Skip to main content

Table 5 Representative set of pathways for processing partially reduced carbon. References [127, 128, 153, 171,172,173,174,175] were used to build this table

From: Electrical energy storage with engineered biological systems

Cycle or pathway

Substrate

Product

ATP requirements

NAD(P)H

Number of substrate molecules

Number of each product

ATPs per substrate molecules

Key enzyme(s)

Specific activity of key enzyme(s) (μmol/min/mg protein)

Note

Reference

Naturally Evolved Under Aerobic Conditions

Serine cycle

Formaldehyde (CH2O) + CO2, methanol (CH4O) + CO2, methane (CH4) + CO2

Acetyl-CoA (C2H3O-CoA)

2

2

1 + 1

1

1

A. Serine hydroxymethyltransferase (SHMT) (EC 2.1.2.1) (e.g. Geobacillus stearothermophilus, 37°C, pH 7.4)

A. 5

This cycle has been found in methane-assimilating microorganisms.

Anthony et al. [171], Berg et al. [153]

Ribulose monophosphate (RuMP) pathway- Entner–Doudoroff (EDD)-variant

Formaldehyde (CH2O), methanol (CH4O), methane (CH4)

3-phosphoglycerate (C3H7O7P)

2

1

3

1

0.6

A. 6-phosphogluconate dehydratase (EC 4.2.1.12)

A. 0.033

This pathway loses one carbon in the decarboxylation of pyruvate to acetyl-CoA.

Kalyuzhnaya et al. [172]

B. 2-keto-3-deoxy-6-phosphogluconate aldolase (EC 4.1.2.14) (e.g. Methylomicrobium alcaliphilum, 28°C, pH 9)

B. 0.062

Artificially Evolved Under Aerobic Conditions

Reductive glycine pathway (RGP or rGly)

Formate (HCO2-) + CO2

Pyruvate (C3H3O3-)

2

3

2 + 1

1

0.6

A. Formate dehydrogenase (EC 1.17.1.9) (e.g. Mycobacterium vaccae, 30°C, pH 6.5)

A. 3.24

This pathway is reversible and Yishai et al. believe this is the most efficient pathway, even though it needs an extra CO2.

Yishai et al. [128], Yishai et al. [173]

B. Tetrahydrofolate (THF) dehydrogenase (EC 1.5.1.3) (e.g. Plasmodium falciparum, 25°C, pH 7)

B. 0.82

Methanol condensation cycle (MCC)

Formaldehyde (CH2O), methanol (CH4O), methane (CH4)

Acetyl-CoA (C2H3O-CoA)

0

0

2

1

0

A. Phosphoketolase (EC 4.1.2.9) (e.g. Clostridium acetobutylicum, 37°C, pH 6.5)

A. 2.01

This pathway avoids the decarboxylation of pyruvate and achieves complete carbon conservation with the loss of only water.

Bogorad et al. [174]

Formolase (dihydroxy-acetone variant)

Formate (HCO2-)

Glycerate 3P (C3H7O7P)

5

2

1

1

5

A. Formate-tetrahydrofolate ligase (FTL), (EC 6.3.4.3) (e.g. Homo sapiens)

A. 23

The main barrier in this pathway is that formaldehyde as an intermediate limiting cell growth even at low concentrations.

Bar-even et al. [127], Siegel et al. [175]

Serine−threonine pathway, a variant of the methylotrophic serine pathway

Formate (HCO2-) + CO2

Acetyl-CoA (C2H3O-CoA)

10

4

1 + 1

1

5

A. Serine hydroxymethyltransferase (EC 2.1.2.1) (e.g. Geobacillus stearothermophilus, 37°C, pH 7.4)

A. 5

This pathway is considered to be a highly promising pathway.

Yishai et al. [173]

B. Formate-tetrahydrofolate ligase (FTL), (EC 6.3.4.3) (e.g. Homo sapiens)

B. 23

Artificially evolved under anaerobic conditions

pyruvate formatelyase- Phosphoketolase (PFL-PKT)

Formate (HCO2-)

Glycerate 3P (C3H7O7P)

6

2

1

1

6

A. Pyruvate formate-lyase (EC 2.3.1.54) (eg Streptococcus mutans)

A. 12

A synthetic autocatalytic formate- assimilation cycle that is not dependent on fixation of inorganic carbon.

Bar-even et al. [127]

B. Phosphoketolase (EC 4.1.2.9) (e.g. Lactobacillus pentosus)

B. 4.5