Carbon metabolism is the most basic aspect of life.

Carbon metabolism is the most basic aspect of life

https://reasonandscience.catsboard.com/t2986-carbon-metabolism-is-the-most-basic-aspect-of-life

Autotrophic CO2 fixation represents the most important biosynthetic process in biology. 5 None of the chemolithoautotrophic archaea seems to use the Calvin cycle for CO2 fixation, even though in some species one of the key enzymes, ribulose1,5-bisphosphate carboxylase–oxygenase (RubisCO), is present. Instead, these organisms use diverse CO2 fixation mechanisms to generate acetyl-coenzyme A (acetyl-CoA), from which the biosynthesis of building blocks can start.

Autotrophic organisms use several routes of assimilation of Co2, each with its own biochemical reactions requiring its own enzymes and reducing power of a specific nature.2
Plants and cyanobacteria fix CO2 use the  Calvin cycle, Calvin-Benson cycle. There are, at least, five additional carbon fixation pathways known to exist in autotrophic bacteria and archaea, which differ in reducing compounds, energy source, and oxygen sensitivity of enzymes. 4  Besides the well-known Calvin-Benson cycle, five other totally different autotrophic mechanisms are known today. 5  Today, six autotrophic CO2 fixation mechanisms are known, raising the question of why so many pathways are necessary.

It has been proposed that the first autotrophic pathway was akin to either the reductive TCA cycle or the reductive acetyl-CoA pathway (11, 17, 35, 45, 58)  The reductive TCA cycle has the characteristics of an autocatalytic cycle and leads to a complex cyclic reaction network from which other anabolic pathways could have evolved (11, 58): e.g., the oxidative TCA cycle (8, 45)

My comment: This challenges the central biological dogma of the biochemical unity of life and common ancestry.

None of the autotrophic archaea seems to use the Calvin cycle for CO2 fixation. Instead, they use three different CO2 fixation mechanisms to generate acetyl-coenzyme A (acetyl-CoA), from which the biosynthesis of building blocks can start. 6

Organisms capable of autotrophic metabolism assimilate inorganic carbon into organic carbon. They form an integral part of ecosystems by making an otherwise unavailable form of carbon available to other organisms, a central component of the global carbon cycle. For many years, the doctrine prevailed that the Calvin-Benson-Bassham (CBB) cycle is the only biochemical autotrophic CO2 fixation pathway of significance in the ocean. However, ecological, biochemical, and genomic studies carried out over the last decade have not only elucidated new pathways but also shown that autotrophic carbon fixation via pathways other than the CBB cycle can be significant. This has ramifications for our understanding of the carbon cycle and energy flow in the ocean. 3 Autotrophic organisms have the ability to build all cell material solely from inorganic carbon. This makes autotrophic processes a crucial component of the global carbon cycle by providing the organic carbon used by heterotrophic organisms, which oxidize organic carbon back to inorganic carbon, completing the carbon cycle. The balance between autotrophy and heterotrophy is a key factor regulating CO2 and O2 concentrations in the atmosphere, and it also affects the overall redox balance of Earth. Although the standing stock of primary producers is much smaller in the ocean compared with the land, approximately half of the global primary production occurs in the ocean due to a much higher turnover of biomass

Below map presents an overall view of central carbon metabolism, where the number of carbons is shown for each compound denoted by a circle, excluding a cofactor (CoA, CoM, THF, or THMPT) that is replaced by an asterisk. The map contains carbon utilization pathways of glycolysis (map00010), pentose phosphate pathway (map00030), and citrate cycle (map00020), and six known carbon fixation pathways (map00710 and map00720) as well as some pathways of methane metabolism (map00680). The six carbon fixation pathways are:  1


1. reductive pentose phosphate cycle (Calvin cycle) in plants and cyanobacteria that perform oxygenic photosynthesis, 
2. reductive citrate cycle (rTCA) cycle), or reductive citric acid cycle (Arnon-Buchanan cycle) ) or reductive tricarboxylic acid (rTCA) in photosynthetic green sulfur bacteria and some chemolithoautotrophs, 
3. 3-hydroxypropionate bi-cycle in photosynthetic green nonsulfur bacteria, two variants of 4-hydroxybutyrate pathways in Crenarchaeota 
4. hydroxypropionate-hydroxybutyrate cycle and 
5. dicarboxylate-hydroxybutyrate cycle, and 
6. reductive acetyl-CoA pathway

1. the Calvin-Benson-Bassham cycle (hereafter, the Calvin cycle),
2. the reductive tricarboxylic acid (rTCA) cycle
3, the 3-hydroxypropionate (3-HP) bicycle
4. the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB)
5. the dicarboxylate/4-hydroxybutyrate (DC/4-HB) cycle
6. the reductive Acetyl-CoA Pathway, or Wood-Ljungdahl (WL) pathway

These pathways differ in several ways [e.g., with respect to energy demand, available reducing compounds, requirement for metals (Fe, Co, Ni, and Mo), usage of coenzymes, and oxygen sensitivity of enzymes]. 8


2.The reductive citric acid cycle (Arnon-Buchanan cycle) is found in microaerophiles and anaerobes, such as green sulfur bacteria. In one complete turn of this cycle, four molecules of CO2 are fixed by the enzymes that are sensitive to oxygen, resulting in the production of one molecule of oxaloacetate, which is itself an intermediate of the cycle. 

3. The 3-hydroxypropionate bicycle is found in some green non-sulphur bacteria of the family Chloroflexaceae. In one complete turn of this bicycle, three molecules of bicarbonate are converted into one molecule of pyruvate. In addition, this bicycle provides the secondary benefit of useful intermediates for biosynthesis: acetyl-CoA, glyoxylate, and succinyl-CoA.

4. The hydroxypropionate-hydroxybutyrate cycle  is found in aerobic Crenarchaeota, Acidianus, Metallosphaera, and Sulfolobales. Some of the intermediates and the carboxylation reactions are the same as in the 3-hydroxypropionate bicycle. One complete turn of this cycle generates two molecules of acetyl-CoA, one of which is reutilized in the the cycle and the other is removed for cell material biosynthesis.

5. The dicarboxylate-hydroxybutyrate cycle was named after its intermediates: succinate (a kind of dicarboxylate) and hydroxybutyrate. This cycle has been found only in Ignicoccus hospitals, a strictly anaerobic hyperthermophilic archaea. Recent genome study suggests that this cycle may exist in Desulfurococcales (to which Ignicoccus belongs) and Thermoproteales (a taxon close to the origin of archaea). The first half of the cycle, from acetyl-CoA to succinate-CoA, corresponds to the reductive citric acid cycle and the latter half of the cycle, from succinate-CoA to two molecules of acetyl-CoA, corresponds to the hydroxypropionate-hydroxybutyrate cycle.

6. The reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) is found in strictly anaerobic bacteria and archaea (Proteobacteria, Planctomycetes, Spirochaetes, and Euryarchaeota), some of which are methane-forming. A bifunctional enzyme, carbon monoxide dehydrogenase/acetyl-CoA synthase, catalyzes the reactions from CO2 to CO and from CO2 to a methyl group, and then to generate acetyl-CoA. 
 






CoA, co-enzyme A; F420, deazaflavin factor 420; FAD, flavin adenine dinucleotide; PEP, phosphoenolpyruvate; RubisCO, ribulose 1,5-bisphosphate carboxylase– oxygenase. *Alternative name of pathway is provided in brackets. ‡ In biological processes, when inorganic carbon is used to make organic compounds, 12C is more weakly bonded and reacts more readily than 13C because of its lighter mass. This means that organic matter tends to become enriched in 12C (and depleted in 13C; therefore negative sign) relative to the reservoir of inorganic carbon from which it has been drawn. Carbon stable isotopic fractionations are measured relative to a fossil belemnite standard (the PDB standard). Isotopic fractionations are normally small and so values are measured in parts per thousand (‰) and expressed as d13C values as follows: d13C ‰ = [(13C/12Csample - 13C/12Cstandard) / (13C/12Cstandard)] × 1000. § The presence of biotin-dependent 2-oxoglutarate carboxylase in, for example, Hydrogenobacter thermophilus122, can increase the energy requirements of the cycle. ||NADH in Hydrogenobacter thermophilus123. ¶ Note that reduction of ferredoxin may be energy driven3–5, which would increase the energy demands of the ferredoxin-dependent pathways. 7

Because bacteria and archaea are known for their versatile metabolism, mixotrophy is a widespread phenomenon, especially in aquatic environments. Mixotrophic organisms use several metabolic strategies simultaneously (e.g., incorporating organic carbon into cellular material using light and/or inorganic chemical energy sources), or they can switch between different strategies.

•  Carbohydrate metabolism
  
  
  
  •  Central carbohydrate metabolism
    
    
    
    •  M00001 Glycolysis (Embden-Meyerhof pathway)
      
    •  M00002 Glycolysis, core module involving three-carbon compounds
      
    •  M00307 Pyruvate oxidation
      
    •  M00009 Citrate cycle (TCA cycle, Krebs cycle)
      
    •  M00010 Citrate cycle, first carbon oxidation
      
    •  M00011 Citrate cycle, second carbon oxidation
      
    •  M00004 Pentose phosphate pathway (Pentose phosphate cycle)
      
    •  M00006 Pentose phosphate pathway, oxidative phase
      
    •  M00007 Pentose phosphate pathway, non-oxidative phase
      
    •  M00580 Pentose phosphate pathway, archaea
      
    •  M00005 PRPP biosynthesis
      
    •  M00008 Entner-Doudoroff pathway
      
    •  M00308 Semi-phosphorylative Entner-Doudoroff pathway
      
    •  M00633 Semi-phosphorylative Entner-Doudoroff pathway
      
    •  M00309 Non-phosphorylative Entner-Doudoroff pathway
      
    
    
    
  •  Other carbohydrate metabolism
    
    
    
    •  M00012 Glyoxylate cycle
      
    •  M00373 Ethylmalonyl pathway
      
    •  M00740 Methylaspartate cycle
      
    •  M00532 Photorespiration
      
    •  M00013 Malonate semialdehyde pathway
      
    •  M00741 Propanoyl-CoA metabolism
      
    
    
    
  
  
  
•  Energy metabolism
  
  
  
  •  Carbon fixation
    
    
    
    •  M00165 Reductive pentose phosphate cycle (Calvin cycle)
      
    •  M00166 Reductive pentose phosphate cycle
      
    •  M00167 Reductive pentose phosphate cycle
      
    •  M00168 CAM (Crassulacean acid metabolism), dark
      
    •  M00169 CAM (Crassulacean acid metabolism), light
      
    •  M00172 C4-dicarboxylic acid cycle, NADP - malic enzyme type
      
    •  M00171 C4-dicarboxylic acid cycle, NAD - malic enzyme type
      
    •  M00170 C4-dicarboxylic acid cycle, phosphoenolpyruvate carboxykinase type
      
    •  M00173 Reductive citrate cycle (Arnon-Buchanan cycle)
      
    •  M00376 3-Hydroxypropionate bi-cycle
      
    •  M00375 Hydroxypropionate-hydroxybutylate cycle
      
    •  M00374 Dicarboxylate-hydroxybutyrate cycle
      
    •  M00377 Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway)
      
    •  M00579 Phosphate acetyltransferase-acetate kinase pathway
      
    •  M00620 Incomplete reductive citrate cycle
      
    
    
    
  •  Methane metabolism
    
    
    
