Difference between revisions of "Sarah's Assignment"
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While the similarities are obvious and the BLAST supports that this is, in fact, a deoxyribodipyrimidine photolyase, there are many differences between the two halophiles. | While the similarities are obvious and the BLAST supports that this is, in fact, a deoxyribodipyrimidine photolyase, there are many differences between the two halophiles. | ||
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| + | BLASTs with this other two potential deoxyribodipyrimidine photolyases were not as promising: | ||
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| + | Deoxyribodipyrimidine photolyase-related protein: | ||
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| + | [[Image:photolyase2.png]] | ||
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| + | Only one other whole genome showed significant similarity. | ||
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| + | DNA repair photolyase: | ||
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| + | [[Image:photolyase3.png]] | ||
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| + | Our gene was only matched to its own genome. | ||
'''To edit''': Found several papers that discuss halophiles and their mutational rates in response to UV light or radiation [http://genome.cshlp.org/content/14/6/1025.full]. | '''To edit''': Found several papers that discuss halophiles and their mutational rates in response to UV light or radiation [http://genome.cshlp.org/content/14/6/1025.full]. | ||
Revision as of 15:50, 24 September 2009
I'm interested in the DNA repair mechanisms our species might have. Since or species is in such exposed conditions, how does it evade the mutational effects of UV light?
Commonly found UV-mediated mutations are cyclobutane dimers (pyrimidine dimers) and 6-4 photodimers.
Cyclobutane dimers consist of either C=C binding or T=T binding. UV light creates covalent bonds between adjacent thymidines or cytosines,which can inhibit transcription or replication of DNA. Cytosines that are part of a dimer are also more likely to be deaminated and changed to uracil. This can cause errors in either transcription or replication [1] [2].
Deoxyribodipyrimidine photolyases are partially responsible for correcting cyclobutane dimers by breaking the covalent bonds formed by UV light exposure. The reaction they perform can be characterized by: cyclobutadipyrimidine (in DNA) = 2 pyrimidine residues (in DNA) [3]. Interestingly, these photolysases are not found in placental mammals.
Our species has a deoxyribodipyrimidine photolyase (644033060), a deoxyribodipyrimidine photolyase-related protein (644030931) and a DNA repair photolyase (644032076). In other halophiles, it has been determined that photolyases are light dependent and DNA repair more efficient in the presence of light [4]. Since mutations from UV light are more likely to occur during the day, it stands to reason that the repair mechanism would be light-dependent and function only when necessary.
BLASTing the first dexyribidipyrimidine photolyase brought up a complete match with H. mukohaetaei and loose identification with H. marismortui as shown below:
While the similarities are obvious and the BLAST supports that this is, in fact, a deoxyribodipyrimidine photolyase, there are many differences between the two halophiles.
BLASTs with this other two potential deoxyribodipyrimidine photolyases were not as promising:
Deoxyribodipyrimidine photolyase-related protein:
Only one other whole genome showed significant similarity.
DNA repair photolyase:
Our gene was only matched to its own genome.
To edit: Found several papers that discuss halophiles and their mutational rates in response to UV light or radiation [5].
