Molecule of the Month for April 2015: Alchemase

Structure This month I have chosen the enzyme Alchemase as the subject of my post. The general structure of the enzyme is somewhat different than most enzymes, and moreover, its mechanism of action is unique. Through a series of redox steps, alchemase catalyses the only triple-cofactor dependent transmutation reaction so far identified in living organisms. The other striking feature of alchemase that is novel, is that it is a nucleozyme. Following the demonstration by Szostak and Joyce (see open access publication here), several years ago, that not only RNA, but DNA can provide the structure and reactivity, normally thought of as the preserve of proteins, alchemase was the first example of a naturally occurring DNA enzyme to be isolated. There are many RNA enzymes known, but so far only one deoxyribozyme has been structurally and mechanistically, characterised. The 3 cofactors, which are all variants of Pyridoxal Phosphate, associate with the exposed bases, seen projecting from the central core, which itself comprises the deoxyribose phosphates. Cofactor 1 is purine specific, cofactor 2 is pyrimidine specific, while cofactor 3 seems to show a dual specificity. Each cofactor has a distinctively different redox potential when measured in standard biological buffer at pH7, this is thought to be pivotal to the energetically unfavourable reaction. 

Source The organism from which alchemase was first isolated is Clostridium seaborgii, an obligate anaerobe, found (typically) in the oral cavities of adults over the age of 60, particularly those with a history of high carbohydrate diets. When the carbohydrate diet is supplemented with Bismuth (usually derived from over the counter medication such as Pepto Bismol, well known in the USA, but available now in the UK in a chew formulation at many high street pharmacies), the alchemase is induced. Induction does not follow the usual lac operon model, but occurs through a mechanism in which a site specific nuclease (similar to Type II restriction endonucleases, but with a dependency on Bismuth instead of Magnesium), releases multiple copies of the DNA sequence from the C.seaborgii genome. The alc gene (encoding alchemase), is present in multiple copies, similar to ribosomal RNA genes. 

Chemistry It is during cleavage reaction that Bismuth ions are first activated through cofactor 1 (and subsequently by cofactors 2 and 3), as part of a sequential conversion of the Bismuth nucleus to Gold. The reaction was formally demonstrated by Glenn Seaborg (from where the organism gets its name) over 30 years ago.  Through systematic proton and neutron transfer reactions, the Bismuth (tightly complexed via the phosphate backbone of alchemase), is converted to Gold. Recall from your chemistry that Bismuth (83) is in the post-Transition Metal cluster, whilst Gold (79) is just inside the Transition Metal group. It might not seem like a big jump from Bismuth to Gold, but the energy required is probably equivalent to a day's worth of ATP, confined to the volume of a typical unicellular microbe. So whilst the reaction is therefore pretty slow, compared with many enzymes (and anaerobes are generally known to have much slower doubling times than aerobes), the energy per cubic metre (assume a sphere of radius 1 micron for the anaerobe) is equivalent to that in the  core of a nuclear reactor. The key role of the cofactor triad in this reaction is currently the subject of a major investigation at the Aprilscherztag Institute fur Radiochemie in Berlin through funding by the German Green Party, who are keen to establish an alternative organic programme to solve Germany's energy crisis in the wake of their decision to axe conventional nuclear power. I for one hope that this process can be harnessed soon, since renewable energy is such an important problem to solve globally. 

Applications of alchemase in Synthetic Biology. One of the most promising ideas emerging from the discovery of the alc gene and its enzymatic properties, is the possibility of inducing in situ dental repairs. As you will all no doubt be aware, gold has been shown over many years to be one of the best metals for dental repair. Whist it is still popular in some cultures, the woman on the right is from Tajikistan, where gold teeth are a status symbol, in Europe and the USA, gold has been replaced by materials that match the "ivory" colour of most teeth. The use of metals in the form of amalgams, which combine lead, mercury or increasingly "composites", remains commonplace for dental repairs at the rear of the mouth. Here is where the use of the alc genes comes in. By transplanting the genes (multiple copies, see earlier) for alchemase (based on similar concepts related to the recent CRISPR phenomenon), together with that encoding the alc specific restriction enzyme (CseI), scientists at the Goldgraber Zentrum in Augsburg, Germany have shown evidence of nutrient induced gold deposition by their synthetic microbe. I thought "Synthia" (the name given to Craig Venter's first synthetic microbe) was a bit cheesy, but I quite like the name "Midas"! Whatever your opinion of the name, with the discovery of this novel nucleic acid enzyme, I am certain some interesting fundamental science and subsequent applications will be developed over the coming years that will prove transformative! Finally it would be remiss of me not to acknowledge the help of several colleagues in writing this Blog, in particular Professors Geber, Magnus, Paracelsus and not forgetting many helpful discussions with the late Professor Newton, who is was always a great inspiration to me and whose ideas I have always felt, were not only worth their weight in gold, but bring a certain gravitas to any scientific discussion: he is fondly remembered and affectionately missed, but did live to a ripe old age.