The evolution of biochemical pathways on the example of the citric acid cycle

I. Introduction

How and why did life originate and evolve on earth? These might be two of the earliest questions which arose with the development of a brain that was capable of abstract thinking more than 300 000 years ago. People have used myths and religious beliefs to find answers to these questions, but without success in terms of a widely accepted and evidence-based theory about the origin and evolution of life.

Scientists have not started to address these fundamental questions until much more than 100 years ago and are far from being able to explain why these processes happened and are still going on, but considerable progress has undoubtedly been made in understanding how what we call life developed. But what do we call life? Even if the origin of complex organic substances from methane, ammonium, water and hydrogen in the early earth atmosphere did not lead to the origin of living organisms directly, these events unquestionably represented milestones along this path since from these substances, of which amino acids were a very great part, the formation of nucleotides and ribonucleic acid was only one small step ahead. Since ribonucleic acid is able to carry information and to replicate, two decisive features of what we call life were at this point fulfilled. However, the ability to develop on both ontogenetic and phylogenetic levels represent one more precondition for a cluster of molecules to be considered as life. This characteristic is inseparably linked with the existence of a metabolism because one needs to incorporate energy from the environment and to bring it into a form that can be used by the organism in order to build up anything new.

Before an effective metabolism could develop, the replicating machinery, which used DNA instead of RNA by that time, was surrounded by a membrane separating it from the environment; creating the possibility to harvest energy in form of a molecule whose catabolism could be coupled with energy-consuming anabolic reactions. This molecule, ATP, has kept this function ever since its first occurrence.

The existence of the first prokaryotic organisms with such a kind of basic metabolism has been proven and dated back about 3,5 billion years. 2; 7

Evolution has been going on ever since: Driven by the evolutionary forces of mutation, recombination, migration, genetic drift and selection, more and more complex organisms which were adapted better and better to their respective environments developed.

However, the results from this development which are visible exteriorly such as an organism’s appearance and behaviour are largely due to changes in its metabolism.

Various reactions have been integrated and combined into pathways in different organisms’ metabolisms uncountable times during the evolutionary process. Some of these events happened at a very early stage of phylogeny and, where the respective pathways proved to be effective, the corresponding reaction chains and enzymes can be found in the majority of all species whereas other metabolic pathways that are rather specific are confined to a smaller number of species. If rather complex reaction chains manage to persist within two or even all three domains of life, as is the case for the citric acid cycle (CAC), this suggests that this pathway is both extremely effective and evolved at a very early stage. So the following questions arise: When did this pathway evolve and what makes it so effective?

Another reason why I will use the example of the citric acid to illustrate how biochemical pathways evolve is that it is a cyclic pathway and therefore poses one even more intriguing question: Do cyclic pathways such as the citric acid cycle usually evolve as whole entities in one step or are they rather the result of a combination of previously existing reaction chains in a cyclic way? Thus, analyzing the answers to these questions concerning the central biochemical pathway in eukaryotes can help us to gain a deeper understanding of the evolutionary forces’ influence on the biochemical level.

Figure 1 : overview about the CAC reactions and their initial directions

illustration not visible in this excerpt

Left part of the Right part of the CAC

CAC

Figure 1 : The two major sequential pathways from which the final form of the CAC is composed: ancient bacteria and archeae use the left part of the CAC in the reductive direction (blue arrows) and take the intermediates as e- acceptors (oxaloaxetate and fumarate) or as bases for biosynthetic reactions (oxaloacetate, succinyl CoA and illustration not visible in this excerpt-ketoglutarate)

Some autotrophic bacteria which produceillustration not visible in this excerpt-ketoglutarate out of oxaloacetate and use it for further biosynthesis possess only the right part of the CAC (black arrows).

The final cyclic form of the CAC (inner black arrows) could only be carried out after the creation of two new enzymes which helped to transform illustration not visible in this excerpt-ketoglutarate into succinyl-CoA and further to succinate.

The advantage of this cyclic scheme is that reductive equivalents (NADH and FADH2) are formed as by-products which can be used in the respiratory chain to gain ATP.

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