RNA-cleaving properties of human apurinic/apyrimidinic endonuclease 1 (APE1)
Wan-Cheol Kim1, Dustin King, Chow H Lee
1Chemistry Program, University of Northern British Columbia, 3333 University Way Prince George, BC V2N 4Z9 Canada.
Abstract:
We have recently identified apurinic/apyrimidinic endonuclease 1 (APE1) as an endoribonuclease that cleaves c-myc mRNA in vitro and regulates c-myc mRNA levels and half-life in cells. This study was undertaken to further unravel the RNA-cleaving properties of APE1. Here, we show that APE1 cleaves RNA in the absence of divalent metal ions and, at 2 mM, Zn(2+), Ni(2+), Cu(2+), or Co(2+) inhibited the endoribonuclease activity of APE1. APE1 is able to cleave CD44 mRNA, microRNAs (miR-21, miR-10b), and three RNA components of SARS-corona virus (orf1b, orf3, spike) suggesting that, when challenged, it can cleave any RNAs in vitro. APE1 does not cleave strong doublestranded regions of RNA and it has a strong preference for 3' of pyrimidine, especially towards UA, CA, and UG sites at single-stranded or weakly paired regions. It also cleaves RNA weakly at UC, CU, AC, and AU sites in single-stranded or weakly paired regions. Finally, we found that APE1 can reduce the ability of the Dicer enzyme to process premiRNAs in vitro. Overall, this study has revealed some previously unknown biochemical properties of APE1 which has implications for its role in vivo.
Insights
Apurinic/apyrimidinic endonuclease 1 (APE1) is an endoribonuclease that degrades various RNAs, including c-myc mRNA and microRNAs. This study reveals APE1
Area of Science:
- Biochemistry
- Molecular Biology
- Genetics
Background:
- Apurinic/apyrimidinic endonuclease 1 (APE1) was previously identified as an endoribonuclease affecting c-myc mRNA.
- Further investigation into APE1's RNA-cleaving capabilities is warranted.
Purpose of the Study:
- To elucidate the biochemical properties of APE1's endoribonuclease activity.
- To characterize the substrate specificity and metal ion dependency of APE1.
- To assess the impact of APE1 on microRNA processing.
Main Methods:
- In vitro assays were used to test APE1's RNA cleavage activity.
- The effect of divalent metal ions on APE1 activity was evaluated.
- Cleavage preference for specific RNA sequences and structures was determined.
- APE1's interaction with Dicer enzyme in pre-miRNA processing was assessed.
Main Results:
- APE1 exhibits endoribonuclease activity independently of divalent metal ions.
- Specific divalent metal ions (Zn2+, Ni2+, Cu2+, Co2+) inhibit APE1 activity.
- APE1 cleaves various RNA types, including mRNAs, microRNAs, and viral RNAs, with a preference for single-stranded regions 3' of pyrimidines (UA, CA, UG).
- APE1 inhibits Dicer-mediated pre-miRNA processing in vitro.
Conclusions:
- APE1 possesses broad RNA cleavage capabilities with specific sequence and structural preferences.
- Metal ions can modulate APE1's endoribonuclease activity.
- APE1 influences microRNA biogenesis by inhibiting Dicer activity.
- These findings reveal novel biochemical properties of APE1 with potential in vivo implications for RNA regulation.
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