Metabolism II (CO2 capture) Flashcards
CO2 assimilation
- autotrophic Bacteria and Archaea
assimilate CO2 by at least 5 key pathways:
- Calvin-Benson-Bassham cycle:
-transaldolase variant in chemolithoautotrophic Bacteria and some photolithoautotrophs, namely the Chromatiales.
-sedoheptulose bisphosphatase variant only in photolithoautotrophs - the “Cyanobacteria” (thus in chloroplasts of the Viridiplantae, rhodoplasts of the Rhodophyta etc)
*Arnon-Buchanan cycle – many photolithoautotrophic Bacteria including the ‘green sulfur bacteria’ (the chlorobiota) and chemolithoheterotrophic Epsilonproteobacteria. - Wood-Ljungdahl pathway – acetogenic Bacteria and methanogenic Archaea.
- 3-hydroxypropionate bicycle – ‘green non-sulfur bacteria’ (Chloroflexus etc) in the Chloroflexota, some Archaea,
- hydroxypropionate-hydroxybutyrate pathway in the Archaea:
-one version in e.g. Saccharolobus spp., Metalosphaera spp.
-one version in e.g. Nitrosopumilus spp.
C1 autotrophs – an aside
These are creating their own carbon dioxide instead of getting it from the air.
- there are also a subset of methylotrophs (L09) that assimilate CO2 using the Calvin-Benson-Bassham cycle.
- we call them ‘C1 autotrophs’ – examples:
-Paracoccus denitrificans growing on methanol or formate
-Paracoccus versutus ditto.
[Rhodobacteraceae < Rhodobacterales < Alphaproteobacteria < Pseudomonadota] - Xanthobacter tagetidis growing on methanol or formate
[Xanthobacteraceae < Hyphomicrobiales <Alphaproteobacteria < Pseudomonadota] - they dissimilate their C/E source to CO2 (see L09) then assimilate CO2 rather than assimilating from more reduced levels per the organisms in.
- there are also some legitimate chemolithoautotrophs that can use C1 compounds like dimethylsulfide (DMS, (CH3)2S) and dimethyldisulfide (DMDS, (CH3)2S2)
but they are really using the S(-II) part of the molecule as electron donor and energy source and by virtue of oxidising it to sulfate (S(+VI)), the C atoms end up as CO2 and are assimilated with exogenous CO2 by CBB cycle. Examples: - Thiobacillus thioparus Tk-m on DMS or methanethiol (CH3SH)
- Thiobacillus thioparus E6 on DMDS, DMS or methanethiol
[Thiobacillaceae < Nitrosomonadales < Betaproteobacteria < Pseudomonadota]
CBB cycle: RuBisCO
- CO2 assimilation into biomolecules occurs at ribulose 1,5-bisphosphate carboxylase/oxygenase (RuBisCO, EC 4.1.1.39 – has at least 9 isoenzymes across all 3 Domains of Life) which catalyses:
D-ribulose 1,5-bisphosphate + CO2 + H2O → 2 × 3-phospho-D-glycerate + 2H+ - Next 2 steps of cycle convert 3-phospho-D-glycerate (3PGA) further:
- phosphoglycerate kinase (EC 2.7.2.3):
3-phospho-D-glycerate + ATP → 1,3-bisphosphoglycerate + ADP - glyceraldehyde 3-phosphate dehydrogenase (NADP+
, phosphorylating, EC 1.2.1.59):
1,3-bisphosphoglycerate + NADPH + H+ → D-glyceraldehyde 3-phosphate + NADP+ + Pi - 1/6th of D-glyceraldehyde 3-phosphate (GAP) produced (rest is used up in the cycle) is
used to make hexose sugars (e.g. fructose, glucose etc) which are fed into e.g. glycolytic pathways and Krebs’ cycle to make building blocks for amino acid biosynthesis. - isoenzyme subunit codes: all Form I subtypes are CbbLS; Form II is CbbM
Note many subtypes of each. Older studies may say RbcLS or RbcM – same thing!
Bassham et al. (1950) J Biol Chem 185: 781-787.
I would ignore anything you find online re: Prof Fong discovering it first – highly
contentious matter done long after the fac
When RuBisCO goes wrong…
- ribulose 1,5-bisphosphate carboxylase/oxygenase also
catalyses another reaction – the oxygenation of RuBP:
D-ribulose 1,5-bisphosphate + O2 → 3-phospho-D-glycerate + 2-phospho-D-glycolate + 2H+ - This means autotrophs can waste half of RuBP given 2-phospho-D-glycolate can’t continue in the cycle (2C lost) and no CO2 was assimilated (net 3C lost)!
- Several carbon concentrating mechanisms (CCMs) have evolved e.g.
