Biochemical and Structural Insights into the Mechanism of DNA Recognition by Arabidopsis ETHYLENE INSENSITIVE3

Jinghui Song; Chenxu Zhu; Xing Zhang; Xing Wen; Lulu Liu; Jinying Peng; Hongwei Guo; Chengqi Yi

doi:10.1371/journal.pone.0137439

Biochemical and Structural Insights into the Mechanism of DNA Recognition by Arabidopsis ETHYLENE INSENSITIVE3

PLoS One. 2015 Sep 9;10(9):e0137439. doi: 10.1371/journal.pone.0137439. eCollection 2015.

Authors

Jinghui Song¹, Chenxu Zhu¹, Xing Zhang¹, Xing Wen¹, Lulu Liu¹, Jinying Peng¹, Hongwei Guo¹, Chengqi Yi²

Affiliations

¹ State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China.
² State Key Laboratory of Protein and Plant Gene Research, School of Life Sciences, and Peking-Tsinghua Center for Life Sciences, Peking University, Beijing, China; Department of Chemical Biology and Synthetic and Functional Biomolecules Center, College of Chemistry and Molecular Engineering, Peking University, Beijing, China.

Abstract

Gaseous hormone ethylene regulates numerous stress responses and developmental adaptations in plants by controlling gene expression via transcription factors ETHYLENE INSENSITIVE3 (EIN3) and EIN3-Like1 (EIL1). However, our knowledge regarding to the accurate definition of DNA-binding domains (DBDs) within EIN3 and also the mechanism of specific DNA recognition by EIN3 is limited. Here, we identify EIN3 82-352 and 174-306 as the optimal and core DBDs, respectively. Results from systematic biochemical analyses reveal that both the number of EIN3-binding sites (EBSs) and the spacing length between two EBSs affect the binding affinity of EIN3; accordingly, a new DNA probe which has higher affinity with EIN3 than ERF1 is also designed. Furthermore, we show that palindromic repeat sequences in ERF1 promoter are not necessary for EIN3 binding. Finally, we provide, to our knowledge, the first crystal structure of EIN3 core DBD, which contains amino acid residues essential for DNA binding and signaling. Collectively, these data suggest the detailed mechanism of DNA recognition by EIN3 and provide an in-depth view at molecular level for the transcriptional regulation mediated by EIN3.

Publication types

Research Support, Non-U.S. Gov't

MeSH terms

Arabidopsis / chemistry
Arabidopsis / genetics*
Arabidopsis Proteins / chemistry*
Arabidopsis Proteins / genetics
Binding Sites
Crystallography, X-Ray*
DNA-Binding Proteins / chemistry*
DNA-Binding Proteins / genetics
Electrophoretic Mobility Shift Assay
Ethylenes / metabolism
Gene Expression Regulation, Plant
Inverted Repeat Sequences
Nuclear Proteins / chemistry*
Nuclear Proteins / genetics
Peptide Termination Factors / chemistry
Peptide Termination Factors / genetics
Plants, Genetically Modified
Promoter Regions, Genetic
Protein Conformation
Protein Structure, Tertiary
Signal Transduction
Transcription Factors / chemistry*
Transcription Factors / genetics

Substances

Arabidopsis Proteins
DNA-Binding Proteins
EIL1 protein, Arabidopsis
EIN3 protein, Arabidopsis
Ethylenes
Nuclear Proteins
Peptide Termination Factors
Transcription Factors
eukaryotic release factor 1, Arabidopsis
ethylene

Grants and funding

This work was supported by the National Basic Research Foundation of China (http://www.most.gov.cn/; 2014CB964900 to C.Y.), and the National Natural Science Foundation of China (http://www.nsfc.gov.cn/; 31270838 to C.Y., 21472009 to C.Y.). The funders had no role in study design, data collection and analysis, decision to publish, or preparation of the manuscript.