    •  M00567 Methanogenesis
      
    •  M00357 Methanogenesis
      
    •  M00356 Methanogenesis
      
    •  M00563 Methanogenesis
      
    •  M00174 Methane oxidation, methanotroph
      
    •  M00346 Formaldehyde assimilation, serine pathway
      
    •  M00345 Formaldehyde assimilation, ribulose monophosphate pathway
      
    •  M00344 Formaldehyde assimilation, xylulose monophosphate pathway
      
    •  M00422 Acetyl-CoA pathway
      
    
    
    
  
  
  
•  Amino acid metabolism
  
  
  
  •  Serine and threonine metabolism
    
    
    
    •  M00020 Serine biosynthesis
      
    
    
    
  •  Cysteine and methionine metabolism
    
    
    
    •  M00021 Cysteine biosynthesis
      
    
    
    
  
  
  

1. https://www.genome.jp/kegg-bin/show_pathway?map01200+M00010
2. https://sci-hub.tw/https://link.springer.com/chapter/10.1007/0-306-47954-0_40
3. https://sci-hub.tw/https://www.annualreviews.org/doi/abs/10.1146/annurev-marine-120709-142712?journalCode=marine
4. https://www.genome.jp/dbget-bin/www_bget?ko00720
5. https://aem.asm.org/content/77/6/1925
6. https://www.nature.com/articles/nrmicro2365?draft=marketing
7. https://sci-hub.tw/https://www.nature.com/articles/nrmicro2365
8. https://sci-hub.tw/https://science.sciencemag.org/content/318/5857/1782.full

•  M00173 Reductive citrate cycle (Arnon-Buchanan cycle)
  
•  M00376 3-Hydroxypropionate bi-cycle
  
•  M00375 Hydroxypropionate-hydroxybutylate cycle
  
•  M00374 Dicarboxylate-hydroxybutyrate cycle
  
•  M00377 Reductive acetyl-CoA pathway (Wood-Ljungdahl pathway)
  
•  M00579 Phosphate acetyltransferase-acetate kinase pathway
  
•  M00620 Incomplete reductive citrate cycle
  

https://www.genome.jp/kegg-bin/show_pathway?map00720

•  Carbon fixation
  
  
  
  •  M00165 Reductive pentose phosphate cycle (Calvin cycle)
    
  •  M00166 Reductive pentose phosphate cycle
    
  •  M00167 Reductive pentose phosphate cycle
    
  •  M00168 CAM (Crassulacean acid metabolism), dark
    
  •  M00169 CAM (Crassulacean acid metabolism), light
    
  •  M00172 C4-dicarboxylic acid cycle, NADP - malic enzyme type
    
  •  M00171 C4-dicarboxylic acid cycle, NAD - malic enzyme type
    
  •  M00170 C4-dicarboxylic acid cycle, phosphoenolpyruvate carboxykinase type
    
  
  

https://www.genome.jp/kegg-bin/show_pathway?map00710

NATURAL CO2-FIXATION PATHWAYS

Six natural CO2-fixation pathways have been reported to date, including the 

Calvin-Benson-Bassham cycle (hereafter, the Calvin cycle), 
the 3-hydroxypropionate cycle, 
the Wood-Ljungdahl pathway, 
the reductive tricarboxylic acid (TCA) cycle, 
the dicarboxylate/4-hydroxybutyrate cycle, and 
the 3-hydroxypropionate-4-hydroxybutyrate cycle. 

The Calvin cycle, the 3-hydroxypropionate cycle, and 3-hydroxypropionate- 4-hydroxybutyrate cycle are aerobic, while the other pathways are anaerobic pathways because of the presence of certain oxygen-sensitive enzymes. Aerobic CO2-fixation pathways The Calvin cycle (Figure A below), as the most important CO2-fixation pathway in nature from which all crop biomasses obtain their carbon, has attracted great attention from researchers. It exists widely in plants, algae, cyanobacteria, and other organisms and is driven by light. One Calvin cycle converts three molecules of CO2 to one molecule of glyceraldehyde 3-phosphate, with the consumption of nine ATP molecules and six nicotinamide adenine dinucleotide phosphate (NAD(P)H) molecules. It is the highest energy-consuming pathway among all six natural CO2-fixation pathways. The CO2-fixing enzyme, RuBisCO, is the rate-limiting enzyme in this cycle, with an average activity of 3.5 μmol min–1 mg–1. Moreover, O2 in the air is a substrate of RuBisCO and competes with CO2 for activity sites on the enzyme. Reaction with O2 generates phosphoric glyoxylate, which releases CO2 through subsequent photorespiration pathways. The 3-hydroxypropionate cycle (Figure B) exists in photosynthetic green nonsulfur bacteria and is driven by light. This cycle is the most complex, containing 16 enzymatic reaction steps that are catalyzed by 13 enzymes. In contrast to the Calvin cycle, which converts CO2 to glyceraldehyde 3-phosphate, this cycle converts three molecules of HCO3– into one molecule of pyruvate, with the addition of five ATP and NAD(P)H molecules. There are two CO2-fixing enzymes in this cycle: acetyl-CoA carboxylase and propionyl-CoA carboxylase. Another archaeal aerobic CO2-fixation pathway discovered in 2007 is the 3-hydroxypropionate-4-hydroxybutyrate cycle, which is driven by sulfur and hydrogen (Figure F). This cycle synthesizes one molecule of acetyl coenzyme A from two molecules of HCO3–, four molecules of ATP, and four equal molecules of NAD(P)H. The two CO2-fixing enzymes used are the same as those of the 3-hydroxypropionate cycle.

Anaerobic CO2-fixation pathways
The Wood-Ljungdahl pathway (Figure C), which exists mainly in acetate-producing anaerobes, was identified in the 1970s by Harland G. Wood and Lars G. Ljungdahl and uses hydrogen as its energy source. It is the only non-cycle CO2-fixation pathway, contains the fewest reaction steps, and consumes the least amount of energy. This pathway converts two molecules of CO2 (or one molecule of CO2 and one molecule of carbon monoxide) into one molecule of acetyl coenzyme A, using one ATP and four NAD(P)H molecules. It is therefore called the anaerobic acetyl coenzyme A pathway. The reductive TCA cycle (Figure D) exists in photosynthetic green sulfur bacteria and anaerobic bacteria. This cycle generates one molecule of acetyl coenzyme A via two molecules of CO2, with the consumption of two ATP and four NAD(P)H molecules. The two CO2-fixing enzymes in this cycle are α-ketoglutarate synthase and isocitrate dehydrogenase. The enzyme α-ketoglutarate synthase is strictly anaerobic, with unknown activity. Isocitrate dehydrogenase has the highest activity amongst all CO2-fixing enzymes listed in Table 1. The archaeal anaerobic CO2-fixation pathway—the dicarboxylate/ 4-hydroxybutyrate cycle (Figure E)—was discovered in 2008. This cycle uses sulfur and hydrogen as energy sources. One molecule each of CO2 and HCO3 – are used to synthesize one molecule of acetyl coenzyme A, consuming three ATP and four NAD(P)H molecules. The CO2-fixing enzymes in this cycle are pyruvate synthase and phosphoenolpyruvate carboxylase. Pyruvate synthase is another strictly anaerobic enzyme with unknown activity. It is reported that the KM of phosphoenolpyruvate carboxylase to HCO3 – is the smallest amongst all carboxylases listed in Table 1, demonstrating its high affinity for HCO3 –. Notably, the doubling time of autotrophic archaea Ignicoccus hospitalis, which utilizes this CO2-fixation pathway, is only 1h under optimal growth conditions. This may be partly contributed by the strong affinity of phosphoenolpyruvate carboxylase.







1. https://sci-hub.tw/https://link.springer.com/article/10.1007/s11427-016-0304-2

The existence of the biosphere today depends on its capacity to fix inorganic Co2 into living matter.  One can assume that the global biological carbon cycle has always been based on Co2.

Comparing gene-profiles across the metabolic cores of deep-branching organisms and requiring that they are capable of synthesizing all their biomass components leads to the surprising conclusion that the most common form for deep-branching autotrophic carbon-fixation combines two disconnected sub-networks, each supplying carbon to distinct biomass components. 1

My comment: This is not good news for proponents of common ancestry.

This tree requires few instances of lateral gene transfer or convergence and instead suggests a simple evolutionary dynamic in which all divergences have primary environmental causes. The root of this tree combines the reductive citric acid cycle and the Wood-Ljungdahl pathway into a single connected network. This linked network lacks the selective optimization of modern fixation pathways but its redundancy leads to a more robust topology, making it more plausible than any modern pathway as a primitive universal ancestral form.

Most discussions of autotrophy in the origin of life are complicated because they combine chemical requirements for carbon and energy uptake with considerations of whether organisms or syntrophic ecosystems were required to complete the required pathways. ( syntrophy is the phenomenon of one species living off of the products of another species ) The modern biosphere may be described, most fundamentally, as implementing a biological carbon cycle based on An external file that holds a picture, illustration, etc. Co2, in which carbon fixation is the metabolic anchor embedding life within geochemistry. If the earliest ecosystems were also autotrophic, then a carbon cycle based on Co2 must have existed continuously to have supported biosynthesis.

The finely tuned  and regulated carbon cycle, essential for life
http://reasonandscience.heavenforum.org/t2464-the-finely-tuned-carbon-cycle-essential-for-life
And what carbon does is cycle, a process essential to life on Earth. It’s a carefully regulated process so that the planet can maintain critical balances. Call it the Goldilocks Principle: not too much carbon, not too little, but just the right amount. For instance, without CO2 and other greenhouse gases Earth would be a frozen ball of rock. With too many greenhouse gases, however, Earth would be like hothouse Venus. Just right means balancing between the two extremes, which helps to keep the planet’s temperature relatively stable. It’s like the thermostat in your house. If it gets too warm, the cycle works to cool things off and vice versa. Of course, the planet’s thermostat gets overwhelmed at times, resulting periods of rapid warming or cooling (think Ice Ages).

Scientists have shown how geologic process regulates the amount of carbon dioxide in the atmosphere. Researchers have documented evidence suggesting that part of the reason that Earth has become neither sweltering like Venus nor frigid like Mars lies with a built-in atmospheric carbon dioxide regulator — the geologic cycles that churn up the planet’s rocky surface. Plate tectonics makes possible the carbon cycle, which is essential to our planet’s habitability. 10 This cycle is actually composed of a number of organic and inorganic subcycles, all occurring on different timescales. These cycles regulate the exchange of carbon-containing molecules among the atmosphere, ocean, and land. Since the Earth is a closed system with a finite supply of essential elements such as hydrogen (H), oxygen (O), carbon (C), nitrogen (N), sulfur (S) and phosphorus (P), recycling of these elements is fundamental to avoid exhaustion. 

Fortunately, the miraculous carbon cycles keeps working, scrubbing excess CO2 out of the atmosphere or adding more if necessary. Who does all this regulatory work?  green, growing plants and. Photosynthesis is the process by which carbon is transferred from sky to soil. It’s what makes the Goldilocks principle tick.The process by which atmospheric CO2 gets converted into soil carbon requires is sunlight, green plants, water, nutrients, and soil microbes.

My comment: The current scientific claim is that photosynthesis evolved about 2 billion years after the formation of the earth. If that were true, the carbon cycle would never have taken off, and consequently, life, as we know it, would never have emerged on earth. Life is an all or nothing business. Either the ecological balance based on the energy cycles which are interlinked and interdependent emerged together, all at once, or our planet would be lifeless like all others in the universe. This gives strong support to the Genesis account, where God created planet earth and all life-forms during the creation week. 