- Many “Cyanobacteria” (and chemolithoautotrophic Bacteria) contain carboxysomes (protein
‘houses’ for RuBisCO and carbonic anhydrase) to keep pCO2 high around RuBisCO and to exclude oxygen. - The Streptophyta have various solutions including the Hatch-Slack pathway (in C4 plants of the Poales) and crassulacean acid metabolism (in CAM plants – cacti and succulents).
- Some Bryophyta (viz. Anthocerotophyta) and Chlorophyta etc use pyrenoids to concentrate CO2 similarly to carboxysomes in general principles but not in structure or function!
Thiobacillus thioparus transmission electron micrograph – electron dense bodies in lower half of cell are carboxysomes
LEFT: Sorghum bicolor (L.) Moench. of the Poales, a C4 plant.
RIGHT: Crassula ovata (Miller) Druce of the Saxifragales, a CAM plant (the archetypal CAM plant!)
LEFT: Chlamydomonas reinhardtii P.D.Dang. of the chlorophyta, the ‘flower-like’ structure on the right is the pyrenoid inside of a cup-shaped chloroplast (electrondense).
RIGHT: chloroplast of Anthoceros agrestis (Paton) Damsholt of the Anthocerotophyta – the pyrenoid is the dark structure in the centre.
Carboxysomes
- proteinaceous cell compartments that share an evolutionary ancestor with the enterosome.
- first seen in the “Cyanobacteria” (Drews and Niklowitz (1956) Arch. Mikrobiol. 24:147-162*) and were referred to as
“polyhedral bodies” until “carboxysomes” was proposed
(Shively et al. (1973) Science 182: 584-586) when studied in
Halothiobacillus neapolitanus ParkerXT.
[Halothiobacillaceae < Chromatiales < Gammaproteobacteria < Pseudomonadota] - contain a specific isozyme of RuBisCO
- two types of pores in the protein sheets of the shells – BMC-H (for bicarbonate) and BMC-T (for organic substrates – open and close for them).
- interior is packed with RuBisCO and carbonic anhydrase (EC 4.2.1.1), which catalyses cleavage of carbonic acid (H2CO3):
H2CO3 → CO2 + H2O
Carboxysomes contain a specific form of the enzyme RuBisCO and have two types of pores in their protein shell: BMC-H for bicarbonate and BMC-T for organic substrates. The interior of carboxysomes is packed with RuBisCO and carbonic anhydrase, which catalyzes the cleavage of carbonic acid into carbon dioxide and water.
More on Carboxysomes
Bicarbonate ions (HCO3-) are the dominant form of dissolved inorganic carbon (DIC) at pH 7.2, which is the typical pH inside the cytoplasm of a cell.
This means that in the cellular environment, bicarbonate ions are the most prevalent form of carbon that is dissolved in the fluid.
Carbonic anhydrase catalyzes the conversion of bicarbonate ions into carbonic acid (H2CO3), which then spontaneously dissociates into protons (H+) and carbon dioxide (CO2).
Carbonic anhydrase is an enzyme that accelerates this conversion process.
The dissociation of carbonic acid releases protons and carbon dioxide.
The high concentration of carbon dioxide inside the carboxysome, compared to the cytoplasm, ensures that RuBisCO primarily performs the carboxylation reaction rather than oxygenation.
The carboxysome maintains a much higher concentration of CO2 compared to the cytoplasm.
This high concentration of CO2 ensures that RuBisCO mainly catalyzes the carboxylation reaction, where CO2 is added to a molecule during photosynthesis, rather than the oxygenation reaction, which can be wasteful.
RuBisCO can only use CO2 as a substrate and cannot utilize carbonate, bicarbonate, or carbonic acid.
RuBisCO, or ribulose-1,5-bisphosphate carboxylase/oxygenase, is an enzyme involved in the first major step of carbon fixation during photosynthesis.
It specifically requires CO2 as the substrate for its reaction and cannot use other forms of carbon.
Carboxysome types
- α-carboxysomes (on cso operon) found in some of the
“Cyanobacteria”, chemolithoautotrophic Bacteria (Thiobacillus thioparus, Halothiobacillus neapolitanus, Thiomicrospira spp., Thiomicrorhabdus spp., Hydrogenovibrio spp.). - 100-160 nm diameter.
- contain Form IAc RuBisCO (Form IAq is cytoplasmic).
- β-carboxysomes (on csm operon) found in some
“Cyanobacteria”. - 200-400 nm diameter.
- contain Form IBc RuBisCO (Form IBq is cytoplasmic).
how does DIC get to carboxysomes?
Transport into the cell: DIC, which primarily exists as bicarbonate ions (HCO3-) in the surrounding environment, needs to be transported into the cell. This transport process often involves specialized membrane transport proteins that facilitate the movement of DIC across the cell membrane.
