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Ray S, Tillo D, Assad N, Ufot A, Porollo A, Durell SR, Vinson C. Altering the Double-Stranded DNA Specificity of the bZIP Domain of Zta with Site-Directed Mutagenesis at N182. ACS OMEGA 2022; 7:129-139. [PMID: 35036684 PMCID: PMC8756438 DOI: 10.1021/acsomega.1c04148] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/03/2021] [Accepted: 11/23/2021] [Indexed: 06/14/2023]
Abstract
Zta, the Epstein-Barr virus bZIP transcription factor (TF), binds both unmethylated and methylated double-stranded DNA (dsDNA) in a sequence-specific manner. We studied the contribution of a conserved asparagine (N182) to sequence-specific dsDNA binding to four types of dsDNA: (i) dsDNA with cytosine in both strands ((DNA(C|C)), (ii, iii) dsDNA with 5-methylcytosine (5mC, M) or 5-hydroxymethylcytosine (5hmC, H) in one strand and cytosine in the second strand ((DNA(5mC|C) and DNA(5hmC|C)), and (iv) dsDNA with methylated cytosine in both strands in all CG dinucleotides ((DNA(5mCG)). We replaced asparagine with five similarly sized amino acids (glutamine (Q), serine (S), threonine (T), isoleucine (I), or valine (V)) and used protein binding microarrays to evaluate sequence-specific dsDNA binding. Zta preferentially binds the pseudo-palindrome TRE (AP1) motif (T-4G-3A-2G/C 0T2C3A4 ). Zta (N182Q) changes binding to A3 in only one half-site. Zta(N182S) changes binding to G3 in one or both halves of the motif. Zta(N182S) and Zta(N182Q) have 34- and 17-fold weaker median dsDNA binding, respectively. Zta(N182V) and Zta(N182I) have increased binding to dsDNA(5mC|C). Molecular dynamics simulations rationalize some of these results, identifying hydrogen bonds between glutamine and A3 , but do not reveal why serine preferentially binds G3 , suggesting that entropic interactions may mediate this new binding specificity.
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Affiliation(s)
- Sreejana Ray
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Desiree Tillo
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
- Cancer
Genetics Branch, National Cancer Institute,
National Institutes of Health, Building 37, Bethesda, Maryland 20892, United States
| | - Nima Assad
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Aniekanabasi Ufot
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
| | - Aleksey Porollo
- Center
for Autoimmune Genomics and Etiology, Division of Biomedical Informatics, Cincinnati Children’s Hospital Medical Center, Cincinnati, Ohio 45229, United States
- Department
of Pediatrics, University of Cincinnati
College of Medicine, Cincinnati, Ohio 45267, United States
| | - Stewart R. Durell
- Laboratory
of Cell Biology, National Cancer Institute,
National Institutes of Health, Building 37, Bethesda, Maryland 20892, United States
| | - Charles Vinson
- Laboratory
of Metabolism, National Cancer Institute,
National Institutes of Health, Room 5000, Building 37, Bethesda, Maryland 20892, United States
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