scholarly journals Unlocking p53 response elements: DNA shape is the key

2021 ◽  
pp. 1905489
Author(s):  
Marina Farkas ◽  
Steven McMahon
2013 ◽  
Vol 42 (4) ◽  
pp. 2789-2797 ◽  
Author(s):  
Xiaojun Zhang ◽  
Ana Carolina Dantas Machado ◽  
Yuan Ding ◽  
Yongheng Chen ◽  
Yan Lu ◽  
...  

Abstract The tumor suppressor protein p53 regulates numerous signaling pathways by specifically recognizing diverse p53 response elements (REs). Understanding the mechanisms of p53-DNA interaction requires structural information on p53 REs. However, such information is limited as a 3D structure of any RE in the unbound form is not available yet. Here, site-directed spin labeling was used to probe the solution structures of REs involved in p53 regulation of the p21 and Bax genes. Multiple nanometer distances in the p21-RE and BAX-RE, measured using a nucleotide-independent nitroxide probe and double-electron-electron-resonance spectroscopy, were used to derive molecular models of unbound REs from pools of all-atom structures generated by Monte-Carlo simulations, thus enabling analyses to reveal sequence-dependent DNA shape features of unbound REs in solution. The data revealed distinct RE conformational changes on binding to the p53 core domain, and support the hypothesis that sequence-dependent properties encoded in REs are exploited by p53 to achieve the energetically most favorable mode of deformation, consequently enhancing binding specificity. This work reveals mechanisms of p53-DNA recognition, and establishes a new experimental/computational approach for studying DNA shape in solution that has far-reaching implications for studying protein–DNA interactions.


2007 ◽  
Vol 35 (9) ◽  
pp. 2986-3001 ◽  
Author(s):  
Buyong Ma ◽  
Yongping Pan ◽  
Jie Zheng ◽  
Arnold J. Levine ◽  
Ruth Nussinov

2014 ◽  
Vol 133 (12) ◽  
pp. 1467-1476 ◽  
Author(s):  
Xuting Wang ◽  
Gary S. Pittman ◽  
Omari J. Bandele ◽  
Jason J. Bischof ◽  
Gang Liu ◽  
...  

2008 ◽  
Vol 36 (11) ◽  
pp. 3828-3833 ◽  
Author(s):  
Ilya G. Lyakhov ◽  
Annangarachari Krishnamachari ◽  
Thomas D. Schneider

PLoS ONE ◽  
2013 ◽  
Vol 8 (7) ◽  
pp. e69152 ◽  
Author(s):  
Ivan Raimondi ◽  
Yari Ciribilli ◽  
Paola Monti ◽  
Alessandra Bisio ◽  
Loredano Pollegioni ◽  
...  

BMC Genomics ◽  
2015 ◽  
Vol 16 (1) ◽  
Author(s):  
Toma Tebaldi ◽  
Sara Zaccara ◽  
Federica Alessandrini ◽  
Alessandra Bisio ◽  
Yari Ciribilli ◽  
...  

2017 ◽  
Vol 483 (1) ◽  
pp. 516-521 ◽  
Author(s):  
Václav Brázda ◽  
Jana Čechová ◽  
Michele Battistin ◽  
Jan Coufal ◽  
Eva B. Jagelská ◽  
...  

2006 ◽  
Vol 282 (7) ◽  
pp. 4765-4771 ◽  
Author(s):  
Somdutta Roy ◽  
Martin Tenniswood

Histone deacetylase (HDAC) inhibitors are being investigated as possible adjuvant therapies for a number of diseases, including cancer. In addition to stabilization of acetylated histones, HDAC inhibitors stabilize the acetylation of a number of transcription factors, including p53. This study investigates the action of two HDAC inhibitors, CG-1521 and trichostatin A, which stabilize Ac-Lys-373 p53 and Ac-Lys-382 p53, respectively, in LNCaP prostate cancer cells. Real-time PCR demonstrates that CG-1521 induces p21 transcription whereas trichostatin A does not alter the steady state level of p21 mRNA. Co-immunoprecipitation demonstrates that the selective acetylation of p53 directs the recruitment of mutually exclusive coactivator complexes on the p53 response elements in the p21 promoter. Furthermore, the co-activator complexes initiate the recruitment of the components of the basal transcription apparatus to the basal promoter with markedly different outcomes because only Ac-Lys-373 p53 promotes the assembly of the basal transcriptional apparatus on the p21 promoter. These data highlight the profound effects of post-translational modification, including acetylation, on the function of p53. The data also suggest a novel and critically important role for protein acetylation/deacetylation in the assembly of active transcription processes that may be as important as classical phosphorylation/dephosphorylation.


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