Richa Prakash, MSc, Central University of Punjab
DNA or Deoxyribonucleic Acid is a complex molecular structure containing all the genetic information inside the cells required for the development and functioning of any organism. DNA damage occurs every day by the byproducts formed during cellular metabolism and ionizing radiations. DNA damage is any change in the basic DNA structure leading to genetic instability, mutations and failure of functioning of replication machinery in organisms. DNA integrity and stability are very crucial for the normal functioning of organisms and repairing any damage caused to DNA becomes more significant. DNA repair is a process in which a cell identifies and makes corrections to the damage caused to DNA to maintain the integrity and stability of DNA. Failing to do so will lead to an accumulation of genotoxic intermediates and cytotoxic mutagens in the cell and hence causing cell death and cancer.
What are DNA Repair Enzymes?
In response to DNA damage, certain enzymes recognize and process the repairing of the damage caused in the DNA base pairs by a process known as Base Excision Repair (BER). BER is a cellular process involving a cascade of 5 steps enzymatic processes. The enzymes are conserved in bacteria and humans. Glycosylase firstly cleaves the damaged base pairs creating an apurinic or apyrimidinic (AP) site at the DNA damage site. This is followed by the incision of the phosphodiester backbone with the help of AP endonucleases. The next step is gap creation by exonuclease followed by gap-filling by a polymerase. It also restores the excised base pair and removes the nucleobase-less phosphodiester backbone. The last step is the nick-sealing by the ligase enzyme. The two most important enzymes in this cascade are exonuclease III (ExoIII) and polymerase I (Pol I). But, the mechanism of coordination of these enzymatic reactions was unknown.
The Study
Scientists from the Gwangju Institute of Science and Technology (GIST), Korea have used single-molecule fluorescence resonance energy transfer (smFRET) to get an insight into the coordination mechanism of these enzymes. The study has been published in Science Advances. They reported that ExoIII cuts 5’ to the AP site as it belongs to the type II AP endonuclease family and then cuts the DNA in 3’-5’ direction. ExoIII has a higher affinity to the 5’ AP site. The gap size created by ExoIII depends on the physical constraints. It is highly influenced by salt concentration and is restricted to few base pairs only in order to maintain genomic stability. Both Exo III and Pol I have an affinity for the 3’ AP site but Pol 1 outcompetes ExoIII and binds at the 3’ AP site. It starts synthesizes DNA 3’-5’ direction and removes AP site with the help of its 5’-dRPase (deoxyribo-5’-phosphatase) activity. Ligase seals the nick created. According to Dr Gwangrog Lee (the scientist leading the study), “Interestingly, there is perfect temporal and spatial regulation between the gap creation activity of ExoIII and the gap-filling activity of Pol I, such that genomic stability is always maintained.”
Figure 1. Base Excision Repair Mechanism (Source: & Centers for Disease Control and Prevention, US)
Significance of the study
Understanding the functioning of ExoIII in the base excision repair process has opened a lot many doors for further investigations. Cancer cells express more AP endonuclease as compared to normal cells. So, we can use AP endonuclease as a biomarker for cancer diagnosis and treatment. Further research in this area can lead to technologies for drug development and targeted gene repair.
Also read: The Dodging Biofilms of P. aeruginosa in Cystic Fibrosis
References
- Yoo, J., Lee, D., Im, H., Ji, S., Oh, S., Shin, M., … & Lee, G. (2021). The mechanism of gap creation by a multifunctional nuclease during base excision repair. Science Advances, 7(29), eabg0076. https://www.science.org/doi/epdf/10.1126/sciadv.abg0076
- on Smoking, O., & Centers for Disease Control and Prevention. (2010). How tobacco smoke causes disease: The biology and behavioral basis for smoking-attributable disease: A report of the surgeon general. https://www.ncbi.nlm.nih.gov/books/NBK53010/figure/ch5.f4/
Author info:
Richa Prakash is a passionate life science researcher with a post-graduation in Life Sciences with a specialization in Microbial Sciences from the Central University of Punjab and a graduation in Biotechnology from Amity University Rajasthan. Currently working as a scientific content writer and aiming for a PhD. Her research fields of interest are microbiology, molecular biology, and genetic engineering.
LinkedIn Profile Link: www.linkedin.com/in/richa-prakash-rp
Publications:
Singh, H., Das, S., Gupta, P. P., Batra, S., Prakash, R., Srivastava, V. K., … & Kaushik, S. (2020). Binding of metronidazole to Enterococcus faecalis homoserine kinase: Binding studies, docking studies, and molecular dynamics simulation studies. Pharmacognosy Magazine, 16(5), 553. https://www.phcog.com/text.asp?2020/16/5/553/301892
Publications at BioXone:
- Prakash, R. (2021, August 3). Children with Autism have underdeveloped gut microbiota. BioXone. https://bioxone.in/news/worldnews/children-with-autism-have-underdeveloped-gut-microbiota/
- Prakash, R. (2021, July 28). Chronic lung diseases patients are “primed” for severe Coronavirus infections. BioXone. https://bioxone.in/news/worldnews/people-with-chronic-lung-diseases-are-primed-for-severe-coronavirus-infections/
- Prakash, R. (2021, July 10). The journey that led to the discovery of Bryum bharatiensis. BioXone. https://bioxone.in/news/worldnews/the-journey-that-led-to-the-discovery-bryum-bharatiensis/
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