sufficiently reactive to originate new compounds in prebiotically plausible environments. Ideally, this derivative should be able to undergo reactions in various directions, without prohibitively high energy barriers, thus allowing the production of different classes of potentially prebiotic compounds. Formamide fulfils all these requirements and, due to its significantly higher boiling point (210 °C), enables chemical synthesis in a much broader temperature range than water.

Prebiotic chemistry

Current living forms on Earth are essentially composed of four types of molecular entities: (i) nucleic acids, (ii) proteins, (iii) carbohydrates, and (iv) lipids. Nucleic acids (DNA and RNA) embody and express the genetic information and, together, constitute the genome and the apparatus for its expression (the genotype). Proteins, carbohydrates, and lipids form the structures, which harness and handle energy from the environment for organizing matter according to the instructions specified by the genotype, aiming to its conservation and transmission. The ensemble of proteins, carbohydrates, lipids and nucleic acids constitute the phenotype. Life is thus made of the interaction of metabolism and genetics, of the genotype with the phenotype. Both are built around the chemistry of the most common elements of the universe (hydrogen, oxygen, nitrogen, and carbon), important although ancillary roles being played by phosphorus and sulphur, and by other elements.

Given the overwhelming variety of the chemically conceivable molecules, the fact that in biological systems we observe only a small subset of organic molecules has raised questions how and which different reaction pathways could have plausibly lead to the synthesis of pre-biological molecules on the primordial Earth. These are the main objectives of prebiotic chemistry research.

Precursor of biogenic molecules

Figure 1. Relationship between formamide and other prebiotic feedstock molecules, such as HCN and ammonium formate(NH₄⁺HCOO⁻).

Figure 1 summarizes the basic chemistry of formamide and its chemical connection with HCN and ammonium formate (NH₄⁺HCOO⁻), considering selected examples of preparative and degradative reactions.

The synthesis of purine from formamide was first reported in 1980. A series of studies building on this observation was started 20 years later: the synthesis of a large panel of prebiotically relevant compounds (including purine, adenine, cytosine, and 4(3H)pyrimidinone) in good yields was reported in 2001. These products were obtained by heating formamide in the presence of simple catalysts such as calcium carbonate (CaCO₃), silica (SiO₂), or alumina (Al₂O₃).

In addition to nucleobases, sugars, carboxylic acids, amino acids, as well as heterogeneous compounds of various classes, (including urea and carbodiimide) were also synthesized. The catalysts studied include, in addition to those mentioned, titanium oxides, clays, cosmic dust analogues, phosphates, iron sulphide minerals, zirconium minerals, borate minerals, or numerous materials of meteoritic origin  encompassing iron, stony-iron, chondrites, and achondrites meteorites.

Various energy sources, including thermal energy, UV-radiation, irradiation with high-energy (terawatt) laser pulses, or slow protons were tested. Mimics of different formamide-based prebiotic scenarios have been reconstructed and analyzed, including space-wise solar wind irradiation of meteorites, dynamic chemical gardens, and meteorites in aqueous environments. It has been suggested that the stepwise decrease of the temperature of the prebiotic environment could induce a sequence of strongly non-equilibrium chemical events that led to the emergence of more and more complex species from formamide on the early Earth.

For each studied combination of catalyst/energy source/environment, formamide condensed into a variety of different prebiotically relevant compounds, each combination giving rise to a specific set of relatively complex molecules, usually encompassing several nucleobases, amino acids, and carboxylic acids. The highest level of complexity was attained for the formamide/meteorite system, using proton irradiation as the energy source, where the one-pot synthesis of four nucleosides (uridine, cytidine, adenosine, thymidine) was observed. So far, no other one-carbon atom compound has shown the versatility of products that can be formed from formamide under plausible prebiotic conditions in a one-pot chemistry (see Figure 2).

Figure 2. Main prebiotic building blocks that can be synthesized from formamide under plausible prebiotic conditions.

