Origins of Cell Respiration
Assuming the origin of genes and proteins could have been fuelled with acyl
phosphates as central currency of “high energy bonds” generated by substrate level
phosphorylation
Once increasing chemical complexity transforms conventional evolution of
genetically encoded proteins, the invention of new functions potentially becomes a
very fast process
Advent of ATP as the universal energy currency was an important step, displacing
acetyl phosphate (postulate) – though ATP is universal, it is not the sole energy
currency
Has been argued that deep differences between archaebacterial and eubacteria
reflect comparatively recent environmental adaptations – specific claim that
archaebacterial adapted very recently
- However, many eubacteria thrive in hyperthermophilic environments without
going to trouble of replacing all their membranes and walls, DNA replication et c,
while plenty archaebacterial thrive in mesophilic environments archaea are
not better adapted than eubacteria
- Also interpreted as adaptations to energy stress – though acetogens and
methanogens live at lower end of free energy spectrum
- Simplest explanation as to why ATP rose to prominence was due to the substrate
specificity of rotor-stator type ATPase
Quinones, cytochrome complexes, quinone-based charge translocation is lacking in
methanogens and acetogens, possess no complexes I, II, III, no terminal oxidases,
and only a single coupling (ion pumping) site each
- Energy metabolic pahtwyas differ so fundamentally from normal respiratory
pathways in E.coli or mitochondria, biochemists have only recently uncovered te
basic energetics
- Despite the biochemical differences, the bioenergetics of methanogens and
acetogens feature some basics of chemiosmotic circuits – coupling proteins, ion
electrochemical gradients over membranes and ATP synthase
- Methanogens (no ATP consumption involved in methanogenesis – energy currency
is low-potential reduced ferredoxin Fdred) + Acetogens lack cytochromes (eg.
Methanobacterium marbugensis) use specialised version of Wood-Ljungdahl
pathway
Both reduce CO2 to a methyl group using electrons from H2 flavin based
electron bifurcation – splitting of electron pairs from hydrogen at a flavin –
electron goes to generate reduced low-potential ferredoxins, with energy
provided by second electron going a high potential acceptor (eg.
heterodisulphide CoM-S-S-CoB of methanogens)
Can then reduce CO2 in energetically difficult situations – electron bifurcation
may be (among strict anaerobes) an ancient biochemical mechanism, one that was
apparently a prerequisite for a lifestyle of reducing CO2 with electrons from
, H2, how organisms use acetyl-CoA pathway for carbon and energy metabolism to
survive (which can used to drive net ATP synthesis via ATP synthase or in case
of M. marbugensis – reduce ferredoxin via energy converting hydrogenase Ech)
Chemiosmotic circuits
System is the same , though components
differ structurally
Respiratory proteins are nanomachines,
coupled in series – how did they evolve?
Chemiosmotic Theory
1. Exergonic series of redox reactions
between members of the ETC on the IMM
2. Exergonic redox reactions drive 3 proton
pumps which transport H+ from matrix to
intermembrane space, thus a proton
gradient generated across IMM
3. Dissipation of proton gradient coupled to the phosphorylation of ADP to ATP
Different types of pumping
a) Conformational change
Complex I and complex IV transfer protons
by conformational change of protein
Reduction of redox centre (eg. cytochrome
or FeS cluster) alters conformation of
protein, opens gated channel across
membrane, allowing transfer of H+ from one side of membrane to other
AH2 donating electrons complex – electrons then reduce another protein in the
membrane. Diffuses to second complex, transferred to C
More difficult to evolve? Involves shape change of a highly complex protein
b) Redox Loops
, Complex III operates via a redox loop
across the membrane (Q cycle, Peter
Mitchell, 1975)
Less requirement for conformational
change in proteins, so seems less
sophisticated, but still needs mechanism to
transfer electrons back through complex
to an acceptor on the inside
From simple circuit in methanogens and acetogens to complex respiratory chains
Methanogens and acetogens are analogous in their chemiosmotic circuits – neither
has quinones or cytochromes, Na+/H+ pumping requires conformational change in a
relatively simple integral membrane protein (Rnf/Mtr/Ech) (Ech became a pump
rather than a pore)
2 mechanisms to generate pmf – redox loops
Key inventions: quinones and cytochromes
Respiratory chains modular
Respiratory chains maximise energy conservation from redox span between electron
donor and terminal acceptor
Arguments for early emergence of methanogenesis
1. Early branching on some phyogenetic trees
- Methanogens genuinely ancient or derived? Problem with deep branching in
phylogenetic trees: different trees recover different branching, so impossible
to say which groups associated with particular forms of respiration arose first)
- Some studies Cox et al., 2008 show methanogens branching early but there are
also systematic problems… (use concatenated sequences – use many sequences or
protein genes but still has problems)
- Methanopyrus genome predicts protein content – including membrane proteins –
note there is a single membrane pump (methyl transferase but no quinones or
cytochromes) (Slaserev et al., 2008)
- Acetogens also branch deeply in some trees (Ciccarelli et al., 2006) but not in
others, depending on genes selected and precise methodology
