Cell Reports (Feb 2024)
Readthrough events in plants reveal plasticity of stop codons
- Yuqian Zhang,
- Hehuan Li,
- Yanting Shen,
- Shunxi Wang,
- Lei Tian,
- Haoqiang Yin,
- Jiawei Shi,
- Anqi Xing,
- Jinghua Zhang,
- Usman Ali,
- Abdul Sami,
- Xueyan Chen,
- Chenxuan Gao,
- Yangtao Zhao,
- Yajing Lyu,
- Xiaoxu Wang,
- Yanhui Chen,
- Zhixi Tian,
- Shu-Biao Wu,
- Liuji Wu
Affiliations
- Yuqian Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China; School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia
- Hehuan Li
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Yanting Shen
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China
- Shunxi Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Lei Tian
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Haoqiang Yin
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Jiawei Shi
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Anqi Xing
- Department of Plant and Environmental Sciences, Clemson University, Clemson, SC 29634, USA
- Jinghua Zhang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Usman Ali
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Abdul Sami
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Xueyan Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Chenxuan Gao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Yangtao Zhao
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Yajing Lyu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Xiaoxu Wang
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Yanhui Chen
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China
- Zhixi Tian
- State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing 100101, China; College of Advanced Agriculture Sciences, University of Chinese Academy of Sciences, Beijing 100049, China; Corresponding author
- Shu-Biao Wu
- School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Corresponding author
- Liuji Wu
- National Key Laboratory of Wheat and Maize Crop Science, Collaborative Innovation Center of Henan Grain Crops, College of Agronomy, Henan Agricultural University, Zhengzhou 450046, Henan, China; School of Environmental and Rural Science, University of New England, Armidale, NSW 2351, Australia; Corresponding author
- Journal volume & issue
-
Vol. 43,
no. 2
p. 113723
Abstract
Summary: Stop codon readthrough (SCR) has important biological implications but remains largely uncharacterized. Here, we identify 1,009 SCR events in plants using a proteogenomic strategy. Plant SCR candidates tend to have shorter transcript lengths and fewer exons and splice variants than non-SCR transcripts. Mass spectrometry evidence shows that stop codons involved in SCR events can be recoded as 20 standard amino acids, some of which are also supported by suppressor tRNA analysis. We also observe multiple functional signals in 34 maize extended proteins and characterize the structural and subcellular localization changes in the extended protein of basic transcription factor 3. Furthermore, the SCR events exhibit non-conserved signature, and the extensions likely undergo protein-coding selection. Overall, our study not only characterizes that SCR events are commonly present in plants but also identifies the recoding plasticity of stop codons, which provides important insights into the flexibility of genetic decoding.