In addition to its dual function of substrate and solvent in one-pot syntheses affording prebiotic compounds as complex as nucleosides and long aliphatic chains, it has been observed that formamide plays a role in the generation of molecules which are closer to the biological domain. In the presence of a phosphate source (e.g., phosphate minerals), formamide promotes the phosphorylation of nucleosides, leading to the formation of nucleotides and strongly stimulates the non-enzymatic polymerization of 3’,5’ cyclic nucleotides, leading to the abiotic synthesis of RNA oligomers. This is the reason why formamide is considered a plausible medium for prebiotic phosphorylation reactions also in the “discontinuous synthesis” scenario of the origin of life. As well as phosphorylation, formamide has been shown to be a competent medium for the production of amino acid derivatives from their simple aldehyde and nitrile precursors, demonstrating that water is not the only solvent that this process can occur in.  Most notably, formamide provides a medium for the prebiotic synthesis of cysteine derivatives, not considered previously considered plausible in strictly aqueous prebiotic environments.

Oxygen cycle

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Oxygen_cycle 

Main reservoirs and fluxes — in the biosphere (green), marine biosphere (blue), lithosphere (brown), and atmosphere (grey).
The major fluxes between these reservoirs are shown in colored arrows, where the green arrows are related to the terrestrial biosphere, blue arrows are related to the marine biosphere, black arrows are related to the lithosphere, and the purple arrow is related to space (not a reservoir, but also contributes to the atmospheric O₂₎.
The value of photosynthesis or net primary productivity (NPP) can be estimated through the variation in the abundance and isotopic composition of atmospheric O₂.
The rate of organic carbon burial was derived from estimated fluxes of volcanic and hydrothermal carbon.

Oxygen cycle refers to the movement of oxygen through the atmosphere (air), biosphere (plants and animals) and the lithosphere (the Earth’s crust). The oxygen cycle demonstrates how free oxygen is made available in each of these regions, as well as how it is used. The oxygen cycle is the biogeochemical cycle of oxygen atoms between different oxidation states in ions, oxides, and molecules through redox reactions within and between the spheres/reservoirs of the planet Earth. The word oxygen in the literature typically refers to the most common oxygen allotrope, elemental/diatomic oxygen (O₂), as it is a common product or reactant of many biogeochemical redox reactions within the cycle. Processes within the oxygen cycle are considered to be biological or geological and are evaluated as either a source (O₂ production) or sink (O₂ consumption).

Oxygen is one of the most common elements on Earth and represents a large portion of each main reservoir. By far the largest reservoir of Earth's oxygen is within the silicate and oxide minerals of the crust and mantle (99.5% by weight). The Earth's atmosphere, hydrosphere, and biosphere together hold less than 0.05% of the Earth's total mass of oxygen. Besides O₂, additional oxygen atoms are present in various forms spread throughout the surface reservoirs in the molecules of biomass, H₂O, CO₂, HNO₃, NO, NO₂, CO, H₂O₂, O₃, SO₂, H₂SO₄, MgO, CaO, Al2O3, SiO₂, and PO₄.

Atmosphere

The atmosphere is 21% oxygen by volume, which equates to a total of roughly 34 × 10¹⁸ mol of oxygen. Other oxygen-containing molecules in the atmosphere include ozone (O₃), carbon dioxide (CO₂), water vapor (H₂O), and sulphur and nitrogen oxides (SO₂, NO, N₂O, etc.).

Biosphere

The biosphere is 22% oxygen by volume, present mainly as a component of organic molecules (C_xH_xN_xO_x) and water.

Hydrosphere

The hydrosphere is 33% oxygen by volume present mainly as a component of water molecules, with dissolved molecules including free oxygen and carbolic acids (H_xCO₃).

Lithosphere

The lithosphere is 46.6% oxygen by volume, present mainly as silica minerals (SiO₂) and other oxide minerals.

Sources and sinks

While there are many abiotic sources and sinks for O₂, the presence of the profuse concentration of free oxygen in modern Earth's atmosphere and ocean is attributed to O₂ production from the biological process of oxygenic photosynthesis in conjunction with a biological sink known as the biological pump and a geologic process of carbon burial involving plate tectonics. Biology is the main driver of O₂ flux on modern Earth, and the evolution of oxygenic photosynthesis by bacteria, which is discussed as part of the Great Oxygenation Event, is thought to be directly responsible for the conditions permitting the development and existence of all complex eukaryotic metabolism.

Biological production

The main source of atmospheric free oxygen is photosynthesis, which produces sugars and free oxygen from carbon dioxide and water:

${\displaystyle 6\mathrm{C}{\mathrm{O}}_2+6{\mathrm{H}}_2\mathrm{O}+\mathrm{e}\mathrm{n}\mathrm{e}\mathrm{r}\mathrm{g}\mathrm{y}⟶{\mathrm{C}}_6{\mathrm{H}}_{12}{\mathrm{O}}_6+6{\mathrm{O}}_2}$

Photosynthesizing organisms include the plant life of the land areas, as well as the phytoplankton of the oceans. The tiny marine cyanobacterium Prochlorococcus was discovered in 1986 and accounts for up to half of the photosynthesis of the open oceans.

