Evolution of the aerobic iron oxidation metabolism

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Evolution of the aerobic iron oxidation metabolism

Every living organism needs energy to survive and reproduce. We humans get our energy from food, mainly in the form of fats, sugars, protein, and perhaps some alcohol. Bacteria and other microorganisms are able to use other sources such as light and metals. In this master thesis I aim to find out how the cellular machinery needed for the aerobic oxidation of iron evolved throughout history in several different microorganisms.

Antonie van Leeuwenhoek, a famous maker of microscopes, was the first person to document what we today know as bacteria. In the 1840s, some 150 years after the first documentation of bacteria, S. F. Stiebel already recorded the presence of bacteria in iron-rich ground water (see picture). He also observed the formation of a ‘brown-red’ substance (rust) in these waters. What he was witnessing was the oxidation of iron by bacteria in iron rich ground waters.

Iron atoms can be present in multiple states when dissolved in water, including in its ferrous form (Fe2+) and ferric form (Fe3+). These bacteria use certain proteins such as Cyc2 and Sulfocyanin to perform the oxidation of iron, which turns Fe2+ into Fe3+ outside the cell and releases an electron in the process. This electron is shuttled into the bacterial cell, and is then used to turn oxygen into water. This generates the energy needed for the survival of the cell. The Fe3+ which is formed on the outside of the cell isn’t as soluble as Fe2+. The Fe3+ precipitates on the outside of the cell, forming the rust as seen in the picture.

But where did this mechanism come from?
In this thesis I studied the generation of energy by the process described above in a wide range of microorganisms. Not only bacteria, but also archaea (commonly described as ancient microorganisms) can perform this process. The organisms use a wide range of different proteins to perform the process, and I collected all protein sequences related to this process from the literature. By using several different tools (software) which compare the different proteins to each other, one can have insights on how a certain protein evolved over time.

One of the goals of this thesis was to see if the proteins related to this process had a common origin, just like the muscle proteins in mammals have a common origin. Using the software described above, I found out that most of the pathways evolved independently, just like flight in birds and bats evolved independently from each other. I also found several several signs of ’horizontal gene transfer’, a process which is often seen in microorganisms but rare in mammals. It means that a gene is directly transferred between species, and might provide the species receiving the gene with an advantage such as faster growth, or a the ability to use a new coumpound from the enviroment.

Master’s Degree Project in Bioinformatics 45 credits 2018
Department of Biology, Lund University

Advisor: Filipa L. Sousa
Archaea Biology and Ecogenomics Division, Universität Wien

• author: van Ham, Joost
• supervisor: Filipa Sousa
• organization: Degree Projects in Bioinformatics
• course: BINP51 20191
• year: 2019
• type: H2 - Master's Degree (Two Years)
• subject: Biology and Life Sciences
• language: English
• id: 8996967
• date added to LUP: 2019-10-22 15:01:21
• date last changed: 2019-10-22 15:01:21