It has been observed that all anabolic pathways originate from five universal precursors:

acetyl-CoA,
pyruvate,
oxaloacetate,
succinyl-CoA and
alpha-ketoglutarate,

and that all of these are intermediates in the citric acid (TCA) cycle.





1. https://www.ncbi.nlm.nih.gov/pmc/articles/PMC3334880/

The Calvin-Benson-Bassham cycle (hereafter, the Calvin cycle)



The following is a brief summary of each enzyme and its role in the regeneration of ribulose 1,5-bisphosphate in the order it appears in this specific phase.

1. RuBisCO catalyzes the carboxylation of ribulose-1,5-bisphosphate
2. phosphoglycerate kinase catalyzes the phosphorylation of 3-PGA by ATP
3. glyceraldehyde 3-phosphate dehydrogenase catalyzes the reduction of 1,3BPGA by NADPH
4. Triose phosphate isomerase: converts all G3P molecules into DHAP
5. Aldolase and fructose-1,6-bisphosphatase: converts G3P and DHAP into fructose 6-phosphate
6. Transketolase: removes two carbon molecules in fructose 6-phosphate to produce erythrose 4-phosphate (E4P); the two removed carbons are added to G3P to produce xylulose-5-phosphate (Xu5P)
7. Aldolase: converts E4P and a DHAP to sedoheptulose-1,7-bisphosphate
8. Sedoheptulase-1,7-bisphosphatase: cleaves the sedohetpulose-1,7-bisphosphate into sedoheptulase-7-phosphate (S7P)
9. Transketolase: removes two carbons from S7P and two carbons are transferred to one of the G3P molecules producing ribose-5-phosphate (R5P)and another Xu5P
10. Phosphopentose isomerase: converts the R5P into ribulose-5-phosphate (Ru5P)
11. Phosphopentose epimerase: converts the Xu5P into Ru5P
12. Phosphoribulokinase: phosphorylates Ru5P into ribulose-1,5-bisphosphate

in the first stage:
1.Rubisco
2.phosphoglycerate kinase
3.glyceraldehyde 3-phosphate dehydrogenase
in the second stage:
1.Triosephosphate isomerase Fructose 1,6-bisphosphatase
2.Aldolase
3.Transketolase
4.Sedoheptulose-bisphosphatase
5.Sedoheptulose-1,7-bisphosphatase
6.Ribose-5-phosphate isomerase
7.phosphopentose epimerase
in the last stage:
1.phosphoribulokinase

Why would natural chemical reactions produce three enzymes that are uniquely used in the Calvin cycle ( they are not used in any other metabolic reaction ), that is Rubisco, sedoheptulose bisphosphatase, and Phosphoribulokinase, if they have function only in the Calvin Cycle?

Plastid Calvin cycle enzymes in Plantae
1.  Ribulose-1,5-bisphosphate carboxylase large subunit 
     Ribulose-1,5-bisphosphate carboxylase small subunit
2.  Phosphoglycerate kinase
3.  Glyceraldehyde-3-phosphate dehydrogenase subunit A 
     Glyceraldehyde-3-phosphate dehydrogenase subunit B
4.  Triosephosphate isomerase
5.  Fructose-1,6-bisphosphate aldolase class I
     Fructose-1,6-bisphosphate aldolase class II   
6.  Fructose-1,6-bisphosphatase
7.  Sedoheptulose-1,7-bisphosphatase
8.  Transketolase
9.  Ribulose-phosphate 3-epimerase
10. Ribose 5-phosphate isomerase
11. Phosphoribulokinase

Calvin-Benson-Bassham Cycle
The complete CBB cycle (or reductive pentose phosphate cycle) was described in 1954 by the research group of Melvin Calvin (Bassham et al. 1954), and it was thought for quite some time that the CBB cycle might be the only carbon fixation pathway on Earth. The characteristic enzyme involved in the cycle is ribulose 1,5-bisphosphate carboxylase/oxygenase (RubisCO), which catalyzes the primary carboxylation of ribulose 1,5-bisphosphate, yielding two molecules of 3- phosphoglycerate. First described in 1957, RubisCO was and still is intensively studied. Presently, four different types of RubisCO proteins are known (forms I–IV). However, only forms I, II, and III catalyze the carboxylation reaction, whereas form IV—the RubisCO-like protein—is involved in other reactions (Tabita et al. 2007). Nevertheless, phylogenetic analyses support a common origin of all types of RubisCO that predates the split between bacteria and archaea. Apart from RubisCO, the enzyme phosphoribulokinase is essential for a functional CBB cycle. The CBB cycle probably evolved in cyanobacteria, and it is the only carbon fixation pathway operating in eukaryotes (algae and plants) as a result of the endosymbiotic acquisition of a cyanobacterium that evolved into the chloroplasts. Overall, the phylogenetic diversity of bacterial groups using the CBB cycle is rather limited (Figure 1). Besides cyanobacteria, the CBB cycle occurs in photo- and (aerobic) chemoautotrophic Alpha-, Beta-, and Gammaproteobacteria. In addition, some Gram-positives (Sulfobacillus spp., Firmicutes) and members of the Oscillochloridaceae (Chloroflexi) use this cycle. 2

Some taxa known to possess this pathway include  : Arabidopsis thaliana col, Arabidopsis thaliana Ws, Chlamydomonas reinhardtii, Nicotiana tabacum, Synechococcus elongatus PCC 7942, Synechocystis sp. PCC 6803 3

https://bio.libretexts.org/Bookshelves/Microbiology/Book%3A_Microbiology_(Boundless)/5%3A_Microbial_Metabolism/5.12%3A_Biosynthesis/5.12E%3A_Regulation_of_the_Calvin_Cycle
2. https://sci-hub.tw/https://www.annualreviews.org/doi/abs/10.1146/annurev-marine-120709-142712?journalCode=marine
3. https://biocyc.org/META/NEW-IMAGE?object=CALVIN-PWY&&redirect=T

Reductive Tricarboxylic Acid Cycle or Reverse Krebs cycle (Arnon-Buchanan cycle)

Reductive citrate cycle (Arnon-Buchanan cycle)
https://www.genome.jp/kegg-bin/show_module?M00173


Structure of the rTCA cycle.
Panel A: sequence of the substrates and reactions. Reactions are labeled according to the reaction types described on panel B. The autocatalytic structure of the cycle derives from the branching point associated with citrate cleavage.



1, malate dehydrogenase (EC 1.1.1.37); 
2, fumarate hydratase (fumarase) (EC 4.2.1.2); 
3, fumarate reductase; 
4, succinyl-CoA synthetase (EC 6.2.1.5); 
5, 2-oxoglutarate:ferredoxin oxidoreductase (EC 1.2.7.3); 
6, isocitrate dehydrogenase (EC 1.1.1.42); 
7, aconitate hydratase (aconitase) (EC 4.2.1.3); 
8, ATP citrate lyase (ACL) (EC 2.3.3.8 );  
9, pyruvate:ferredoxin oxidoreductase (EC 1.2.7.1).

Most of the enzymes of the two pathways are shared, with the exception of three key enzymes that allow the cycle to run in reverse:

8. ATP citrate lyase,
5. 2-oxoglutarate: ferredoxin oxidoreductase,
3. fumarate reductase.

Oxoglutarate: ferredoxin oxidoreductase catalyzes the carboxylation of succinyl-CoA to 2-oxoglutarate, ATP citrate lyase the ATP-dependent cleavage of citrate to acetyl-CoA and oxaloacetate, and fumarate reductase the reduction of fumarate forming succinate. The presence of these enzyme activities in autotrophically grown bacteria and archaea is indicative of a functioning reductive TCA cycle (5, 28, 46, 48, 49).

Oxoglutarate:ferredoxin oxidoreductase (OGOR) is the key enzyme in this cycle that fixes carbon dioxide. 6

The reductive TCA cycle is essentially the oxidative TCA cycle running in reverse, leading to the fixation of two molecules of CO2 and the production of one molecule of acetyl-CoA

The reductive tricarboxylic acid (rTCA) cycle is an important pathway mediating carbon fixation in many autotrophic Bacteria and Archaea. Members of the Aquificaceae family, which is phylogenetically located in the oldest branch in the domain Bacteria, are found in harsh environments such as hot springs, sulfur pools, and hydrothermal vents where they grow autotrophically using the rTCA cycle. Hydrogenobacter thermophilus strain TK-6 is a thermophilic, aerobic, obligate chemolithotrophic, hydrogen-oxidizing bacterium within the family Aquificaceae. Analyses of the enzymes of the rTCA cycle in this organism has revealed various significant differences compared to those in other organisms, e.g. novel citrate cleavage reactions catalyzed by citryl-CoA synthetase and citryl-CoA lyase, novel carboxylation reaction of 2-oxoglutarate catalyzed by CFI (carboxylating factor for ICDH), two novel five-subunits type 2-oxoacid oxidoreductase, and an NADH-dependent fumarate reductase.

2-Oxoglutarate:ferredoxin oxidoreductase (OGOR) is a key enzyme in the rTCA cycle, and a member of the 2-oxoacid oxidoreductase (OR) family of enzymes. These enzymes catalyze the oxidative decarboxylation of 2-oxoacids to their acyl- or aryl-CoA derivatives. In the oxidative TCA cycle, OGOR catalyzes the oxidative decarboxylation of 2-oxoglutarate to succinyl-CoA. Conversely, in the rTCA cycle, the enzyme acts as a 2-oxoglutarate synthase and assimilates carbon dioxide. Reducing energy is required for this carboxylation reaction, and ferredoxin is believed to be the electron donor. Strain TK-6 expresses two different OGORs, designated For and Kor

The reductive tricarboxylic acid (TCA) cycle is a carbon dioxide fixation pathway found in autotrophic eubacteria and archaea (there is a report of the pathway also operating in a strain of the green algae Chlamydomonas reinhardtii). It is considered to be a primordial pathway for production of starting organic molecules for biosynthesis of sugars, lipids, amino acids, pyrimidines and pyrroles 5

The tricarboxylic acid (TCA) cycle is an energy-producing pathway for aerobic organisms. However, it is widely accepted that the phylogenetic origin of the TCA cycle is the reductive TCA cycle, which is a non-Calvin-type carbon-dioxide-fixing pathway. Most of the enzymes responsible for the oxidative and reductive TCA cycles are common to the two pathways, the difference being the direction in which the reactions operate. Because the reductive TCA cycle operates in an energetically unfavorable direction, some specific mechanisms are required for the reductive TCA cycle- utilizing organisms. 

Recently, the molecular mechanism for the “citrate cleavage reaction” and the “reductive carboxylating reaction from 2-oxoglutarate to isocitrate” in Hydrogenobacter thermophilus have been demonstrated. Both of these reactions comprise two distinct consecutive reactions, each catalyzed by two novel enzymes. Sequence analyses of the newly discovered enzymes revealed phylogenetic and functional relationships between other TCA cycle-related enzymes. The occurrence of novel enzymes involved in the citrate-cleaving reaction seems to be limited to the family Aquificaceae. In contrast, the key enzyme in the reductive carboxylation of 2-oxoglutarate appears to be more widely distributed in extant organisms. New enzyme systems involved in the reductive TCA cycle of Hydrogenobacter thermophilus TK-6 (which belongs to the order Aquificales) have been demonstrated. Interestingly, the new enzyme systems found in H. thermophilus seem to be present in Aquifex aeolicus (which also belongs to the order Aquificales), but are quite different from those reported from C. limicola. This observation indicates that the reductive TCA cycle is not a completely uniform system.

My comment: It also falsifies the claim of common ancestry. Why would evolution produce two different enzymes in the same pathway, with the same function ( convergent evolution ?! ) if that would not confer any survival advantage compared to the regular rTCA cycle? 