Abiotic production

An additional source of atmospheric free oxygen comes from photolysis, whereby high-energy ultraviolet radiation breaks down atmospheric water and nitrous oxide into component atoms. The free hydrogen and nitrogen atoms escape into space, leaving O₂ in the atmosphere:

${\displaystyle 2{\mathrm{H}}_2\mathrm{O}+\mathrm{e}\mathrm{n}\mathrm{e}\mathrm{r}\mathrm{g}\mathrm{y}⟶4\mathrm{H}+{\mathrm{O}}_2}$

${\displaystyle 2{\mathrm{N}}_2\mathrm{O}+\mathrm{e}\mathrm{n}\mathrm{e}\mathrm{r}\mathrm{g}\mathrm{y}⟶4\mathrm{N}+{\mathrm{O}}_2}$

Biological consumption

The main way free oxygen is lost from the atmosphere is via respiration and decay, mechanisms in which animal life and bacteria consume oxygen and release carbon dioxide.

Capacities and fluxes

The following tables offer estimates of oxygen cycle reservoir capacities and fluxes. These numbers are based primarily on estimates from (Walker, J. C. G.): More recent research indicates that ocean life (marine primary production) is actually responsible for more than half the total oxygen production on Earth.

Reservoir	Capacity (kg O2)	Flux in/out (kg O2 per year)	Residence time (years)
Atmosphere	1.4×1018	3×1014	4500
Biosphere	1.6×1016	3×1014	50
Lithosphere	2.9×1020	6×1011	500000000

Table 2: Annual gain and loss of atmospheric oxygen (Units of 10¹⁰ kg O₂ per year)

Photosynthesis (land)	16,500
Photosynthesis (ocean)	13,500
Photolysis of N2O	1.3
Photolysis of H2O	0.03
Total gains	~30,000
Losses - respiration and decay
Aerobic respiration	23,000
Microbial oxidation	5,100
Combustion of fossil fuel (anthropogenic)	1,200
Photochemical oxidation	600
Fixation of N2 by lightning	12
Fixation of N2 by industry (anthropogenic)	10
Oxidation of volcanic gases	5
Losses - weathering
Chemical weathering	50
Surface reaction of O3	12
Total losses	~30,000

Ozone

Main article: Ozone-oxygen cycle

The presence of atmospheric oxygen has led to the formation of ozone (O₃) and the ozone layer within the stratosphere:

${\displaystyle {\mathrm{O}}_2+\mathrm{u}\mathrm{v}\mathrm{l}\mathrm{i}\mathrm{g}\mathrm{h}\mathrm{t}⟶2\mathrm{O}(\lambda \lesssim 200\text{nm})}$

${\displaystyle \mathrm{O}+{\mathrm{O}}_2⟶{\mathrm{O}}_3}$

O + O₂ :- O₃

The ozone layer is extremely important to modern life as it absorbs harmful ultraviolet radiation:

${\displaystyle {\mathrm{O}}_3+\mathrm{u}\mathrm{v}\mathrm{l}\mathrm{i}\mathrm{g}\mathrm{h}\mathrm{t}⟶{\mathrm{O}}_2+\mathrm{O}(\lambda \lesssim 300\text{nm})}$

Biological carbon fixation

From Wikipedia, the free encyclopedia

https://en.wikipedia.org/wiki/Biological_carbon_fixation

Cyanobacteria such as these carry out photosynthesis. Their emergence foreshadowed the evolution of many photosynthetic plants and oxygenated Earth's atmosphere.

Biological carbon fixation or сarbon assimilation is the process by which inorganic carbon (particularly in the form of carbon dioxide) is converted to organic compounds by living organisms. The compounds are then used to store energy and as structure for other biomolecules. Carbon is primarily fixed through photosynthesis, but some organisms use a process called chemosynthesis in the absence of sunlight.

