Radical SAM enzymes are ancient, essential enzymes. They perform radical chemical reactions in virtually all living organisms and are involved in producing antibiotics, generating greenhouse gases, human health, and likely many other essential roles that have yet to be established. A wide variety of reactions have been characterized from this group of enzymes, including hydrogen abstractions, the transferring of methylthio groups, complex cyclization and rearrangement reactions, and others. However, many radical SAM enzymes have yet to be identified or characterized. There have been great leaps forward in the amount of enzyme sequences that are available in public databases, but experiments to investigate what chemical reactions the enzymes perform take a great deal of time. In our work, we utilize Hidden Markov Models to identify possible radical SAM enzymes and predict their possible functions through BLAST alignments and homology modelling. We also explore their distribution across the tree of life and determine how it is correlated with organism oxygen tolerances, because the core iron-sulfur cluster is oxygen sensitive. Trends in the abundances of radical SAM enzymes depending on oxygen tolerances were more apparent in prokaryotes than in eukaryotes. Although eukaryotes tend to have fewer radical SAM enzymes than prokaryotes, we were able to analyze uncharacterized radical SAM enzymes from both an aerobic eukaryote (Entamoeba histolytica) and a eukaryote capable of oxygenic photosynthesis (Gossypium barbadense), and predict the reactions they catalyze. This work sets the stage for the functional characterization of these essential yet elusive enzymes in future laboratory experiments. / Master of Science in Life Sciences / Radical SAM enzymes are ancient, essential enzymes that perform chemical reactions in virtually all living organisms. We do know that they are involved in producing antibiotics, human health, and generating greenhouse gases. We also know that there are many radical SAM enzymes whose functions remain a mystery. There have been great leaps forward in the amount of enzyme sequences that are available in public databases, but experiments to investigate what chemical reactions enzymes perform take a great deal of time. The experiments are especially difficult for radical SAM enzymes because the oxygen we breathe can break the enzymes down in a laboratory. In our work, we utilize computational techniques to identify possible radical SAM enzymes and predict what reactions they might catalyze. Because these enzymes are vulnerable to oxygen in laboratory environments, we also explore whether organisms that breathe oxygen have fewer of these enzymes than organisms that perform anaerobic respiration instead. We found that does seem to be the case in microbes like bacteria and archaea, but the results were not as consistent for eukaryotes. We then chose radical SAM enzymes we had identified from both an aerobic eukaryote (Entamoeba histolytica) and a eukaryote capable of producing oxygen (Gossypium barbadense), and predicted the reactions they catalyze. This work sets the stage for the functional characterization of these essential yet elusive enzymes in future laboratory experiments.
| Identifer | oai:union.ndltd.org:VTETD/oai:vtechworks.lib.vt.edu:10919/98736 |
| Date | 03 June 2020 |
| Creators | Gagliano, Elisa |
| Contributors | Biochemistry, Brown, Anne M., Allen, Kylie D., Lemkul, Justin A. |
| Publisher | Virginia Tech |
| Source Sets | Virginia Tech Theses and Dissertation |
| Detected Language | English |
| Type | Thesis |
| Format | ETD, application/pdf, video/quicktime, application/vnd.openxmlformats-officedocument.spreadsheetml.sheet, video/quicktime |
| Rights | In Copyright, http://rightsstatements.org/vocab/InC/1.0/ |
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