Assuming the origin of genes and proteins could have been fuelled with acyl
phosphates as central currency of “high energy bonds” generated by substrate level
phosphorylation
Once increasing chemical complexity transforms conventional evolution of
genetically encoded proteins, the invention of new functions potentially becomes a
very fast process
Advent of ATP as the universal energy currency was an important step, displacing
acetyl phosphate (postulate) – though ATP is universal, it is not the sole energy
currency
Has been argued that deep differences between archaebacterial and eubacteria
reflect comparatively recent environmental adaptations – specific claim that
archaebacterial adapted very recently
- However, many eubacteria thrive in hyperthermophilic environments without
going to trouble of replacing all their membranes and walls, DNA replication et c,
while plenty archaebacterial thrive in mesophilic environments archaea are
not better adapted than eubacteria
- Also interpreted as adaptations to energy stress – though acetogens and
methanogens live at lower end of free energy spectrum
- Simplest explanation as to why ATP rose to prominence was due to the substrate
specificity of rotor-stator type ATPase
Quinones, cytochrome complexes, quinone-based charge translocation is lacking in
methanogens and acetogens, possess no complexes I, II, III, no terminal oxidases,
and only a single coupling (ion pumping) site each
- Energy metabolic pahtwyas differ so fundamentally from normal respiratory
pathways in E.coli or mitochondria, biochemists have only recently uncovered te
basic energetics
- Despite the biochemical differences, the bioenergetics of methanogens and
acetogens feature some basics of chemiosmotic circuits – coupling proteins, ion
electrochemical gradients over membranes and ATP synthase
- Methanogens (no ATP consumption involved in methanogenesis – energy currency
is low-potential reduced ferredoxin Fdred) + Acetogens lack cytochromes (eg.
Methanobacterium marbugensis) use specialised version of Wood-Ljungdahl
pathway
Both reduce CO2 to a methyl group using electrons from H2 flavin based
electron bifurcation – splitting of electron pairs from hydrogen at a flavin –
electron goes to generate reduced low-potential ferredoxins, with energy
provided by second electron going a high potential acceptor (eg.
heterodisulphide CoM-S-S-CoB of methanogens)
Can then reduce CO2 in energetically difficult situations – electron bifurcation
may be (among strict anaerobes) an ancient biochemical mechanism, one that was
apparently a prerequisite for a lifestyle of reducing CO2 with electrons from
, H2, how organisms use acetyl-CoA pathway for carbon and energy metabolism to
survive (which can used to drive net ATP synthesis via ATP synthase or in case
of M. marbugensis – reduce ferredoxin via energy converting hydrogenase Ech)
Chemiosmotic circuits
System is the same , though components
differ structurally
Respiratory proteins are nanomachines,
coupled in series – how did they evolve?
Chemiosmotic Theory
1. Exergonic series of redox reactions
between members of the ETC on the IMM
2. Exergonic redox reactions drive 3 proton
pumps which transport H+ from matrix to
intermembrane space, thus a proton
gradient generated across IMM
3. Dissipation of proton gradient coupled to the phosphorylation of ADP to ATP
Different types of pumping
a) Conformational change
Complex I and complex IV transfer protons
by conformational change of protein
Reduction of redox centre (eg. cytochrome
or FeS cluster) alters conformation of
protein, opens gated channel across
membrane, allowing transfer of H+ from one side of membrane to other
AH2 donating electrons complex – electrons then reduce another protein in the
membrane. Diffuses to second complex, transferred to C
More difficult to evolve? Involves shape change of a highly complex protein
b) Redox Loops
, Complex III operates via a redox loop
across the membrane (Q cycle, Peter
Mitchell, 1975)
Less requirement for conformational
change in proteins, so seems less
sophisticated, but still needs mechanism to
transfer electrons back through complex
to an acceptor on the inside
From simple circuit in methanogens and acetogens to complex respiratory chains
Methanogens and acetogens are analogous in their chemiosmotic circuits – neither
has quinones or cytochromes, Na+/H+ pumping requires conformational change in a
relatively simple integral membrane protein (Rnf/Mtr/Ech) (Ech became a pump
rather than a pore)
2 mechanisms to generate pmf – redox loops
Key inventions: quinones and cytochromes
Respiratory chains modular
Respiratory chains maximise energy conservation from redox span between electron
donor and terminal acceptor
Arguments for early emergence of methanogenesis
1. Early branching on some phyogenetic trees
- Methanogens genuinely ancient or derived? Problem with deep branching in
phylogenetic trees: different trees recover different branching, so impossible
to say which groups associated with particular forms of respiration arose first)
- Some studies Cox et al., 2008 show methanogens branching early but there are
also systematic problems… (use concatenated sequences – use many sequences or
protein genes but still has problems)
- Methanopyrus genome predicts protein content – including membrane proteins –
note there is a single membrane pump (methyl transferase but no quinones or
cytochromes) (Slaserev et al., 2008)
- Acetogens also branch deeply in some trees (Ciccarelli et al., 2006) but not in
others, depending on genes selected and precise methodology