Organisms that grow by fixing carbon are called autotrophs, which include photoautotrophs (which use sunlight), and lithoautotrophs (which use inorganic oxidation). Heterotrophs are not themselves capable of carbon fixation but are able to grow by consuming the carbon fixed by autotrophs or other heterotrophs. "Fixed carbon", "reduced carbon", and "organic carbon" may all be used interchangeably to refer to various organic compounds. Chemosynthesis is carbon fixation driven by chemical energy, rather than from sunlight. Sulfur- and hydrogen-oxidizing bacteria often use the Calvin cycle or the reductive citric acid cycle.

Net vs. gross CO₂ fixation

Graphic showing net annual amounts of CO₂ fixation by land and sea-based organisms.

The primary form of inorganic carbon that is fixed is carbon dioxide (CO₂). It is estimated that approximately 250 billion tons of carbon dioxide are converted by photosynthesis annually. The majority of the fixation occurs in terrestrial environments, especially the tropics. The gross amount of carbon dioxide fixed is much larger since approximately 40% is consumed by respiration following photosynthesis. Historically it is estimated that approximately 2×10¹¹ billion tons of carbon has been fixed since the origin of life.

Overview of pathways

Seven autotrophic carbon fixation pathways are known. The Calvin cycle fixes carbon in the chloroplasts of plants and algae, and in the cyanobacteria. It also fixes carbon in the anoxygenic photosynthesis in one type of Pseudomonadota called purple bacteria, and in some non-phototrophic Pseudomonadota.

Of the five other autotrophic pathways, two are known only in bacteria (the reductive citric acid cycle and the 3-hydroxypropionate cycle), two only in archaea (two variants of the 3-hydroxypropionate cycle), and one in both bacteria and archaea (the reductive acetyl CoA pathway).

List of pathways

Calvin cycle

The Calvin cycle accounts for 90% of biological carbon fixation. Consuming ATP and NADPH, the Calvin cycle in plants accounts for the preponderance of carbon fixation on land. In algae and cyanobacteria, it accounts for the preponderance of carbon fixation in the oceans. The Calvin cycle converts carbon dioxide into sugar, as triose phosphate (TP), which is glyceraldehyde 3-phosphate (GAP) together with dihydroxyacetone phosphate (DHAP):

3 CO₂ + 12 e⁻ + 12 H⁺ + P_i → TP + 4 H₂O

An alternative perspective accounts for NADPH (source of e⁻) and ATP:

3 CO₂ + 6 NADPH + 6 H⁺ + 9 ATP + 5 H₂O → TP + 6 NADP⁺ + 9 ADP + 8 P_i

The formula for inorganic phosphate (P_i) is HOPO₃²⁻ + 2H⁺. Formulas for triose and TP are C₂H₃O₂-CH₂OH and C₂H₃O₂-CH₂OPO₃²⁻ + 2H⁺

Reverse Krebs cycle

The reverse Krebs cycle, also known as reverse TCA cycle (rTCA) or reductive citric acid cycle, is an alternative to the standard Calvin-Benson cycle for carbon fixation. It has been found in strict anaerobic or microaerobic bacteria (as Aquificales) and anaerobic archea. It was discovered by Evans, Buchanan and Arnon in 1966 working with the photosynthetic green sulfur bacterium Chlorobium limicola. In particular, it is one of the most used pathways in hydrothermal vents by the Campylobacterota. This feature is very important in oceans. Without it, there would be no primary production in aphotic environments, which would lead to habitats without life. So this kind of primary production is called "dark primary production".

The cycle involves the biosynthesis of acetyl-CoA from two molecules of CO₂. The key steps of the reverse Krebs cycle are:

• Oxaloacetate to malate, using NADH + H⁺

  ${\displaystyle \text{Oxaloacetate}+\text{NADH}/{\text{H}}^{+}⟶\text{Malate}+{\text{NAD}}^{+}}$

• Fumarate to succinate, catalyzed by an oxidoreductase, Fumarate reductase

  ${\displaystyle \text{Fumarate}+{\text{FADH}}_2^{}\stackrel{-\rightharpoonup }{\leftharpoondown -}\text{Succinate}+\text{FAD}}$

• Succinate to succinyl-CoA, an ATP dependent step

  ${\displaystyle \text{Succinate}+\text{ATP}+\text{CoA}⟶\text{Succinyl}-\text{CoA}+\text{ADP}+\text{Pi}}$

• Succinyl-CoA to alpha-ketoglutarate, using one molecule of CO₂

  ${\displaystyle \text{Succinyl}-\text{CoA}+{\text{CO}}_2^{}+\text{Fd}(\text{red})⟶\text{alpha}-\text{ketoglutarate}+\text{Fd}(\text{ox})}$