Changing DIC species: Once inside the cell, DIC may undergo chemical transformations to change its chemical species. For example, it may be converted to other forms such as carbon dioxide (CO2) or carbonic acid (H2CO3), depending on the cellular conditions and metabolic requirements.
Protection as bicarbonate: Bicarbonate ions (HCO3-) are a common form of DIC inside the cell and are often protected to prevent their loss or unwanted reactions. This protection may involve sequestering bicarbonate ions in specific cellular compartments or binding them to proteins that stabilize their concentration.
Flipping DIC species: If DIC undergoes transformation into other chemical species within the cell, mechanisms may exist to reverse these changes and convert them back to bicarbonate ions or other preferred forms for subsequent metabolic processes.
Arnon-Buchanan cycle enzymes
- DIC fixation steps:
2-oxoglutarate synthase (EC 1.2.7.3, OorABCD and
For ABGDE isoenzymes) is not found in Krebs’ cycle and
uses ferredoxin (Fd) as cofactor to convert C4 to C5
species by adding C from CO2:
succinyl-CoA + CO2 + Fd(red) → 2-oxoglutarate + CoA + Fd(ox) isocitrate dehydrogenase (NADP+, EC 1.1.1.42, Icd1) is
found in Krebs’ cycle and converts C5 to C6 species by
adding C from CO2):
2-oxoglutarate + CO2 + NADPH + H+ →isocitrate + NADP+
most intermediates are the same as Krebs cycle but with different enzymes.
Arnon-Buchanan cycle
- sometimes called “rTCA”, “reverse TCA”, “reverse Krebs’ cycle”, “reductive TCA” etc. All have issues with trueness and so Arnon-Buchanan cycle has superseded them
[there are many TCA cycles of which one is Krebs’ cycle, which operates clockwise; Arnon-Buchanan cycle is another TCA cycle (not the only reverse or reductive one) that operates anticlockwise] - same intermediates as Krebs’ cycle but not the same enzymes!
- cycle found in many thermophilic organisms near to the root of the Bacteria –may be an ancient cycle? (Chlorobium, Thermotoga etc).
[Chlorobiaceae < Chlorobiales < “Chlorobiia” < Chlorobiota]
[Thermotogaceae < Thermotogales < Thermotogae < Thermotogota] - some steps can happen at high temperature and low pH with metal catalysts and Life is not required (Muchowska et al. (2017) Nature Ecol. Evol. 1: 1716-1721) –compare and contrast with the Krebs’ cycle origin theory of ächtershäuser (1988) Syst. Appl. Microbiol. 10: 207-210; Wächtershäuser (2000) Science 289: 1307-1308.
Wood-Ljungdahl pathway enzymes
- DIC fixation steps are the same in both cycles found in:
- homoacetogenic Bacteria (Acetobacterium woodii, for example).
[Eubacteriaceae < Eubacteriales < Clostridia < Bacillota < Bacteria] - autotrophic methanogenic Archaea (Methanosarcina thermophila, for example).
[Methanosarcinaceae < Methanosarcinales < “Methanomicrobia” < “Methanobacteriota” < Archaea]
CO2 is first reduced to carbon monoxide (CO) by anaerobic carbon-monoxide dehydrogenase (EC 1.2.7.4)
CO2 + 2Fd(red) + 2H+ → CO + H2O + 2Fd(ox)
CO is then fixed into acetyl-CoA by carbon-monoxide-methylating acetyl-CoA synthase (EC 2.3.1.169)
CO + CoA + [(Co(III))] → acetyl CoA + [Me(Co(I))]
(where [stuff in brackets] are corrinoid cofactors (bit like heme but Co not Fe) inside of a protein– v common in methyl-accepting enzymes)
3-hydroxypropionate bicycle enzymes
- found in Archaea like Acidianus spp. and in Bacteria like Chloroflexus spp. [latter is genes only, no evidence they can or do use it]
[Sulfolobaceae < Sulfolobales < Thermoprotei < Thermoproteota < Archaea]
[Chloroflexaceae < Chloroflexales < Chloroflexia < Chloroflexota < Bacteria]
bicarbonate is fixed into malonyl-CoA by acetyl-CoA carboxylase (EC 6.4.1.2):
HCO3- + acetyl-CoA + ATP → malonyl-CoA + ADP + Pi
…and also into (S)-methylmalonyl-CoA by propionyl-CoA carboxylase (EC 6.4.1.3):
HCO3- + propionyl-CoA + ATP → (S)-methylmalonyl-CoA + ADP + Pi
even though organism lives in pH1 inside the cytoplasm is pH7 so in order to avoid the use of carboxysomes they use bicarbonate instead of CO2
