and 2-oxoglutarate to isocitrate. This pathway was originally discovered in the green
sulfur bacterium Chlorobium (Chlorobi), but it has since been found in anaerobic or
microaerobic members of the Aquificae (Aquifex, Hydrogenobacter), Proteobacteria
(especially Deltaproteobacteria and Epsilonproteobacteria), and the Nitrospirae.
Some Aquificae that use this pathway can grow up to 95
C.
The reductive acetyl-CoA pathway, also known as the Wood-Ljungdahl pathway.
Here, one CO 2 is reduced to the level of a methyl group; a second CO 2 molecule is
reduced to carbon monoxide bound to CO dehydrogenase, which also acts as an
acetyl-CoA synthase, combining the two carbons to form acetyl-CoA. Acetyl-CoA
is then carboxylated to pyruvate. As the CO dehydrogenase/acetyl-CoA synthase is
highly oxygen sensitive, functioning of the pathway requires strict anoxic conditions. The Wood-Ljungdahl pathway is the preferred mode of autotrophic CO 2
fixation of acetogenic bacteria and methanogenic archaea, organisms living close
to the thermodynamic limit. The pathway functions also in the anammox bacteria
(Planctomycetes), in autotrophic sulfate-reducing bacteria such as Desulfobacterium
(Deltaproteobacteria), and in autotrophic Archaeoglobales (Euryarchaeota). The
pathway is compatible with life at the upper limits of temperature: it is used by a
Methanopyrus strain that can multiply at 122
C.
The 3-hydroxypropionate bi-cycle, also known as the Fuchs-Holo bi-cycle. Figure 5 in Berg (2011) gives a detailed description of this complex pathway. The CO 2
fixation steps are the carboxylation of acetyl-CoA to malonyl-CoA and of propionylCoA to (S)-methylmalonyl-CoA. The 3-hydroxypropionate bi-cycle operates in the
green non-sulfur phototrophs of the Chloroflexaceae family (phylum Chloroflexi),
which preferentially grow as photoheterotrophs. The key carboxylase activities of
biotin-dependent acetyl-CoA/propionyl-CoA carboxylase are virtually irreversible
and use bicarbonate as substrate. This may be advantageous during growth at high
pH. However, the energy costs are high: seven ATP equivalents are needed for the
synthesis of pyruvate and three additional ATPs for its conversion to triose
phosphate.
The
3-hydroxypropionate/4-hydroxybutyrate
and
dicarboxylate/4hydroxybutyrate cycles. Here acetyl-CoA and two inorganic carbons are converted
to succinyl-CoA, the carboxylation reactions being the conversion of acetyl-CoA to
pyruvate and phosphoenolpyruvate to oxaloacetate in the first case and conversion of
acetyl-CoA to malonyl-CoA and of propionyl-CoA to (S)-methylmalonyl-CoA in
the second case. The enzymes of the 3-hydroxypropionate/4-hydroxybutyrate cycle
are oxygen-tolerant. The pathway is found in (micro)aerobic Sulfolobales, while the
dicarboxylate/4-hydroxybutyrate cycle is found in mostly anaerobic members of the
Crenarchaeota orders Desulfurococcales and Thermoproteales. Both cycles are
energetically expensive, the anaerobic one being less costly. The thermotolerance
of these pathways may be an important feature explaining why they were adopted by
the hyperthermophilic crenarchaeotes (Berg 2011).
Another interesting case of multiple biochemical pathways used by different
microorganisms to achieve the same goal is the incorporation of methane-derived
carbon into the biomass of cells that grow on methane as single carbon source. None
of the known methanotrophs uses RuBisCo and the enzymes of the Calvin cycle for
174
A. Oren
sulfur bacterium Chlorobium (Chlorobi), but it has since been found in anaerobic or
microaerobic members of the Aquificae (Aquifex, Hydrogenobacter), Proteobacteria
(especially Deltaproteobacteria and Epsilonproteobacteria), and the Nitrospirae.
Some Aquificae that use this pathway can grow up to 95
C.
The reductive acetyl-CoA pathway, also known as the Wood-Ljungdahl pathway.
Here, one CO 2 is reduced to the level of a methyl group; a second CO 2 molecule is
reduced to carbon monoxide bound to CO dehydrogenase, which also acts as an
acetyl-CoA synthase, combining the two carbons to form acetyl-CoA. Acetyl-CoA
is then carboxylated to pyruvate. As the CO dehydrogenase/acetyl-CoA synthase is
highly oxygen sensitive, functioning of the pathway requires strict anoxic conditions. The Wood-Ljungdahl pathway is the preferred mode of autotrophic CO 2
fixation of acetogenic bacteria and methanogenic archaea, organisms living close
to the thermodynamic limit. The pathway functions also in the anammox bacteria
(Planctomycetes), in autotrophic sulfate-reducing bacteria such as Desulfobacterium
(Deltaproteobacteria), and in autotrophic Archaeoglobales (Euryarchaeota). The
pathway is compatible with life at the upper limits of temperature: it is used by a
Methanopyrus strain that can multiply at 122
C.
The 3-hydroxypropionate bi-cycle, also known as the Fuchs-Holo bi-cycle. Figure 5 in Berg (2011) gives a detailed description of this complex pathway. The CO 2
fixation steps are the carboxylation of acetyl-CoA to malonyl-CoA and of propionylCoA to (S)-methylmalonyl-CoA. The 3-hydroxypropionate bi-cycle operates in the
green non-sulfur phototrophs of the Chloroflexaceae family (phylum Chloroflexi),
which preferentially grow as photoheterotrophs. The key carboxylase activities of
biotin-dependent acetyl-CoA/propionyl-CoA carboxylase are virtually irreversible
and use bicarbonate as substrate. This may be advantageous during growth at high
pH. However, the energy costs are high: seven ATP equivalents are needed for the
synthesis of pyruvate and three additional ATPs for its conversion to triose
phosphate.
The
3-hydroxypropionate/4-hydroxybutyrate
and
dicarboxylate/4hydroxybutyrate cycles. Here acetyl-CoA and two inorganic carbons are converted
to succinyl-CoA, the carboxylation reactions being the conversion of acetyl-CoA to
pyruvate and phosphoenolpyruvate to oxaloacetate in the first case and conversion of
acetyl-CoA to malonyl-CoA and of propionyl-CoA to (S)-methylmalonyl-CoA in
the second case. The enzymes of the 3-hydroxypropionate/4-hydroxybutyrate cycle
are oxygen-tolerant. The pathway is found in (micro)aerobic Sulfolobales, while the
dicarboxylate/4-hydroxybutyrate cycle is found in mostly anaerobic members of the
Crenarchaeota orders Desulfurococcales and Thermoproteales. Both cycles are
energetically expensive, the anaerobic one being less costly. The thermotolerance
of these pathways may be an important feature explaining why they were adopted by
the hyperthermophilic crenarchaeotes (Berg 2011).
Another interesting case of multiple biochemical pathways used by different
microorganisms to achieve the same goal is the incorporation of methane-derived
carbon into the biomass of cells that grow on methane as single carbon source. None
of the known methanotrophs uses RuBisCo and the enzymes of the Calvin cycle for
174
A. Oren