• Alpha-ketoglutarate to isocitrate, using NADPH + H⁺ and another molecule of CO₂

  ${\displaystyle \text{Alpha}-\text{ketoglutarate}+{\text{CO}}_2^{}+\text{NAD}(\text{P})\text{H}/{\text{H}}^{+}⟶\text{Isocitrate}+\text{NAD}{(\text{P})}^{+}}$

• Citrate converted into oxaloacetate and acetyl-CoA, this is an ATP dependent step and the key enzyme is the ATP citrate lyase

  ${\displaystyle \text{Citrate}+\text{ATP}+\text{CoA}⟶\text{Oxaloacetate}+\text{Acetyl}-\text{CoA}+\text{ADP}+\text{Pi}}$

This pathway is cyclic due to the regeneration of the oxaloacetate.

The bacteria Gammaproteobacteria and Riftia pachyptila switch from the Calvin-Benson cycle to the rTCA cycle in response to concentrations of H₂S.

Reductive acetyl CoA pathway

The reductive acetyl CoA pathway (CoA) pathway, also known as the Wood-Ljungdahl pathway uses CO₂ as electron acceptor and carbon source, and H₂ as an electron donor to form acetic acid. This metabolism is wide spread within the phylum Bacillota, especially in the Clostridia.

The pathway is also used by methanogens, which are mainly Euryarchaeota, and several anaerobic chemolithoautotrophs, such as sulfate-reducing bacteria and archaea. It is probably performed also by the Brocadiales, an order of Planctomycetota that oxidize ammonia in anaerobic condition. Hydrogenotrophic methanogenesis, which is only found in certain archaea and accounts for 80% of global methanogenesis, is also based on the reductive acetyl CoA pathway.

The Carbon Monoxide Dehydrogenase/Acetyl-CoA Synthase is the oxygen-sensitive enzyme that permits the reduction of CO₂ to CO and the synthesis of acetyl-CoA in several reactions.

One branch of this pathway, the methyl branch, is similar but non-homologous between bacteria and archaea. In this branch happens the reduction of CO₂ to a methyl residue bound to a cofactor. The intermediates are formate for bacteria and formyl-methanofuran for archaea, and also the carriers, tetrahydrofolate and tetrahydropterins respectively in bacteria and archaea, are different, such as the enzymes forming the cofactor-bound methyl group.

Otherwise, the carbonyl branch is homologous between the two domains and consists of the reduction of another molecule of CO₂ to a carbonyl residue bound to an enzyme, catalyzed by the CO dehydrogenase/acetyl-CoA synthase. This key enzyme is also the catalyst for the formation of acetyl-CoA starting from the products of the previous reactions, the methyl and the carbonyl residues.

This carbon fixation pathway requires only one molecule of ATP for the production of one molecule of pyruvate, which makes this process one of the main choice for chemolithoautotrophs limited in energy and living in anaerobic conditions.

3-Hydroxypropionate bicycle

The 3-Hydroxypropionate bicycle, also known as 3-HP/malyl-CoA cycle, discovered only in 1989, is utilized by green non-sulfur phototrophs of Chloroflexaceae family, including the maximum exponent of this family Chloroflexus auranticus by which this way was discovered and demonstrated. The 3-Hydroxipropionate bicycle is composed of two cycles and the name of this way comes from the 3-Hydroxyporopionate which corresponds to an intermediate characteristic of it.

The first cycle is a way of synthesis of glyoxylate. During this cycle, two equivalents of bicarbonate are fixed by the action of two enzymes: the Acetyl-CoA carboxylase catalyzes the carboxylation of the Acetyl-CoA to Malonyl-CoA and Propionyl-CoA carboxylase catalyses the carboxylation of propionyl-CoA to methylamalonyl-CoA. From this point a series of reactions lead to the formation of glyoxylate which will thus become part of the second cycle.

In the second cycle, glyoxylate is approximately one equivalent of propionyl-CoA forming methylamalonyl-CoA. This, in turn, is then converted through a series of reactions into citramalyl-CoA. The citramalyl-CoA is split into pyruvate and Acetyl-CoA thanks to the enzyme MMC lyase. At this point the pyruvate is released, while the Acetyl-CoA is reused and carboxylated again at Malonyl-CoA thus reconstituting the cycle.