The only common feature of the two families of green bacteria, Chlorobiaceae (green sulfur bacteria) and Chloroflexaceae (green gliding bacteria), is their type of light-harvesting chlorophyll and the organization of these pigments into chlorosomes. In most other respects, including metabolism, photosynthetic apparatus, and phylogeny, they are very different and far apart. Each of the two most studied genera possesses a unique pathway for autotrophic fixation of the reductive tricarboxylic acid cycle used by Chlorobium and the newly discovered 3-hydroxypropionate cycle used by Chloroflexus. 1 

Citrate-cleaving pathway 
The citrate-condensing reaction in the oxidative TCA cycle is catalyzed by citrate synthase (CS). The reaction catalyzed by citrate synthase CS is exergonic and almost irreversible. Thus, to drive the cycle in the reductive direction, another enzyme capable of catalyzing the citrate cleavage reaction, ATP citrate lyase (ACL) is required. Although ATP citrate lyase ACL was thought to be the only enzyme that catalyzes the citrate cleavage reaction in the reductive TCA cycle, recent studies have demonstrated that H. thermophilus does not possess ACL, but instead utilizes two enzymes [citryl-CoA synthetase (CCS) and citryl-CoA lyase (CCL)] to mediate the same reaction. CCS catalyzes the ATP-dependent formation of citryl-CoA that corresponds to the first step of the citrate cleavage reaction. CCL catalyzes the cleavage of citrylCoA into acetyl-CoA and oxaloacetate that corresponds to the second step of the citrate cleavage reaction. In the ACL catalyzed reaction, citryl-CoA is a hypothetical intermediate that is not released from the enzyme. By contrast, CCS releases citryl-CoA into solution as an intermediate. citryl-CoA synthetase (CCS) and citryl-CoA lyase (CCL) are both novel enzymes that have previously never been reported from other organisms.

The discovery of the two-enzyme system was rather more striking from the aspect of phylogenic relationships.

citrate synthase (CS). 
ATP citrate lyase 
citryl-CoA synthetase (CCS) 
citryl-CoA lyase (CCL)]

The sequencing analyses revealed that the former enzyme in the two-enzyme system, citryl-CoA synthetase (CCS), is a homologue of succinyl-CoA synthetase (SCS), and the latter enzyme, citryl-CoA lyase (CCL), is a homologue of citrate synthase CS. These observations indicate that CCS and SCS evolved from a common ancestral enzyme, and CCL and CS share an origin. SCS is the enzyme involved in both the reductive and oxidative TCA cycles. In the reductive TCA cycle, SCS activates succinate by using energy derived from ATP hydrolysis. In contrast, in the oxidative TCA cycle, SCS is involved in the substrate level ATP production (often via the GTP production). Hence, the newly discovered enzymes from H. thermophilus may represent an evolutionary trail of the oxidative TCA-cycle enzymes (SCS and CS). Furthermore, sequence comparisons revealed that ACL (accession numbers BAB21376 and BAB21375 for the C. limicola enzyme) is a fused form of CCS and CCL. This observation indicates that ACL evolved from CCS and CCL by gene fusion. It should be noted that the evolutionary history of ACL involves another gene fusion. 

The citrate-condensing reaction in the oxidative TCA cycle is catalyzed by citrate synthase (CS). The reaction catalyzed by citrate synthase CS is exergonic and almost irreversible. Thus, to drive the cycle in the reductive direction, another enzyme capable of catalyzing the citrate cleavage reaction, ATP citrate lyase (ACL) is required. Although ATP citrate lyase ACL was thought to be the only enzyme that catalyzes the citrate cleavage reaction in the reductive TCA cycle, recent studies have demonstrated that H. thermophilus does not possess ACL, but instead utilizes two enzymes [citryl-CoA synthetase (CCS) and citryl-CoA lyase (CCL)] to mediate the same reaction. CCS catalyzes the ATP-dependent formation of citryl-CoA that corresponds to the first step of the citrate cleavage reaction. CCL catalyzes the cleavage of citrylCoA into acetyl-CoA and oxaloacetate that corresponds to the second step of the citrate cleavage reaction. In the ACL catalyzed reaction, citryl-CoA is a hypothetical intermediate that is not released from the enzyme. By contrast, CCS releases citryl-CoA into solution as an intermediate. citryl-CoA synthetase (CCS) and citryl-CoA lyase (CCL) are both novel enzymes that have previously never been reported from other organisms.

The discovery of the two-enzyme system was rather more striking from the aspect of phylogenic relationships.

The sequencing analyses revealed that the former enzyme in the two-enzyme system, citryl-CoA synthetase (CCS), is a homologue of succinyl-CoA synthetase (SCS), and the latter enzyme, citryl-CoA lyase (CCL), is a homologue of citrate synthase CS. These observations indicate that CCS and SCS evolved from a common ancestral enzyme, and CCL and CS share an origin. SCS is the enzyme involved in both the reductive and oxidative TCA cycles. In the reductive TCA cycle, SCS activates succinate by using energy derived from ATP hydrolysis. In contrast, in the oxidative TCA cycle, SCS is involved in the substrate level ATP production (often via the GTP production). Hence, the newly discovered enzymes from H. thermophilus may represent an evolutionary trail of the oxidative TCA-cycle enzymes (SCS and CS). Furthermore, sequence comparisons revealed that ACL (accession numbers BAB21376 and BAB21375 for the C. limicola enzyme) is a fused form of CCS and CCL. This observation indicates that ACL evolved from CCS and CCL by gene fusion. It should be noted that the evolutionary history of ACL involves another gene fusion. Although prokaryotic ACL is composed of 

The rTCA cycle was first proposed in 1966 to act as a CO2 fixation pathway in Chlorobium thiosulfatophilum (now Chlorobium limicola). However, it took until 1980 for this pathway to become generally accepted. Over the last 10 years, the understanding of the biochemistry, evolution, and ecology of the rTCA cycle has increased considerably. Model organisms for elucidating the biochemistry of the pathway included the green sulfur bacteria C. limicola and Chlorobaculum tepidum, as well as Hydrogenobacter thermophilus (Aquificales). The rTCA cycle is essentially a reversal of the oxidative TCA cycle, or Krebs cycle (Figure a). 


Alternative pathways of autotrophic CO2 fixation: 
a. the reductive tricarboxylic acid (rTCA) cycle;
b, the 3-hydroxypropionate (3-HP) bicycle;
c. the reductive acetyl-CoA, or Wood-Ljungdahl (WL) pathway in methanogenic bacteria.;
d. the 3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB)
e. the dicarboxylate/4-hydroxybutyrate (DC/4-HB) cycles

The biochemical reactions involved, as well as the enzymes (red ) catalyzing the reactions, are depicted. Note that the reductive acetyl-CoA pathway is so far the only known CO2 fixation pathway used by bacteria as well as archaea.

Whereas the oxidative TCA cycle is used in heterotrophic organisms to oxidize acetyl-CoA to CO2, thereby generating reducing power for the synthesis of adenosine triphosphate (ATP), the rTCA cycle can be used for the reverse process, the biosynthesis of acetyl-CoA from two molecules of CO2.Most enzymes (malate dehydrogenase, fumarate hydratase, succinyl- CoA synthetase, isocitrate dehydrogenase, aconitate hydratase) can be used in both variants of the cycle because they catalyze fully reversible reactions. Unique enzymes of the reductive TCA cycle are fumarate reductase, 2-oxoglutarate synthase (2-oxoglutarate:ferredoxin oxidoreductase), and the citrate cleaving enzymes. Two carboxylation reactions are involved: the reductive carboxylation of succinyl-CoA to 2-oxoglutarate, catalyzed by 2-oxoglutarate synthase, and the reductive carboxylation of 2-oxoglutarate to isocitrate. The latter reaction can be accomplished either by isocitrate dehydrogenase, as shown for C. limicola , or by the enzymes 2- oxoglutarate carboxylase and oxalosuccinate reductase, with oxalosuccinate as a free intermediate, as described for H. thermophilus .The ATP-dependent cleavage of citrate to acetyl- CoA and oxaloacetate can be considered the key reaction of the rTCAcycle. This complex reaction can be achieved either by ATP citrate lyase or by the combined action of citryl-CoA synthetase and citryl-CoA lyase. In order to get pyruvate from acetyl-CoA, another carboxylation reaction, catalyzed by pyruvate synthase, is required.

Phylogenetic distribution. 
The rTCA cycle is present in quite diverse groups of bacteria; however, due to the oxygen sensitivity of the enzymes 2-oxoglutarate and pyruvate synthase, the cycle appears to be restricted to anaerobic or microaerophilic bacteria . Enzymatic as well as genomic data suggest that all members of the obligate photoautotrophic and anaerobic green sulfur bacteria (Chlorobiales) use the rTCA cycle for carbon fixation. Other bacterial groups in which all autotrophic members are believed to use the rTCA cycle are the Aquificales and the Epsilonproteobacteria. Enzymatic evidence has been obtained for several strains of Aquificales and Epsilonproteobacteria, and the sequenced genomes also provide evidence for the comprehensive use of this pathway in these groups . The operation of the rTCA cycle has also been reported for members of other bacterial groups, including the magnetotactic Alphaproteobacterium Magnetococcus sp.MC-1 , the Deltaproteobacterium Desulfobacter hydrogenophilus, and “Candidatus Endoriftia persephone,” the gammaproteobacterial endosymbiont of the giant tubeworm Riftia pachyptila. In the case of the Riftia symbiont, the rTCA cycle seems to be used in addition to the CBB cycle, making it the first bacterium that most likely expresses two different carbon fixation pathways simultaneously. In addition, genome analyses of acidophilic iron-oxidizing Leptospirillum spp. strongly suggest the operation of the rTCA cycle in autotrophic members of Nitrospirae. This group also contains the nitriteoxidizing genus Nitrospira, and recent genomic and isotopic data suggest the usage of the rTCA cycle in “Candidatus Nitrospira defluvii” as well. Initially, it was thought that the rTCA cycle also operates in certain archaea (e.g., Thermoproteus neutrophilus or Pyrobaculum islandicum; ; however, recent data suggest that they use the DC/4-HB cycle for carbon fixation.

Some taxa known to possess this pathway include  : Aquifex pyrophilus, Candidatus Arcobacter sulfidicus, Chlorobaculum tepidum, Chlorobaculum thiosulfatiphilum, Chlorobium limicola, Desulfobacter hydrogenophilus, Pyrobaculum islandicum, Pyrobaculum neutrophilum, Sulfurimonas denitrificans, Thermoproteus tenax 3

The reductive TCA cycle appears to operate in phylogenetically diverse autotrophic bacteria and archaea, including genera of anoxic phototrophic bacteria (Chlorobium) (14, 18, 28), sulfate-reducing bacteria (Desulfobacter) (48), microaerophilic, hyperthermophilic hydrogen-oxidizing bacteria (Aquifex and Hydrogenobacter) (5, 49), and sulfur-reducing Crenarchaeota (Thermoproteus and Pyrobaculum) (5, 24, 46). 


