This project provides an introspection into what are motifs in molecular biology and their biological importance together with methods to detect DNA and protein sequence motifs. The application of this work is focused on the hyperthermophilic archaeon Pyrococcus Furiosus and a genetically tractable Pyrococcus Furiosus strain called COM1 that has the particular characteristics to resist to gamma irradiation despite that a number of DNA repair proteins are actually or potentially disrupted. The known diversity of metabolic strategies and physiological adaptations of archaeal species to extreme environments is extraordinary and in this project, some possible mechanisms of metabolic adaptation of COM1 are studied by searching for overrepresented DNA sequence motifs related to radioresistance. The results show that the DNA sequence motif GARGADRHTGHGGMAGAGDTY, which is detected by the software MEME using a set of 8 Ferritin-like DNA sequence genes involved in the protection against oxidative damage, is overrepresented in COM1 with respect to the reference P. Furiosus genome. Notice that the DNA sequence motif is Guanine enriched and this reminds us the property of genes imparting resistant to radiation in radioresistant bacteria, such as D. Radiodurans, that have enriched promoter-PG4 motifs. This can suggest that the radioresistance of COM1 is due to amplification of genes encoding proteins which belong to Ferritin family, or of genes with similar functions, following the destruction or inactivation of DNA repair genes.
Mainly The MEME Suite 5.5.1 plus Python 3.9 (the code is in pdf file Motifs_ManuelaCarriero.pdf).
- Pyrococcus furiosus COM1, complete genome https://www.ncbi.nlm.nih.gov/nuccore/CP003685
- Pyrococcus furiosus DSM 3638, complete sequence https://www.ncbi.nlm.nih.gov/nuccore/NC_003413.1