The ancient cyanobacterial part of our genome and its major consequences for our evolution

Lactate dehydrogenase (LDH) is a key metabolic enzyme. In eukaryotes, and in humans in particular, it contributes to the maintenance of an essential metabolic pathway, glycolysis, in the event of anaerobic stress. It is also involved in cell-to-cell communication mechanisms. These include interactions between healthy and cancerous cells and communication between neurons. In fact, it is one of the most studied enzymes. Structurally, human LDHs can be distinguished from their bacterial counterparts by the presence of long N-terminal extensions that contribute to tetrameric assembly. Bacterial LDHs are shorter and undergo structural reorganisations that allow them to be regulated by a process of allosteric activation. A property that no longer exists in eukaryotic enzymes. It was long thought that the loss of allosteric regulation in human LDHs was due to the presence of extensions that prevented the conformational changes associated with allostery. In practice, no experiments supporting or contradicting this hypothesis had been carried out until this study, and no evolutionary scenario explaining the presence of LDHs in eukaryotes existed.

Adeline Robin, Eric Girard and Dominique Madern from IBS/ELMA and Céline Brochier-Armanet from the Laboratoire de Biométrie et Biologie Evolutive (LBBE) first elucidated the process by which LDHs appeared in eukaryotes. This is linked to a very ancient gene transfer from a cyanobacterium to a primitive eukaryotic cell. Indeed, it has been possible to identify a group of cyanobacteria that possess LDHs with sequence characteristics typical of eukaryotes, notably the presence of long N-terminal extensions. Unexpectedly, the biochemical properties of LDH from cyanobacterium aponinum (C. apon) showed that the enzyme was under allosteric control by activation. The researchers also determined the structure of the inactive and active forms of C. apon LDH and were able to observe the associated conformational changes. These observations invalidated the hypothesis that extensions play a role in the loss of allosteric regulation in eukaryotes.

The researchers then analysed the amino acid substitution trajectory along the different eukaryotic lineages (plants, metazoans, etc) and proposed that the extinction of allostery in eukaryotic LDHs was the consequence of a mutation, in a key region of the enzyme, unique and specific to each major lineage. In order to validate this observation, the C. apon LDH, taken as a starting point, was used to probe the consequences of the introduction of these unique mutations. A first single mutant of C. apon LDH perfectly mimics the properties of plant LDHs and the second possesses most of the properties of a human LDH.

This work demonstrates the relevance of the combined approaches of evolutionary biochemistry and structural biology and makes it possible to explain not only the establishment of the last stage of glycolysis during evolution in eukaryotes but also the molecular mechanism of the extinction of allostery in human LDHs.

Deciphering Evolutionary Trajectories of Lactate Dehydrogenases Provides New Insights into Allostery. Robin AY, Brochier-Armanet C, Bertrand Q, Barette C, Girard E, Madern D. Mol Biol Evol. 2023 Oct 4 ;40(10):msad223. doi : 10.1093/molbev/msad223.

Contact : Dominique Madern (IBS/Extremophiles and Large Molecular Assemblies Group)