The reductive TCA cycle is largely the oxidative, catabolic TCA cycle in reverse. Most of the enzymes of the TCA cycle work reversibly and could catalyze both directions. Only three counteracting enzyme pairs are thought to determine the oxidative or reductive direction of the cycle. These three enzymes are 

EC 2.3.3.8, ATP citrate synthase; 
EC 1.2.7.3, 2-oxoglutarate synthase; 
EC 1.3.5.4, fumarate reductase (quinol) 

Both organisms contained activities of the key enzymes of the reductive tricarboxylic acid cycle, 

ATP citrate lyase, 2-oxoglutarate:ferredoxin oxidoreductase, and pyruvate:ferredoxin oxidoreductase. Furthermore, no activities of key enzymes of other CO2 fixation pathways, such as the Calvin cycle, the reductive acetyl coenzyme A pathway, and the 3-hydroxypropionate cycle, could be detected

(the enzymes listed here are those catalyzing the reductive direction). It should be noted that these enzymes may participate in other pathways (for example, EC 1.2.7.3, 2-oxoglutarate synthase also participates in the oxidative TCA cycle found in Helicobacteraceae). Nonetheless, the presence of these enzyme activities in autotrophically grown bacteria and archaea is considered indicative of the presence of the reductive TCA cycle.

1. https://sci-hub.tw/https://link.springer.com/chapter/10.1007/0-306-47954-0_40
2. https://www.nature.com/articles/ismej201028
3. https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=P23-PWY
4. https://sci-hub.tw/https://link.springer.com/article/10.1007/s00253-007-0893-0
5. https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=P23-PWY
6. https://agris.fao.org/agris-search/search.do?recordID=US201301718505

3-Hydroxypropionate Bicycle



The complete 3-hydroxypropionate cycle, as studied in C. aurantiacus.

1. Acetyl-CoA carboxylase,
2. malonyl-CoA reductase,
3. propionyl-CoA synthase,
4. propionyl-CoA carboxylase,
5. methylmalonyl-CoA epimerase,
6. methylmalonyl-CoA mutase,
7. succinyl-CoA:(S)-malate-CoA transferase,
8. succinate dehydrogenase,
9. fumarate hydratase,
10. a, b, c] (S)-malyl-CoA/β-methylmalyl-CoA/(S)-citramalyl-CoA (MMC) lyase,
11.  mesaconyl-C1-CoA hydratase (β-methylmalyl-CoA dehydratase),
12.  mesaconyl-CoA C1-C4 CoA transferase,
13.  mesaconyl-C4-CoA hydratase.

Carbon-labeling patterns during the interconversion of propionyl-CoA plus glyoxylate to pyruvate plus acetyl-CoA via C5 compounds are shown. 14C carbon atoms derived from [1-14C]propionyl-CoA are marked by ▴, and 13C carbon atoms derived from [1,2,3-13C]propionyl-CoA are marked by ■. Note that the cleavage of citramalyl-CoA requires that the CoA moiety be shifted finally from the “right” carboxyl group of β-methylmalyl-CoA to the “left” carboxyl group of citramalyl-CoA. This shifting is accomplished by an intramolecular CoA transfer (reaction 12). Otherwise, citramalyl-CoA cleavage into pyruvate and acetyl-CoA would not be feasible.


The 3-hydroxypropionate bicycle (also 3-HP/malyl-CoA cycle) operates in the green nonsulfur bacterium Chloroflexus aurantiacus and most likely in other members of Chloroflexaceae as well. Initially,Helge Holo questioned
the operation of the CBB cycle in C. aurantiacus and suggested a novel CO2 fixation pathway with 3-hydroxypropionate as intermediate. Yet, it took another 20 years of research in the laboratory of Georg Fuchs to completely elucidate this pathway. As shown in Figure b, two cycles are involved in this CO2 fixation pathway, and, consequently, the name 3-HP bicycle has now been proposed. In the first cycle, two molecules of bicarbonate are fixed and glyoxylate is formed as the first CO2 fixation product. In the second cycle, glyoxylate and propionyl-CoA are disproportionated to pyruvate and acetyl-CoA. In summary, one molecule of pyruvate is formed from three molecules of bicarbonate, involving the carboxylating enzymes acetyl-CoA and propionyl- CoA carboxylase. Only 13 enzymes catalyze the 19 reactions of the pathway due to the involvement of several multifunctional enzymes, including malonyl-CoA reductase, propionyl-CoA synthase, and malyl-CoA/β-methylmalyl-CoA/citramalyl-CoA (MMC) lyase, which can be considered key enzymes for the 3-HP bicycle. Malonyl-CoA reductase catalyzes the two-step reduction of malonyl-CoA to 3-hydroxypropionate, the characteristic intermediate of the pathway. Subsequently, the trifunctional enzyme propionyl-CoA synthase transforms 3-hydroxypropionate to propionyl-CoA. The third key enzyme, MMC lyase, catalyzes three different reactions: 

(a) the cleavage of malyl-CoA to acetyl-CoA and glyoxylate, 
(b) the condensation of glyoxylate with propionyl-CoA, forming methylmalonyl-CoA, and 
(c) the cleavage of citramalyl-CoA to pyruvate and acetyl-CoA 

Other characteristic enzymes of the 3-HP bicycle are two CoA-transferases and two hydratases (Figure b). Until now, the 3-HP bicycle appears to be restricted to Chloroflexaceae. Apart from this, single genes of the pathway
have been detected in various strains of Alpha- and Gammaproteobacteria, yet the complete gene complement is missing.


Divergence time estimates for the Chloroflexi phylum. (A) Cross-calibrated Bayesian molecular clock analysis with a broad sampling across the Chloroflexi phylum (purple branches). The Chloroflexales clade (green branches) marks the members of the phylum that are phototrophic and use the 3HP bicycle. Although this clade was suggested to represent one of the oldest known phototrophic lineages, these analyses instead reveal a much more recent evolution of the Chloroflexales. (B) Phylogenetic distribution of genes that are involved in the 3HP bicycle demonstrates the stepwise acquisition of enzymes that enabled the last remaining enzymes (propionyl-CoA synthase and malyl-CoA lyase; see Fig. 2) to be horizontally acquired and complete a full 3HP bicycle within the Chloroflexales. The distribution of Calvin−Benson cycle enzymes illustrates that members of the Chloroflexales either have a Calvin−Benson cycle or a complete 3HP bicycle, and suggests that autotrophy via the Calvin−Benson cycle preceded the development of 3HP. (C) A metabolic schematic illustrating the complete 3HP bicycle, with enzymes specific to the pathway highlighted by red arrows. 2

Some taxa known to possess this pathway include  : Chloroflexus aggregans, Chloroflexus aurantiacus, Roseiflexus castenholzii, Roseiflexus sp. RS-1 1


1. https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=PWY-5743
2. https://www.pnas.org/content/pnas/114/40/10749.full.pdf

3-hydroxypropionate/4-hydroxybutyrate (3-HP/4-HB)



Enzymes:
1, acetyl-CoA carboxylase;
2, malonyl-CoA reductase (NADPH);
3, malonate semialdehyde reductase (NADPH);
4, 3-hydroxypropionyl-CoA synthetase (AMP-forming);
5, 3-hydroxypropionyl-CoA dehydratase;
6, acryloyl-CoA reductase (NADPH);
7, propionyl-CoA carboxylase;
8, methylmalonyl-CoA epimerase;
9, methylmalonyl-CoA mutase;
10, succinyl-CoA reductase (NADPH);
11, succinate semialdehyde reductase (NADPH);
12, 4-hydroxybutyryl-CoA synthetase (AMP-forming);
13, 4-hydroxybutyryl-CoA dehydratase;
14, crotonyl-CoA hydratase;
15, 3-hydroxybutyryl-CoA dehydrogenase (NAD+);
16, acetoacetyl-CoA β-ketothiolase.

The proposed pathway of glyceraldehyde 3-phosphate synthesis from acetyl-CoA and CO2 is also shown. 3

Enzymes:
17, pyruvate synthase;
18, pyruvate, water dikinase [phosphoenolpyruvate (PEP) synthase];
19, enolase;
20, phosphoglycerate mutase;
21, 3-phosphoglycerate kinase;
22, glyceraldehyde 3-phosphate dehydrogenase.

The activities of pyruvate synthase and PEP synthase at 75°C were 10 to 25 nmol min–1 mg–1 protein (6) and 25 nmol min–1 mg–1 protein, respectively.

3-Hydroxypropionate/4-Hydroxybutyrate Cycle 
The 3-HP/4-HB cycle operates in autotrophic thermoacidophilic members of the crenarchaeal order Sulfolobales . Initially, Kandler & Stetter (1981) suggested an undefined reductive carboxylic acid pathway for Sulfolobus brierleyi (now Acidianus brierleyi ) based on 14CO2-labeling studies. A few years later, the discovery of acetyl-CoA carboxylase activities in Sulfolobus spp. (upregulated in autotrophically grown cells) came by surprise, as archaea lack fatty acids in their membranes and thus do not need this enzyme for fatty acid biosynthesis. Hence, this carboxylase could be involved in carbon fixation, as was already known for the 3-HP bicycle of C. aurantiacus, and indeed, enzymatic studies suggested the operation of a modified 3-HP cycle in A. brierleyi; this was also confirmed for other members of Sulfolobales, including the model organisms Metallosphaera sedula. However, because malyl-CoA lyase activity was absent, the regeneration of acetyl-CoA remained unsolved until Berg et al. (2007) suggested a novel option involving 4-hydroxybutyrate as intermediate and thus reported the outline of the 3-HP/4-HB cycle (Figure d). The first part of the 3-HP/4-HB cycle, the reaction sequence from acetyl-CoA to succinyl- CoA, is identical to the 3-HP bicycle of C. aurantiacus. However, in M. sedula, the transformation of malonyl-CoA to propionyl-CoA involves five different enzymes, whereas in C. aurantiacus, only two multifunctional enzymes are required. Furthermore, the genes coding for the M. sedula enzymes show no sequence similarities to the genes of C. aurantiacus, suggesting a separate evolution of the pathway in Sulfolobales and Chloroflexaceae .

My comment: Or maybe no evolution at all, but distinct, separate creation. 

The second part of the 3-HP/4-HB cycle, the regeneration of acetyl-CoA from succinyl-CoA, clearly differs from the 3-HP bicycle. Succinyl-CoA is transformed to acetoacetyl-CoA, which is then cleaved into two molecules of acetyl-CoA. The most significant enzyme of the 4-HB part of the cycle is 4-hydroxybutyryl-CoA dehydratase, forming crotonyl-CoA from 4-hydroxybutyryl-CoA. Up to this point, the enzyme was only known to act in a few anaerobic bacteria that ferment 4-aminobutyrate. Several enzymes of the 3-HP/4-HB cycle have been studied in M. sedula. Quite interestingly, some enzymes are promiscuous, e.g., acetyl-CoA/propionyl-CoA carboxylase, which catalyzes both carboxylation reactions (H¨ ugler et al. 2003b), or malonyl-CoA/succinyl-CoA reductase, an enzyme reducing malonyl-CoA and succinyl-CoA to the respective semialdehydes (Alber et al. 2006, Kockelkorn & Fuchs 2009). The 3-HP/4-HB cycle seems to be used in all autotrophic members of the Sulfolobales, not only in microaerophilic strains but also in the strictly anaerobic Stygiolobus azoricus. Although all enzyme activities of the complete pathway have been confirmed for only M. sedula and S. azoricus, key enzymes or genes have been detected in several Acidianus spp. and Sulfolobus spp.. In addition, the genome sequences of the mesophilic marine group 1 Crenarchaeota, Cenarchaeum symbiosum and “Ca. Nitrosopumilus maritimus,” suggest the operation of a variant of the 3-HP/4-HP cycle in this ecologically important group . 1