A total of 19 reactions are involved in 3-hydroxypropionate bicycle and 13 multifunctional enzymes are used. The multifunctionality of these enzymes is an important feature of this pathway which thus allows the fixation of three bicarbonate molecules.

It is a very expensive pathway: 7 ATP molecules are used for the synthesis of the new pyruvate and 3 ATP for the phosphate triose.

An important characteristic of this cycle is that it allows the co-assimilation of numerous compounds making it suitable for the mixotrophic organisms.

Cycles related to the 3-hydroxypropionate cycle

A variant of the 3-hydroxypropionate cycle was found to operate in the aerobic extreme thermoacidophile archaeon Metallosphaera sedula. This pathway is called the 3-hydroxypropionate/4-hydroxybutyrate cycle.

Yet another variant of the 3-hydroxypropionate cycle is the dicarboxylate/4-hydroxybutyrate cycle. It was discovered in anaerobic archaea. It was proposed in 2008 for the hyperthermophile archeon Ignicoccus hospitalis.

enoyl-CoA carboxylases/reductases

CO₂ fixation is catalyzed by enoyl-CoA carboxylases/reductases.^[22]

Non-autotrophic pathways

Although no heterotrophs use carbon dioxide in biosynthesis, some carbon dioxide is incorporated in their metabolism. Notably pyruvate carboxylase consumes carbon dioxide (as bicarbonate ions) as part of gluconeogenesis, and carbon dioxide is consumed in various anaplerotic reactions.

6-phosphogluconate dehydrogenase catalyzes the reductive carboxylation of ribulose 5-phosphate to 6-phosphogluconate in E. coli under elevated CO₂ concentrations.

Carbon isotope discrimination

Some carboxylases, particularly RuBisCO, preferentially bind the lighter carbon stable isotope carbon-12 over the heavier carbon-13. This is known as carbon isotope discrimination and results in carbon-12 to carbon-13 ratios in the plant that are higher than in the free air. Measurement of this ratio is important in the evaluation of water use efficiency in plants, and also in assessing the possible or likely sources of carbon in global carbon cycle studies.

Tree of life (biology)

From Wikipedia, the free encyclopedia

 

The tree of life or universal tree of life is a metaphor, conceptual model, and research tool used to explore the evolution of life and describe the relationships between organisms, both living and extinct, as described in a famous passage in Charles Darwin's On the Origin of Species (1859).

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth.

— Charles Darwin

Tree diagrams originated in the medieval era to represent genealogical relationships. Phylogenetic tree diagrams in the evolutionary sense date back to the mid-nineteenth century.

The term phylogeny for the evolutionary relationships of species through time was coined by Ernst Haeckel, who went further than Darwin in proposing phylogenic histories of life. In contemporary usage, tree of life refers to the compilation of comprehensive phylogenetic databases rooted at the last universal common ancestor of life on Earth. Two public databases for the tree of life are TimeTree, for phylogeny and divergence times, and the Open Tree of Life, for phylogeny.

History

Early natural classification

Further information: History of evolutionary thought

Edward Hitchcock's fold-out paleontological chart in his 1840 Elementary Geology

Although tree-like diagrams have long been used to organise knowledge, and although branching diagrams known as claves ("keys") were omnipresent in eighteenth-century natural history, it appears that the earliest tree diagram of natural order was the 1801 "Arbre botanique" (Botanical Tree) of the French schoolteacher and Catholic priest Augustin Augier. Yet, although Augier discussed his tree in distinctly genealogical terms, and although his design clearly mimicked the visual conventions of a contemporary family tree, his tree did not include any evolutionary or temporal aspect. Consistent with Augier's priestly vocation, the Botanical Tree showed rather the perfect order of nature as instituted by God at the moment of Creation.

In 1809, Augier's more famous compatriot Jean-Baptiste Lamarck (1744–1829), who was acquainted with Augier's "Botanical Tree", included a branching diagram of animal species in his Philosophie zoologique. Unlike Augier, however, Lamarck did not discuss his diagram in terms of a genealogy or a tree, but instead named it a tableau ("depiction"). Lamarck believed in the transmutation of life forms, but he did not believe in common descent; instead he believed that life developed in parallel lineages (repeated, spontaneous generation) advancing from more simple to more complex.

