The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution

@article{MelndezHevia2006ThePO,
  title={The puzzle of the Krebs citric acid cycle: Assembling the pieces of chemically feasible reactions, and opportunism in the design of metabolic pathways during evolution},
  author={E. Mel{\'e}ndez-Hevia and T. G. Waddell and M. Cascante},
  journal={Journal of Molecular Evolution},
  year={2006},
  volume={43},
  pages={293-303}
}
The evolutionary origin of the Krebs citric acid cycle has been for a long time a model case in the understanding of the origin and evolution of metabolic pathways: How can the emergence of such a complex pathway be explained. [...] Key Method We have analyzed the Krebs cycle as a problem of chemical design to oxidize acetate yielding reduction equivalents to the respiratory chain to make ATP. Our analysis demonstrates that although there are several different chemical solutions to this problem, the design of…Expand
An appeal to magic? The discovery of a non-enzymatic metabolism and its role in the origins of life
  • M. Ralser
  • Chemistry, Medicine
  • The Biochemical journal
  • 2018
TLDR
It is discussed that, on the basis of non-enzymatic metabolism-like networks, one can elaborate stepwise scenarios for the origin of metabolic pathways, a situation that increasingly renders the origins of metabolism a tangible problem. Expand
Origin and evolution of metabolic pathways.
TLDR
Comparative analyses of genes and genomes from organisms belonging to Archaea, Bacteria and Eukarya revealed that, during evolution, different forces and molecular mechanisms might have driven the shaping of genomes and the arisal of new metabolic abilities. Expand
Reactivity of Metabolic Intermediates and Cofactor Stability under Model Early Earth Conditions
TLDR
This work demonstrates the stability of these metabolic intermediates under anoxic conditions, and shows that even though free cofactors may be stable in a geological environmental setting, an enzyme or other mechanism to promote reaction specificity would likely be necessary for at least this particular reaction to proceed. Expand
Convergent evolution of a modified, acetate-driven TCA cycle in bacteria
TLDR
Evidence is presented that an alternative TCA cycle, in which acetate:succinate CoA-transferase (ASCT) replaces the enzymatic step typically performed by succinyl-CoA synthetase (SCS), has arisen in diverse bacterial groups, including microbial symbionts of animals such as humans and insects. Expand
Sulfate radicals enable a non-enzymatic Krebs cycle precursor
TLDR
The results show that a non-enzymatic precursor of the Krebs cycle is biologically sensible, efficient, and forms spontaneously in the presence of sulfate radicals. Expand
Signatures of Arithmetic Simplicity in Metabolic Network Architecture
TLDR
This work uses metabolic flux constraint-based models to exhaustively search for artificial chemistry pathways that can optimally perform an array of elementary metabolic functions and finds that properties similar to those predicted for the artificial chemistry hold also for real metabolic networks. Expand
Branch-point stoichiometry can generate weak links in metabolism: the case of glycine biosynthesis
TLDR
It may not be possible to ensure that glycine is always synthesized in sufficient quantities to meet optimal metabolic requirements, as a critical weak link is created in glycine biosynthesis by the stoichiometry of the reaction catalyzed by glycine hydroxymethyltransferase. Expand
Central carbon metabolism as a minimal biochemical walk between precursors for biomass and energy.
TLDR
This work finds that central carbon metabolism is built as a minimal walk between the 12 precursor metabolites that form the basis for biomass and one precursor essential for the positive net ATP balance in glycolysis: every pair of consecutive precursors in the network is connected by the minimal number of enzymatic steps. Expand
Arithmetic simplicity beneath metabolic network architecture
Metabolic networks perform some of the most fundamental functions in living cells, including energy transduction and building block biosynthesis. While these are the best characterized networks inExpand
Integrating the universal metabolism into a phylogenetic analysis.
TLDR
The cladogram shows that the earliest pathways to emerge are metabolism of amino acids of groups I and II (Asp, Asn, Glu, and Gln). Expand
...
1
2
3
4
5
...

References

SHOWING 1-10 OF 35 REFERENCES
Optimization of Metabolism: The Evolution of Metabolic Pathways Toward Simplicity Through the Game of the Pentose Phosphate Cycle
TLDR
The results demonstrate that both the design of this pathway and the enzyme mechanisms themselves have been optimized, and it is not possible to find any other set of enzyme mechanisms capable of producing a simpler solution for the pentose phosphate pathway. Expand
Economy of design in metabolic pathways: further remarks on the game of the pentose phosphate cycle.
TLDR
The Calvin cycle in photosynthesis and the "L-type" of the pentose phosphate cycle are analysed arriving at similar conclusions in both cases, which suggest some reflections about the logic in the design of metabolic pathways, and the possible role of the hypothesis of simplicity in cell evolution. Expand
A reverse KREBS cycle in photosynthesis: consensus at last
TLDR
The findings that led the group to the discovery of the reductive carboxylic acid cycle, the nature and resolution of the controversy that followed, and the possible evolutionary implications of the cycle as an ancient mechanism for photosynthetic CO2 assimilation that preceded the pentose cycle and served as a precursor of the Krebs cycle in aerobic metabolism are discussed. Expand
The evolution of metabolic cycles
The function of the citric acid cycle is to convert efficiently the energy released during the combustion of acetate into the energy stored in the pyrophosphate bonds of ATP. The cycle is almostExpand
The game of the pentose phosphate cycle: a mathematical approach to study the optimization in design of metabolic pathways during evolution.
TLDR
The optimization of the pathway structure of the pentose phosphate cycle is studied by means of abstraction to a model designed as a mathematical game of combinatorial optimization, and a mathematical proof of the optimal solution is given. Expand
Evolutionary roots of the citric acid cycle in prokaryotes.
  • H. Gest
  • Chemistry, Medicine
  • Biochemical Society symposium
  • 1987
TLDR
The extraordinary versatility of citric acid cycle intermediates and reactions for multiple uses raises the possibility that origination of the aerobic cycle, viewed as an evolutionary event, occurred more than once. Expand
The Evolution of Metabolic Function
TLDR
Experiments in the Evolution of Catabolic Pathways Using Modern Bacteria using modern Bacteria and an Emerging Outline of the Evolutionary History of Aromatic Amino Acid Biosynthesis. Expand
Optimization of molecular design in the evolution of metabolism: the glycogen molecule.
TLDR
The results demonstrate that the structure of the glycogen molecule is optimized to maximize the total glucose stored in the smallest possible volume, the proportion of it that can be directly released by phosphorylase before any debranching occurs, and the number of non-reducing ends, which maximizes the speed of fuel release. Expand
Acetate oxidation to CO2 in anaerobic bacteria via a novel pathway not involving reactions of the citric acid cycle
In several sulfate-reducing bacteria capable of complete oxidation of acetate (or acetyl CoA), the citric acid cycle is not operative. No 2-oxoglutarate dehydrogenase activity was found in theseExpand
Citric-acid cycle, 50 years on
TLDR
A second pathway for acetyl-CoA oxidation was found and it is shown that sulfur-reducing bacteria and one genus of sulfate reducers use a modified citric-acid cycle with a novel anaplerotic sequence as pathway of terminal respiration, while all other anaerobes use an alternative pathway. Expand
...
1
2
3
4
...