The hydroxypropionate–hydroxybutyrate cycle functions in the autotrophic crenarchaeal order Sulfolobales. This group comprises extreme thermoacidophiles from volcanic areas that grow best at a pH of around 2 and a temperature of 60–90 °C. Most Sulfolobales can grow chemoautotrophically on sulphur, pyrite or H2 under microaerobic conditions. The enzymes of the hydroxypropionate–hydroxybutyrate cycle are oxygen tolerant. Although it is inactivated by oxygen in clostridia, it is sufficiently oxygen insensitive in Sulfolobales to operate under microoxic or even oxic conditions. Therefore, the hydroxypropionate–hydroxybutyrate cycle fits well with the lifestyle of aerobic Crenarchaeota, although it should be noted that is also present in facultative anaerobic and even strictly anaerobic Sulfolobales species. These species might have returned to an anaerobic lifestyle while retaining enzymes that are associated with an aerobic environment. The presence of genes encoding key enzymes of the hydroxypropionate–hydroxybutyrate cycle in the mesophilic marine group I Crenarchaeota suggests that these abundant marine archaea also use this cycle. In the hydroxypropionate–hydroxybutyrate cycle, one molecule of acetyl-CoA is formed from two molecules of bicarbonate. The key carboxylating enzyme is the bifunctional biotin-dependent acetyl-CoA–propionyl-CoA carboxylase. In Bacteria and Eukarya, acetyl- CoA carboxylase catalyses the first step in fatty acid biosynthesis. However, Archaea do not contain fatty acids, so this enzyme obviously has a different metabolic role in these organisms. The hydroxypropionate–hydroxybutyrate cycle can be divided into two parts (FIG. b). The first transforms acetyl-CoA and two bicarbonate molecules through 3-hydroxypropionate to succinyl-CoA, and the second converts succinyl-CoA through 4-hydroxybutyrate to two acetyl-CoA molecules. The product of the acetyl-CoA carboxylase reaction, malonyl-CoA, is reduced to malonic semialdehyde and then to 3-hydroxypropionate, which is further reductively converted to propionyl-CoA. Propionyl-CoA is carboxylated to (S)-methylmalonyl-CoA by the same carboxylase. (S)-methylmalonyl-CoA is isomerized to (R)-methylmalonyl-CoA, followed by carbon rearrangement to succinyl-CoA by coenzyme B12- dependent methylmalonyl-CoA mutase. Succinyl-CoA is then converted to 4-hydroxybutyrate and then to two acetyl-CoA molecules; this second reaction sequence involving 4-hydroxybutyrate is apparently common to the autotrophic Crenarchaeota.



A 3-Hydroxypropionate/4-Hydroxybutyrate Autotrophic Carbon Dioxide Assimilation Pathway in Archaea 4
an autotrophic member of the archaeal order Sulfolobales, Metallosphaera sedula, fixed CO2 with acetyl–coenzyme A (acetyl-CoA)/propionyl-CoA carboxylase as the key carboxylating enzyme. In this system, one acetyl-CoA and two bicarbonate molecules were reductively converted via 3-hydroxypropionate to succinyl-CoA. This intermediate was reduced to 4-hydroxybutyrate and converted into two acetyl-CoA molecules via 4-hydroxybutyryl-CoA dehydratase. The key genes of this pathway were found not only in Metallosphaera but also in Sulfolobus, Archaeoglobus, and Cenarchaeum species. Moreover, the Global Ocean Sampling database contains half as many 4-hydroxybutyryl-CoA dehydratase sequences as compared with those found for another key photosynthetic CO2-fixing enzyme, ribulose-1,5-bisphosphate carboxylase-oxygenase. This indicates the importance of this enzyme in global carbon cycling.


Some taxa known to possess this pathway include  : Metallosphaera sedula, Pyrobaculum neutrophilum V24Sta, Sulfurisphaera tokodaii 2


1. https://www.semanticscholar.org/paper/Beyond-the-Calvin-cycle%3A-autotrophic-carbon-in-the-H%C3%BCgler-Sievert/58882b2fe25636d109064e74f653c20b3689d2db
2. https://biocyc.org/META/new-image?object=PWY-5789
3. https://science.sciencemag.org/content/318/5857/1782/tab-figures-data
4. https://sci-hub.tw/https://science.sciencemag.org/content/318/5857/1782.full

Enzymes Catalyzing Crotonyl-CoA Conversion to Acetoacetyl-CoA During the Autotrophic CO2 Fixation in Metallosphaera sedula
https://www.frontiersin.org/articles/10.3389/fmicb.2020.00354/full

Structural Insight into Substrate Specificity of 3-Hydroxypropionyl-Coenzyme A Dehydratase from Metallosphaera sedula
https://www.nature.com/articles/s41598-018-29070-w?WT.feed_name=subjects_nanocrystallography

Dicarboxylate/4-hydroxybutyrate (DC/4-HB) cycle

The oxygen-sensitive dicarboxylate–hydroxybutyrate cycle is restricted to the anaerobic Thermoproteales and Desulfurococcales 3



Enzymes: 1
1, pyruvate synthase (reduced MV);
2, pyruvate:water dikinase;
3, PEP carboxylase;
4, malate dehydrogenase (NADH);
5, fumarate hydratase;
6, fumarate reductase (reduced MV);
7, succinate thiokinase (ADP forming);
8, succinyl-CoA reductase (reduced MV);
9, succinate semialdehyde reductase (NADPH);
10, 4-hydroxybutyryl-CoA synthetase (AMP forming);
11, 4-hydroxybutyryl-CoA dehydratase;
12, crotonyl-CoA hydratase;
13, 3-hydroxybutyryl-CoA dehydrogenase (NAD+);
14, acetoacetyl-CoA β-ketothiolase. Label from [1,4-13C2]succinate

The outlines of the sixth CO2 fixation pathway, the dicarboxylate/4-hydroxybutyrate (DC/4-HB) cycle, were described only recently by Huber et al. (2008). The pathway was elucidated in the thermophilic crenarchaeon Ignicoccus hospitalis (Desulfurococcales), but it is also present in other Crenarchaeota. In 2003, a survey of carbon-fixation enzyme activities in different Crenarchaeaota led to the suggestion of a novelCO2 fixation pathway in Ignicoccus spp. Later, Jahn et al. (2007) proposed pyruvate synthase and PEP carboxylase as carboxylating enzymes for the novel pathway. Only after the discovery of the 3-HP/4-HB cycle did it become clear that I. hospitalis uses the same reaction sequence for the formation of acetyl-CoA from succinyl-CoA, and the pathway was completely solved. The DC/4-HB cycle (Figure e) partly involves enzymes of the rTCA cycle (the enzymes converting oxaloacetate to succinyl-CoA) as well as enzymes of the 4-HB part of the 3-HP/4-HB cycle (the enzymes converting succinyl-CoA to acetyl-CoA). Three additional enzymes (pyruvate synthase, pyruvate:water dikinase, and PEP carboxylase) are required in order to convert acetyl- CoA to oxaloacetate. Quite interestingly, the DC/4-HB cycle has no enzymes that are unique to this pathway, necessitating the measurement of a combination of enzymes to be able to determine the operation of this cycle. Because many enzymes of the rTCA cycle are also required for the DC/4-HB cycle, early investigations in the crenarchaeon T. neutrophilus (Thermoproteales) suggested the operation of the rTCA cycle in this organism. However, reinvestigations confirmed the usage of the DC/4-HB cycle. In addition, the genes of the cycle are present within the genomes of other Thermoproteales (e.g., Pyrobaculum islandicum, P. calidifontis). Only recently have enzyme activity measurements also confirmed the operation of theDC/4-HB cycle in Pyrolobus fumarii (Desulfurococcales).Thus, presently, it looks as if all autotrophic members of the crenarchaeal orders Desulfurococcales and Thermoproteales use this pathway for carbon fixation.

The dicarboxylate–4-hydroxybutyrate cycle (shortened to the dicarboxylate–hydroxybutyrate cycle) functions in the anaerobic or microaerobic autotrophic members of the crenarchaeal orders Thermoproteales and Desulfurococcales. Many grow as strict anaerobes by reducing elemental sulphur with H2 to H2S, but some grow under microaerobic or denitrifying conditions. The dicarboxylate–hydroxybutyrate cycle can be divided into two parts: in the first part, acetyl- CoA, one CO2 and one bicarbonate are transformed through C4 dicarboxylic acids to succinyl-CoA, and in the second part, succinyl-CoA is converted through 4-hydroxybutyrate into two molecules of acetyl-CoA

(FIG. a). 


Pathways of autotrophic co2 fixation in crenarchaeota. 
dicarboxylate–hydroxybutyrate cycle functions in Desulfurococcales and Thermoproteales (a) and the hydroxypropionate–hydroxybutyrate cycle functions in Sulfolobales (b). Note that succinyl-coenzyme A (succinyl-CoA) reductase in Thermoproteales and Sulfolobales uses NADPH and reduced methyl viologen (possibly as a substitute for reduced ferredoxin) in Desulfurococcales13,15. In Sulfolobales, pyruvate might be derived from succinyl-CoA by C4 decarboxylation. CoASH, coenzyme A; Fdred 2–, reduced ferredoxin; Fdox, oxidized ferredoxin; PEP, phosphoenolpyruvate.

One acetyl-CoA can be used for biosynthesis and the second serves as a CO2 acceptor for the next round of the cycle. The dicarboxylate–hydroxybutyrate cycle starts with the reductive carboxylation of acetyl-CoA to pyruvate, a reaction that is catalysed by pyruvate synthase (also known as pyruvate: ferredoxin oxidoreductase). This oxygen-sensitive enzyme is common in strict anaerobes, bacteria and archaea. Pyruvate is converted to phosphoenolpyruvate (PEP), followed by carboxylation of PEP to oxaloacetate, which is catalysed by an archaeal PEP carboxylase. The subsequent reduction to succinyl-CoA involves an incomplete reductive citric acid cycle. Originally, a complete reductive citric acid cycle was thought to operate. However, succinyl-CoA is not converted to 2-oxoglutarate but is further reduced to succinic semialdehyde and then to 4-hydroxybutyrate. 4-Hydroxybutyrate is then converted into two acetyl-CoA molecules, a process that requires 4-hydroxybutyryl-CoA dehydratase, a key enzyme in the dicarboxylate–hydroxybutyrate cycle. 4-Hydroxybutyryl-CoA dehydratase contains a 4Fe–4S centre and flavin adenine dinucleotide and catalyses the elimination of water from 4-hydroxybutyryl- CoA by a ketyl radical mechanism. Its product, crotonyl-CoA, is converted into two molecules of acetyl-CoA through a normal β-oxidation reaction. The active CO2 species in the dicarboxylate– hydroxybutyrate cycle are CO2 as the co-substrate for pyruvate synthase and bicarbonate (HCO3–) as the co-substrate for PEP carboxylase. Pyruvate formation in this cycle requires five ATP equivalents, and one energy-rich pyrophosphate is formed (the fate of which is unknown); this is compared with the seven ATP equivalents per pyruvate in the Calvin cycle. A comparison with the 3 hydroxypropionate–4-hydroxybutyrate cycle (shortened to the hydroxypropionate– hydroxybutyrate cycle; discussed below) reveals that the dicarboxylate–hydroxybutyrate cycle preferentially uses reduced ferredoxin instead of NADH or NADPH as the reductant. The oxygen sensitivity of some of its enzymes (for example, pyruvate synthase) and electron carriers (for example, ferredoxin) restricts this cycle to anaerobic, or at best microaerobic,
Crenarchaeota.