In 1840, the American geologist Edward Hitchcock (1793–1864) published the first tree-like paleontology chart in his Elementary Geology, with two separate trees for the plants and the animals. These are crowned (graphically) with the Palms and Man.

The first edition of Robert Chambers' Vestiges of the Natural History of Creation, published anonymously in 1844 in England, contained a tree-like diagram in the chapter "Hypothesis of the development of the vegetable and animal kingdoms". It shows a model of embryological development where fish (F), reptiles (R), and birds (B) represent branches from a path leading to mammals (M). In the text this branching tree idea is tentatively applied to the history of life on earth: "there may be branching".

In 1858, a year before Darwin's Origin, the paleontologist Heinrich Georg Bronn (1800–1862) published a hypothetical tree labelled with letters. Although not a creationist, Bronn did not propose a mechanism of change.

• 
  Augustin Augier's 1801 Arbre botanique ("Botanical Tree")
   
• 
  Jean-Baptiste Lamarck's 1809 depiction of the origins of animal groups in his Philosophie zoologique with branching evolutionary paths, not considered an evolutionary tree
   
• 
  Diagram in Robert Chambers's 1844 Vestiges of the Natural History of Creation

Darwin

Further information: Evolution and Common descent

Charles Darwin (1809–1882) used the metaphor of a "tree of life" to conceptualise his theory of evolution. In On the Origin of Species (1859) he presented an abstract diagram of a portion of a larger timetree for species of an unnamed large genus (see figure). On the horizontal base line hypothetical species within this genus are labelled A – L and are spaced irregularly to indicate how distinct they are from each other, and are above broken lines at various angles suggesting that they have diverged from one or more common ancestors. On the vertical axis divisions labelled I – XIV each represent a thousand generations. From A, diverging lines show branching descent producing new varieties, some of which become extinct, so that after ten thousand generations descendants of A have become distinct new varieties or even sub-species a¹⁰, f¹⁰, and m¹⁰. Similarly, the descendants of I have diversified to become the new varieties w¹⁰ and z¹⁰. The process is extrapolated for a further four thousand generations so that the descendants of A and I become fourteen new species labelled a¹⁴ to z¹⁴. While F has continued for fourteen thousand generations relatively unchanged, species B,C,D,E,G,H,K and L have gone extinct. In Darwin's own words: "Thus the small differences distinguishing varieties of the same species, will steadily tend to increase till they come to equal the greater differences between species of the same genus, or even of distinct genera." Darwin's tree is not a tree of life, but rather a small portion created to show the principle of evolution. Because it shows relationships (phylogeny) and time (generations), it is a timetree. In contrast, Ernst Haeckel illustrated a phylogenetic tree (branching only) in 1866, not scaled to time, and of real species and higher taxa. In his summary to the section, Darwin put his concept in terms of the metaphor of the tree of life:

The affinities of all the beings of the same class have sometimes been represented by a great tree. I believe this simile largely speaks the truth. The green and budding twigs may represent existing species; and those produced during each former year may represent the long succession of extinct species. At each period of growth all the growing twigs have tried to branch out on all sides, and to overtop and kill the surrounding twigs and branches, in the same manner as species and groups of species have tried to overmaster other species in the great battle for life. The limbs divided into great branches, and these into lesser and lesser branches, were themselves once, when the tree was small, budding twigs; and this connexion of the former and present buds by ramifying branches may well represent the classification of all extinct and living species in groups subordinate to groups. Of the many twigs which flourished when the tree was a mere bush, only two or three, now grown into great branches, yet survive and bear all the other branches; so with the species which lived during long-past geological periods, very few now have living and modified descendants. From the first growth of the tree, many a limb and branch has decayed and dropped off; and these lost branches of various sizes may represent those whole orders, families, and genera which have now no living representatives, and which are known to us only from having been found in a fossil state. As we here and there see a thin straggling branch springing from a fork low down in a tree, and which by some chance has been favoured and is still alive on its summit, so we occasionally see an animal like the Ornithorhynchus or Lepidosiren, which in some small degree connects by its affinities two large branches of life, and which has apparently been saved from fatal competition by having inhabited a protected station. As buds give rise by growth to fresh buds, and these, if vigorous, branch out and overtop on all sides many a feebler branch, so by generation I believe it has been with the great Tree of Life, which fills with its dead and broken branches the crust of the earth, and covers the surface with its ever branching and beautiful ramifications.

— Darwin, 1859.

