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Biosynthesis of Carbon compounds

©2001 Timothy Paustian, University of Wisconsin-Madison

Organotrophs obtain carbon for biosynthesis from preformed organic compounds. Often the source of electrons (which is an organic molecule) will also serve as a source of cell carbon. Pseudomonas cepacia is capable of growth on benzene (an organic molecule) alone, generating energy, via respiration and synthesizing all needed carbon molecules from it.

The most abundant form of carbon on earth is in the form of CO2 and many other microbes are capable, given enough ATP and NADH of incorporating CO2 into cell carbon. This process is termed CO2 fixation. Organisms capable of fixing CO2 are classified as autotrophs and include phototrophs and lithotrophs.

There are four pathways that are used to for the fixation of CO2, the ribulose bisphosphate pathway (RuBP), the reductive tricarboxylic acid pathway (rTCA) the reductive acetyl-CoA pathway (rACA) and the 3-Hydroxypropionate cycle. In this section we will take a brief look at each pathway.

Ribulose bisphosphate pathway (The Calvin Cycle)

RuBP is one of the most important biosynthetic cycles on earth. It is used by most photosynthetic organisms (plants, cyanobacteria, purple and green bacteria) to incorporate CO2 into cell carbon. All higher organisms eventually obtain their carbon from the products of this cycle. RuBP is not just the providence of photosynthetic organisms however, many other autotrophs use RuBP and it is by far the most commonly found method for CO2 fixation in nature. Because of its prevalence, it was discovered first and a great deal of research has revealed much about the cycle. It is the best understood of the three pathways.

Calvincycle picture

Figure 1 - The RuBP pathway.

There are three phases in RuBP and three unique enzymes found only operating in the cycle. The three phases of the cycle are...

  1. Carboxylation - CO2 is combined with ribulose bisphosphate a 5 carbon compound that immediately splits to form two 3-phosphoglycerate molecules (3 carbon compounds). The enzyme that catalyzes the reaction is ribulose bisphosphate carboxylase and it is the most abundant and arguable the most important enzyme on earth. The evolution of this catalytic ability contributed to the emergence of photosynthetic organisms and their presence allowed for the explosive abundance of life.

    The rest of RuBP has two goals. Create fructose, that is siphoned off for cellular metabolism and regenerate the ribulose bisphosphate molecule, for another turn of the cycle.

  2. Reduction - In this phase, the two 3-phosphoglycerate molecules are reduced, using ATP and NADPH to glyceraldehyde-3-phosphate (an intermediate in glycolysis). One of the glyceraldehyde-3-phosphates is then converted to dihydroxyacetone phosphate. Next the glycolytic enzyme aldolase is used in reverse, combining glyceraldehyde-3-phosphate and dihydroxyacetone phosphate to form fructose-1,6-bisphosphate. Finally, this is converted into Fructose-6-phosphate.

  3. Regeneration - The rest of the steps of RuBP involve reforming the ribulose bisphosphate. Regeneration involves a complex series reactions and two enzymes unique to the RuBP are important in the process (See Figure). One ATP is expended to regenerate Ribulose bisphosphate.

Energy Balance of RuBP

To generate one extra fructose-6-phosphate molecule that can be removed from the cycle, six ribulose bisphosphate molecules have to be carboxylated. (Fructose is a six carbon molecule so six CO2 have to be fixed to generate one fructose). Six ribulose bisphosphates split into twelve 3-phosphoglycerate molecules and reduction of them to glyceraldehyde-3-phosphate costs 12 ATP and 12 NADPH. Adding in the six ATP to regenerate ribulose bisphosphate brings the total cost of synthesizing 1 fructose to 18 ATP and 12 NADPH. The take home message is, CO2 fixation is an expensive process! Photosynthetic organisms have to convert a large amount of light energy into ATP and NADPH to fuel RuBP.

Utilization of Fructose

Fructose is converted into sucrose and this is then used to synthesize all needed carbon intermediates. Needless to say, autotrophs have to be very capable biosynthetically.

Initially, it was assumed that all autotrophs fixed CO2 using RuBP, but work in the last few decades has revealed several strictly anaerobic and microaerophillic autotrophic species that do not use RuBP to assimilate CO2. Two new pathways were discovered. The basic steps of these pathways is now becoming clear, but more research is necessary to obtain information on the regulation of the pathways and the identity of some of enzymes involved. These pathways seem to be only used by microorganisms, at least no example to the contrary have been found. Below is presented each pathway along with a nod to some of the microbes that use them.

Reductive TCA cycle

One alternative strategy for fixing CO2 is to simply reverse the TCA cycle. Instead of breaking down acetyl CoA with the release of 2 CO2 and the generation of energy, acetyl CoA is synthesized by the incorporation of 2 CO2 and the input of 8 H (in the form of NADH and/or FADH), and 2 ATP. Some of the enzymes in the pathway are identical to the TCA cycle, but many of the energy requiring reactions are catalyzed by different enzymes. One of the key enzymes is ATP citrate lyase which cleaves citrate (6 carbons) into oxaloacetate (4 carbons) and acetyl CoA (2 carbons).

Green photosynthetic bacteria (Chlorobium limicola), some thermophillic bacteria that grow on hydrogen, (Hydrogenobacter thermophilus) and certain bacteria that grow by reducing sulfate (Desulfobacter hydrogenophilus ) have been shown to use rTCA.

RedTCA picture

Figure 2 - The reductive TCA cycle.

Reductive Acetyl CoA pathway

Unlike rTCA and RuBP, rACA is a noncyclic pathway. One CO2 is captured on a special cofactor (tetrahydrofolate: T in the figure) and reduced to a methyl group. The other CO2 is reduced to a carobonyl group (C=O) by carbon monoxide dehydrogenase and this enzyme bound carbonyl group is combined with the methyl group to form acetyl CoA by a collection of enzymes termed the acetyl CoA synthase complex. The pathway seems to require hydrogen gas as the electron donor and it is very efficient, requiring only 4H2 per acetate formed.

Some of its practitioners include, acetogens (microbes that generate acetic acid from hydrogen -0 Clostridium thermoaceticum, Acetobacterium woodii), methanogens (Methanobacterium thermoautotrophicum) and most autotrophic sulfate reducers (Defulfobacterium autotrophicum).

RedAcetylCoA picture

Figure 3 - Reaction of the reductive acetyl CoA pathway. Note that the above is a general diagram and the exact reactions in any species can vary. T: tetrahydrofolate, Co: A corrinoid protein (another type of methyl group carrier),

3-Hydroxypropionate cycle

A fourth pathway has been discovered for CO2 assimilation in bacteria, the 3-hydroxypropionate cycle. In this cycle, CO2 is fixed by acetyl-CoA and propionyl-CoA carboxylases eventually forming Malyl-CoA. This is split into acetyl-CoA, to replenish the cycle, and glyoxylate, for use in cell carbon. The electron donors and the nature of the enzymes that catalyze many of the steps are at this time unclear. Past research had demonstrated this pathway only in Chloroflexus, a nonsulfur photosynthetic bacteria, but recent work has detected the pathway in several autotrophic archaea. It seems the pathway is more widespread than previously thought.

3OHPro picture

Figure 4 - The 3-hydroxypropionate cycle. The areas in blue denote the steps where carbon dioxide is incorporated.

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