Acetyl-CoA–propionyl-CoA carboxylase uses bicarbonate as a co-substrate. Pyruvate is probably formed from succinyl-CoA through decarboxylation of malate or oxaloacetate, which requires one and a half turns of the cycle to build succinyl-CoA from four molecules of bicarbonate. The hydroxypropionate–hydroxy butyrate cycle requires nine ATP equivalents to make pyruvate (generating three molecules of pyrophosphate). Pyrophosphate might serve as energy source or might be hydrolysed by pyrophosphatase. Although the 3-hydroxypropionate part of this cycle resembles the first part of the 3-hydroxypropionate bicycle that functions in Chloroflexus aurantiacus (a phototrophic green non-sulphur bacterium), the enzymes used to synthesize propionyl-CoA from malonyl-CoA are not homologous, although the intermediates are the same. Furthermore, in C. aurantiacus acetyl-CoA is regenerated by malyl-CoA cleavage, requiring an additional cycle to assimilate glyoxylate, the second product of this cleavage reaction. Therefore, these pathways that superficially seem to be similar might have evolved independently in Sulfolobales and Chloroflexi.


Postulated distribution of two autotrophic carbon fixation cycles in Crenarchaea. Thermoproteales and Desulfurococcales use the dicarboxylate/4-hydroxybutyrate cycle for autotrophic CO2 fixation, whereas Sulfolobales and, probably, Cenarchaeales possess the 3-hydroxypropionate/4-hydroxybutyrate cycle.2


1. https://www.pnas.org/content/105/22/7851
2. https://jb.asm.org/content/191/13/4286/F5
3. https://www.nature.com/articles/nrmicro2365?draft=marketing

The reductive Acetyl-CoA Pathway, or Wood-Ljungdahl (WL) pathway

Several aspects of the reductive acetyl-CoA pathway are unique, and this pathway might be close to the ancestral autotrophic carbon fixation pathway. 3 The pathway makes extensive use of coenzymes (tetrahydropterin, cobalamin
and others, depending on the systematic position of the organism), metals (Fe, Co, Ni, Mo, or w) and Fe–S centers.  The Wood–Ljungdahl pathway is only found in strictly anaerobic bacteria and archaea. 4

Comment: That rises the question: How did the pathway recruit these metals and coenzymes, since some of them, like tetrahydrobiopterin, are enormously energy consuming, and complex, to be synthesized? 

The reductive Acetyl-CoA Pathway, or Wood-Ljungdahl (WL) pathway. The TCA is the central hub from which all basic building blocks for life are derived, by all three domains of life. So the origin of the TCA is a central OOL problem. The enzymes used in the cycle are:



1, malate dehydrogenase
2, fumarate hydratase (fumarase)
3, fumarate reductase
4, succinyl-CoA synthetase
5, 2-oxoglutarate:ferredoxin oxidoreductase
6, isocitrate dehydrogenase
7, aconitate hydratase (aconitase)
8, ATP citrate lyase
9, ferredoxin oxidoreductase Fdred, reduced ferredoxin.


The reductive acetyl-coenzyme A pathway. 
Two CO2 molecules are reduced in total, one is reduced to CO bound to a nickel atom in the active center of CO dehydrogenase and one to a methyl group bound to the carrier tetrahydropterin. Subsequently, a methyl-transferring corrinoid protein functions in methyl transfer and acetyl-coenzyme A (acetyl-CoA) is synthesized from CO and the methyl group. The enzymes involved in each reaction are: 

1. formylmethanofuran dehydrogenase (reduced ferredoxin (Fdred;  
2. formylmethanofuran: tetrahydromethanopterin formyltransferase 
3. methenyl-tetrahydromethanopterin cyclohydrolase 
4. methylene-tetrahydromethanopterin dehydrogenase (reduced deazaflavin factor 420 (F420); 
5. methylene- tetrahydromethanopterin reductase (reduced F420; 
6. CO dehydrogenase–acetyl-CoA-synthase (probably Fdred; 

Note that in bacteria the pathway differs in that CO2 is reduced to free formate, which becomes activated to N10-formal-tetrahydropterin in an ATP-dependent reaction. The tetrahydropterin also differs. Fdox, oxidized Fd.

The reductive acetyl-CoA pathway, or Wood-Ljungdahl (WL) pathway, was discovered and elucidated in acetogenic bacteria—anaerobic bacteria, which form acetate fromH2 and CO2—mainly in the laboratories of Harland G.Woodand LarsG. Ljungdahl. It is a relatively simple pathway in which two molecules of CO2 are combined directly in a noncyclic way to acetyl-CoA. The pathway can be divided into two branches: the methyl branch, where CO2 is consecutively reduced to a cofactor bound methyl residue, and the carbonyl branch, where another molecule of CO2 is reduced to an enzyme-bound carbonyl residue. The key enzyme of the pathway is CO dehydrogenase/acetyl- CoA synthase, which catalyzes the reduction of CO2 to CO as well as the following step, the synthesis of acetyl-CoA from the methyl and the carbonyl residues. The reduction of CO2 to the methyl group is accomplished by a series of enzymes, most of which are also unique for this pathway. Most acetogens belong to the Gram-positive Clostridiales; however, some Spirochaeta also exhibits an acetogenic lifestyle using the WL-pathway. Apart from acetogenic bacteria, which actually have a versatile metabolism and can also grow heterotrophically, the pathway is used in autotrophic sulfate-reducing bacteria and archaea as well as in methanogenic archaea, and potentially in planctomycetes carrying out the anaerobic oxidation of ammonium (anammox). Thus, the WL-pathway is so far the only carbon fixation pathway present in both bacteria and archaea, in line with the hypothesis that it is the most ancient autotrophic carbon fixation pathway. Yet, distinct variants of the pathway exist in the two domains. Whereas formate is a free intermediate in bacteria, formyl-methanofuran is formed in methanogenic archaea. In addition, the C1 carriers involved—tetrahydrofolate in bacteria, tetrahydropterins in archaea—are different, and thus so are the enzymes involved in the formation of the cofactor-bound methyl group. Only the key enzyme CO dehydrogenase/acetyl- CoA synthase appears to have the same origin in bacteria and archaea.


Schematic views of the archaeal phylogeny including complete genomes available before 2012
(A) and currently (B), based on the literature (see text for details). Fast evolving DPANN lineages are not included as their position is unclear. Red arrows indicate the inferred origin of methanogenesis, with further divergence leading to lineages that retained this metabolism based on experimental characterization or the presence of MCR homologues (in red). Colored circles indicate the type of known and predicted pathways in representatives of the lineages according to the descriptive panel. 2

Some taxa known to possess this pathway include  : Acetitomaculum ruminis, Acetobacterium carbinolicum, Acetobacterium woodii, Blautia producta, Clostridium formicaceticum, Eubacterium limosum, Moorella thermoacetica, Moorella thermoautotrophica, Sporomusa malonica, Sporomusa termitida, Syntrophococcus sucromutans, [Butyribacterium] methylotrophicum 1


1. https://biocyc.org/META/NEW-IMAGE?type=PATHWAY&object=CODH-PWY
2. https://www.semanticscholar.org/paper/Methanogenesis-and-the-Wood%E2%80%93Ljungdahl-Pathway%3A-An-Borrel-Adam/ef21c385ae25c181068abf0e7ffa8d7110ce122d/figure/0
3. https://sci-hub.tw/https://www.nature.com/articles/nrmicro2365
4. https://www.nature.com/articles/nrmicro1847

Carbon Fixation by Marine Ultrasmall Prokaryotes

All corresponding proteins (179,853 proteins for carbon fixation, and 211,781 proteins for ribosomal complexes) were retrieved using the Uniprot mapping tool (http://www.uniprot.org/mapping/) or the KEGG API service (March 2017).


Phylogenetic trees of selected key enzymes in three carbon fixation pathways.
Trees were reconstructed using maximum likelihood on trimmed alignments. The number of informative sites and branch length scale bars (substitutions per site) are shown for each tree. Sequences used are from KEGG, NCBI (CPR and DPANN) and from the TARA Oceans data set. Trees were midpoint rooted. Bootstraps were computed using 1,000 iterations of ultrafast bootstrap approximation. Branches with bootstrap <50% were collapsed, a light blue dot highlights branches with bootstrap values >80%. Environmental sequences are highlighted by a colored bar on the right of each tree. Sequence names: environmental sequences were formatted as (PU, UO, WUO)TARA identifier. KEGG sequences were formatted as phylum_KEGG_identifier. NCBI sequences were formatted as (CPR/DPANN)_phylum_proteinID. For readability, some clades were collapsed and are represented by a dark triangle with the description of the clade’s sequences. Abbreviations: rTCA, reductive tricarboxylic acid cycle; DHC: dicarboxylate–hydroxybutyrate cycle; HBC, 3-hydroxypropionate bi-cycle; PU, Potentially Ultrasmall; UO, Ultrasmall Only; and WUO, Widespread Ultrasmall Only. 1


Heatmap of completeness of six carbon fixation pathways and archaeal and bacterial ribosomal complexes.
The heatmap color scale shows the completeness of pathways or ribosomal complexes, with rows as sampling sites and columns as proteins sets. Black squares highlight sites with pathway completeness >60% and comprising all key enzymes. Rows were clustered using scipy.cluster.hierarchy.linkage (“ward” method). The corresponding dendrogram is shown to the left of the heatmap. Row names indicate sampling sites in the format TARA sampling site id (three digits) _ depth. Depths are: SRF (Surface), DCM (Deep Chlorophyll Maximum), MES (Mesopelagic), and MIX (mixed). Row label colors represent oceanic regions: brown for North Pacific Ocean, green for South Pacific Ocean, purple for Southern Ocean, orange for South Atlantic Ocean, dark blue for Indian Ocean, red for Red Sea, and pink for Mediterranean Sea. The “pool” row represents results for all sampling sites pooled together. Ribosomal complexes from bacteria and archaea contain 55/67 proteins, respectively, and share 31 proteins. Sequencing effort is computed as the proportion of the number of proteins found at a given site and the average number of reads per protein, relatively to the values found at 037_MES sampling site, which showed the maximum values for both indicators.


1. https://europepmc.org/articles/PMC6475129/figure/evz050-F4/

The central problem to get the basic elements to make the building blocks of life on early earth

There is no evidence that the atoms required to make the basic building blocks of life were extant in a usable form on the early earth. A paper published by Nature magazine in 2016 claimed, that the foremost and only known nitrogen-fixing mechanism trough nitrogenase enzymes was extant in the last universal common ancestor. 1 But nitrogenase enzymes are of the HIGHEST complexity, truly marvels of nanomachinery, a molecular sledgehammer. 

The two main constituents of our atmosphere, oxygen (21%) and nitrogen (78%), both play important roles in the makeup of living things. Both are integral parts of the amino acids that join together in long chains to make all proteins, and of the nucleotides which do the same thing to form DNA and RNA. Getting elemental oxygen (O2) to split apart into atoms and take part in the reactions and structures of life is not hard; in fact, oxygen is so reactive that keeping it from getting into where it's not wanted becomes the more challenging job. However, elemental nitrogen poses the opposite problem. Like oxygen, it is diatomic (each molecule contains two N atoms) in its pure form (N2); but, unlike oxygen, each of its atoms is triple-bonded to the other. This is one of the hardest chemical bonds of all to break. So, how can nitrogen be brought out of its tremendous reserves in the atmosphere and into a state where it can be used by living things?

It is claimed that mineral-catalyzed dinitrogen reduction might have provided a significant source of ammonia to the Hadean ocean. But, there is a huge gap to go from such scenario to the ammonia production through nitrogenase enzymes. 