The meaning and importance of Darwin's use of the tree of life metaphor have been extensively discussed by scientists and scholars. Stephen Jay Gould, for one, has argued that Darwin placed the famous passage quoted above "at a crucial spot in his text", where it marked the conclusion of his argument for natural selection, illustrating both the interconnectedness by descent of organisms as well as their success and failure in the history of life. David Penny has written that Darwin did not use the tree of life to describe the relationship between groups of organisms, but to suggest that, as with branches in a living tree, lineages of species competed with and supplanted one another. Petter Hellström has argued that Darwin consciously named his tree after the biblical Tree of Life, as described in Genesis, thus relating his theory to the religious tradition.

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  Page from Darwin's notebooks (c. July 1837) with his first sketch of an evolutionary tree, and the words "I think" at the top
   
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  Diagram in Darwin's On the Origin of Species, 1859.
  It was the book's only illustration.

Haeckel

Ernst Haeckel (1834–1919) constructed several trees of life. His first sketch, in the 1860s, shows "Pithecanthropus alalus" as the ancestor of Homo sapiens. His 1866 tree of life from Generelle Morphologie der Organismen shows three kingdoms: Plantae, Protista and Animalia. This has been described as "the earliest 'tree of life' model of biodiversity". His 1879 "Pedigree of Man" was published in his 1879 book The Evolution of Man. It traces all life forms to the Monera, and places Man (labelled "Menschen") at the top of the tree.

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  Haeckel's Stammbaum der Primaten (1860s)
   
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  Haeckel's tree of life in Generelle Morphologie der Organismen (1866)
   
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  The tree of life as seen by Haeckel in The Evolution of Man (1879)

Developments since 1990

Further information: Kingdom (biology)

Universal phylogenetic tree in rooted form, showing the three domains (Woese, Kandler, Wheelis 1990, p. 4578)

In 1990, Carl Woese, Otto Kandler and Mark Wheelis proposed a novel "tree of life" consisting of three lines of descent for which they introduced the term domain as the highest rank of classification. They suggested and formally defined the terms Bacteria, Archaea and Eukarya for the three domains of life. It was the first tree founded on molecular phylogenetics and microbial evolution as its basis.

The model of a tree is still considered valid for eukaryotic life forms. Trees have been proposed with either four or two supergroups. There does not yet appear to be a consensus; in a 2009 review article, Roger and Simpson conclude that "with the current pace of change in our understanding of the eukaryote tree of life, we should proceed with caution."

In 2015, the third version of TimeTree was released, with 2,274 studies and 50,632 species, represented in a spiral tree of life, free to download.

In 2015, the first draft of the Open Tree of Life was published, in which information from nearly 500 previously published trees was combined into a single online database, free to browse and download. Another database, TimeTree, helps biologists to evaluate phylogeny and divergence times.

In 2016, a new tree of life (unrooted), summarising the evolution of all known life forms, was published, illustrating the latest genetic findings that the branches were mainly composed of bacteria. The new study incorporated over a thousand newly discovered bacteria and archaea.

In 2022, the fifth version of TimeTree was released, incorporating 4,185 published studies and 148,876 species, representing the largest timetree of life from actual data (non-imputed).

Horizontal gene transfer and rooting the tree of life

Further information: Horizontal gene transfer

The prokaryotes (the two domains of bacteria and archaea) and certain animals such as bdelloid rotifers freely pass genetic information between unrelated organisms by horizontal gene transfer. Recombination, gene loss, duplication, and gene creation are a few of the processes by which genes can be transferred within and between bacterial and archaeal species, causing variation that is not due to vertical transfer. There is emerging evidence of horizontal gene transfer within the prokaryotes at the single and multicell level, so the tree of life does not explain the full complexity of the situation in the prokaryotes. This is a major problem for the tree of life because there is consensus that eukaryotes arose from a fusion between bacteria and archaea, meaning that the tree of life is not fully bifurcating and should not be represented as such for that important node. Secondly, unrooted phylogenetic networks are not true evolutionary trees (or trees of life) because there is no directionality, and therefore the tree of life needs a root.

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  Hedges and Kumar's circular timetree of life, of 1,610 families
   
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  Hedges et al.'s 2015 spiral timetree of life of 50,632 species
   
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  David Hillis's 2008 plot of the tree of life, based on completely sequenced genomes
   
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  A 2016 (metagenomic) representation of the tree of life (unrooted) using ribosomal protein sequences