Difference between revisions of "Sarah's Assignment"

Revision as of 16:40, 29 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?

"UV radiation produces many types of photochemical alterations in DNA, ribonucleic acid (RNA), and protein, as well as to structures such as membranes. DNA, however, is the major target for the deleterious effects of UV radiation because it is the largest molecule in the cell, it is present in the fewest copies, it carries the genetic information for a cell, and it absorbs UV radiation very efficiently. In contrast, RNA and proteins are present in multiple copies, so that it is much more difficult to inactivate a significant number of these molecules in a cell by UV irradiation. "[1]

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 [2] [3].

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) [4]. 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 [5]. 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.

From JGI

BLASTn

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.

BLASTp

Blasting the amino acid sequence for each of the three possible photolyases brought more promising results.

DDP:

DDP-related protein:

File:Photolyase2aa.png

DNA repair photolyase:

Most of the organisms that showed significant similarity with our organism's DDP were also halophiles found in salt flats around the world. This suggests that maybe the changes which make our organism's DNA-repair process so efficient have developed independently in many halophiles, while the differences show how different environmental pressures have tweaked the enzymes to fit precise needs.

Strangely, when the amino acid sequences from the DDPs found in our species' genome were BLASTed against one another, very little similarity was found.

DDP and DDP-related protein:

DDP and DNA repair photolyase:

To edit: Found several papers that discuss halophiles and their mutational rates in response to UV light or radiation [6].

Relevant Information

From RAST

According to RAST, our species has 8 enzymes involved in base excision DNA repair. 1 glycosylase, 4 endonucleases, 1 endonuclease and 2 ligases [7]. JGI suggests Base Excision Repair as the only method our organism has for DNA repair and makes no mention of DDP.

What this means

Why do we care about our species' ability to withstand the mutations caused by UV radiation?

Our species presents us with a more efficient version of an old system. Most organisms on the planet use photolyases to correct UV-radiation DNA damage but the halophiles have adapted to their decidedly harsh environment and developed a better compilation of potentially more efficient enzymes to combat this problem.

As we have talked about in class, laboratory conditions are decidedly different from conditions in the "real world". As scientists work to create new organisms that could potentially help in real world situations, they must take into account real world conditions. Most laboratories do not have high levels of UV radiation, unlike the open ocean or a waste dump, yet these are the places that engineered organisms are being sent. If they are unable to survive in the environment they were created to help, then what good can they do? These organisms are also created to very exact specifications. Mutations that do not kill them might render them incapable of performing the function they were meant to or might even alter that function (potentially in a harmful way). WIth knowledge of our organism's (and other halophile's) more efficient UV-radiation-induced DNA damage repair, perhaps genomicists will be able to assist in the development of better bio-tools.