The chief enzyme is nitrogenase. With assistance from an energy source (ATP) and a powerful and specific complementary reducing agent (ferredoxin), nitrogen molecules are bound and cleaved with surgical precision. In this way, a ‘molecular sledgehammer’ is applied to the NN bond, and a single nitrogen molecule yields two molecules of ammonia. The ammonia then ascends the ‘food chain’, and is used as amino groups in protein synthesis for plants and animals. This is a very tiny mechanism but multiplied on a large scale it is of critical importance in allowing plant growth and food production on our planet to continue. 1

One author summed up the situation well by remarking, ‘Nature is really good at it (nitrogen-splitting), so good in fact that we've had difficulty in copying chemically the essence of what bacteria do so well.’ If one merely substitutes the name of God for the word 'nature', the real picture emerges.


The second problem is how to fix carbon dioxide to make glucose. The ultimate origin of  Glucose - sugars is a huge problem for those who believe in life from non-life without requiring a creator. In order to provide credible explanations of how life emerged, a crucial question must be answered: Where did Glucose come from in prebiotic earth? The source of glucose and other sugars used in metabolic processes would have to lie in an energy-collecting process. Without some means to create such sugar, limitations of food supply for metabolic processes would make the origin of life probably impossible. Sugars are by far the most attractive organic energy substrate of primitive anaerobic life, because they are able to provide all the energy and carbon needed for the growth and maintenance of the first organism.  

The hypothesis is that an ensemble of minerals that are capable of catalyzing each of the many steps of the reverse citric acid cycle was present anywhere on the primitive Earth, or that the cycle mysteriously organized itself topographically on a metal sulfide surface.  The lack of a supporting background in chemistry is even more evident in proposals that metabolic cycles can evolve to “life-like” complexity. The most serious challenge to proponents of metabolic cycle theories—the problems presented by the lack of specificity of most nonenzymatic catalysts—has, in general, not been appreciated. If it has, it has been ignored. Theories of the origin of life based on metabolic cycles cannot be justified by the inadequacy of competing theories: they must stand on their own.

But even, if, let's suppose, somehow, carbon fixation would have started on metal sulfide surface, there is an unbridgeable gap from that kind of prebiotic self-organization and carbon production, to even the most simple enzymatic carbon fixation pathway, used in anaerobic bacteria. the reductive tricarboxylic acid cycle rTCA is claimed to be the best candidate. That cycle requires nine sophisticated enzymes, some with complex molybdenum co-factors, which also have to be synthesized in highly ordered sequential multistep production pathways by various enzymes. How did that come to be without evolution? 3

An illustration: On the one side, you have an intelligent agency based system of the irreducible complexity of tight integrated, information-rich functional systems that have ready on hand energy directed for such, that routinely generate the sort of phenomenon being observed.  And on the other side imagine a golfer, who has played a golf ball through a 9 hole course. Can you imagine that the ball could also play itself around the course in his absence? Of course, we could not discard, that natural forces, like wind, tornadoes, or rains or storms could produce the same result, given enough time.  the chances against it, however, are so immense, that the suggestion implies that the non-living world had an innate desire to get through the 9 hole course. 4


Outlining just two elements demonstrates the size of the problem. But overall metabolism is based on seven non-metal elements, H, C, N, 0, P, S, and Se. With these elements, all the major polymers of all cells are made. Hence the major metabolic pathways involve them. In total, over 20 different elements, including heavy elements, like molybdenum, are absolutely essential for life to start.

The emergence of concentrated suites of just the right mix thus remains a central puzzle in origin-of-life research. Life requires the assembly of just the right combination of small molecules into much larger collections - "macromolecules" with specific functions. Making macromolecules is complicated by the fact that for every potentially useful small molecule in the prebiotic soup, dozens of other molecular species had no obvious role in biology. Life is remarkably selective in its building blocks, whereas the vast majority of carbon-based molecules synthesized in prebiotic processes have no obvious biological use. 5

1. https://reasonandscience.catsboard.com/t1585-nitrogenase
2. http://journals.plos.org/plosbiology/article?id=10.1371/journal.pbio.0060018
3. https://reasonandscience.catsboard.com/t1468-irreducible-complexity-the-existence-of-irreducible-interdependent-structures-in-biology-is-an-undeniable-fact#2133
4. https://reasonandscience.catsboard.com/t2419-where-did-glucose-come-from-in-a-prebiotic-world#6109
5. https://reasonandscience.catsboard.com/t2590-origins-what-cause-explains-best-our-existence-and-why#5811

https://reasonandscience.catsboard.com/t2437-essential-elements-and-building-blocks-for-the-origin-of-life#7789

Carbon fixation pathways in prokaryotes - Reference pathway (KO)

Carbon fixation is an important pathway for autotrophs living in various environments. Plants and cyanobacteria fix CO2 as organic compounds using solar energy mainly by the reductive pentose phosphate cycle (also called Calvin cycle, Calvin-Benson cycle, or Calvin-Benson-Bassham cycle) [MD:M00165]. There are, at least, five additional carbon fixation pathways known to exist in autotrophic bacteria and archaea, which differ in reducing compounds, energy source, and oxygen sensitivity of enzymes. (i) The reductive citric acid cycle (Arnon-Buchanan cycle) [MD:M00173] is found in microaerophiles and anaerobes, such as green sulfur bacteria. In one complete turn of this cycle, four molecules of CO2 are fixed by the enzymes that are sensitive to oxygen, resulting in the production of one molecule of oxaloacetate, which is itself an intermediate of the cycle. (ii) The reductive acetyl-CoA pathway (Wood-Ljungdahl pathway) [MD:M00377] is found in strictly anaerobic bacteria and archaea (Proteobacteria, Planctomycetes, Spirochaetes, and Euryarchaeota), some of which are methane-forming. A bifunctional enzyme, carbon monoxide dehydrogenase/acetyl-CoA synthase, catalyzes the reactions from CO2 to CO and from CO2 to a methyl group, and then to generate acetyl-CoA. (iii) The 3-hydroxypropionate bicycle [MD:M00376] is found in some green non-sulphur bacteria of the family Chloroflexaceae. In one complete turn of this bicycle, three molecules of bicarbonate are converted into one molecule of pyruvate. In addition, this bicycle provides the secondary benefit of useful intermediates for biosynthesis: acetyl-CoA, glyoxylate, and succinyl-CoA. (iv) The hydroxypropionate-hydroxybutyrate cycle [MD:M00375] is found in aerobic Crenarchaeota, Acidianus, Metallosphaera, and Sulfolobales. Some of the intermediates and the carboxylation reactions are the same as in the 3-hydroxypropionate bicycle. One complete turn of this cycle generates two molecules of acetyl-CoA, one of which is reutilized in the the cycle and the other is removed for cell material biosynthesis. (v) The dicarboxylate-hydroxybutyrate cycle [MD:M00374] was named after its intermediates: succinate (a kind of dicarboxylate) and hydroxybutyrate. This cycle has been found only in Ignicoccus hospitals, a strictly anaerobic hyperthermophilic archaea. Recent genome study suggests that this cycle may exist in Desulforococcales (to which Ignicoccus belongs) and Thermoproteales (a taxon close to the origin of archaea). The first half of the cycle, from acetyl-CoA to succinate-CoA, corresponds to the reductive citric acid cycle and the latter half of the cycle, from succinate-CoA to two molecules of acetyl-CoA, corresponds to the hydroxypropionate-hydroxybutyrate cycle.





Tomonari Sumi & Kouji Harada: Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea 22 October 2021

L. M. Ward (2019): The fixation of inorganic carbon species like CO2 to more reduced organic forms is one of the most fundamental processes of life as we know it. Although several carbon fixation pathways are known to exist, on Earth today nearly all global carbon fixation is driven by the Calvin cycle in oxygenic photosynthetic plants, algae, and Cyanobacteria. At other times in Earth history, other organisms utilizing different carbon fixation pathways may have played relatively larger roles, with this balance shifting over geological time as the environmental context of life has changed and evolutionary innovations accumulated. Among the most dramatic changes that our planet and the biosphere have undergone are those surrounding the rise of O2 in our atmosphere—first during the Great Oxygenation Event at ~2.3 Ga, and perhaps again during Neoproterozoic or Paleozoic time. These oxygenation events likely represent major step changes in the tempo and mode of biological productivity as a result of the increased productivity of oxygenic photosynthesis and the introduction of O2 into geochemical and biological systems, and likely involved shifts in the relative contribution of different carbon fixation pathways. Here, we review what is known from both the rock record and comparative biology about the evolution of carbon fixation pathways, their contributions to primary productivity through time, and their relationship to the evolving oxygenation state of the fluid Earth following the evolution and expansion of oxygenic photosynthesis.

To date, three novel pathways have been proposed as alternatives to the six known natural carbon-fixation routes. Kono et al. fully described the RHP pathway in the methanogenic Archaea, Methanospirillum hungatei. The carbon metabolism has been shown to involve the enzymes RuBisCO and phosphoribulokinase (PRK), which are the same enzymes found in the CBB cycle. RuBisCO of M. hungatei seems to form a new clade with RuBisCO of another methanogenic Archaea that also has PRK; this clade is different from RuBisCO form III. The coexistence of the RuBisCO and PRK in this Archaea led the authors to propose that M. hungatei fixed carbon. However, the enzymes transketolase, ribulose-5-phosphate and sedoheptulose-1,7-bisphosphatase, which participate in the CBB cycle, are absent from the genome. Archaea are known to lack genes for a transketolase, which is essential in the CBB cycle.1

R. Braakman (2012): :Here we reconstruct the complete early evolutionary history of biological carbon-fixation, relating all modern pathways to a single ancestral form.2

Yuko Ito (2021):: Though it has been revealed that various partial TCA pathways exist in the deep-branching bacteria and archaea that evolved from the LUCA, the reason for the development of this diversity has not been resolved.3

Tomonari Sumi (2021): Currently, there are seven known different autotrophic pathways responsible for carbon fixation, including the newly demonstrated reductive glycine (rGly) pathway 4

J. Asplund-Samuelsson (2021): Organisms that produce biomass by fixation of CO2 are classified as autotrophic. As atmospheric CO2 levels rise, autotrophs offer attractive ecological and biotechnological routes to climate change mitigation and sustainable biomanufacturing. Autotrophs such as Cyanobacteria, algae, and plants already serve as primary producers in most ecosystems. Emphasizing the central role of autotrophic metabolism in evolution and life, the last universal common ancestor possessed the Wood-Ljungdahl pathway for CO2 fixation, possibly in combination with the reductive tri-carboxylic acid (TCA) cycle and the reductive glycine pathway. These three ancient CO2 fixation pathways were later accompanied by the dicarboxylate/4-hydroxybutyrate cycle, the 3-hydroxypropionate/4-hydroxybutyrate cycle, the 3-hydroxypropionate bicycle, and the Calvin-Benson-Bassham (CBB) cycle. 5


1. Lewis M Ward: The evolution and productivity of carbon fixation pathways in response to changes in oxygen concentration over geological time 2019 Aug 20
2. Rogier Braakman: The Emergence and Early Evolution of Biological Carbon-Fixation 2012 Apr; 8
3. Yuko Ito: Discovery of a new kinetic factor that governs the carbon metabolism evolution of ancient microbes 2-DEC-2021
4. Tomonari Sumi: Kinetics of the ancestral carbon metabolism pathways in deep-branching bacteria and archaea  22 October 2021
5. Johannes Asplund-Samuelsson: Wide range of metabolic adaptations to the acquisition of the Calvin cycle revealed by comparison of microbial genomes February 8, 2021